git://source.jalview.org / jabaws.git / commitdiff
? search:
summary | shortlog | log | commit | commitdiff | tree
raw | patch | inline | side by side (parent: 5d5b4fa)
tcoffee updated docs & todo
authorpvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>
Tue, 21 Jun 2011 14:48:37 +0000 (14:48 +0000)
committerpvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>
Tue, 21 Jun 2011 14:48:37 +0000 (14:48 +0000)
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4301 e3abac25-378b-4346-85de-24260fe3988d

TODO.txt patch | blob | history
website/prog_docs/tcoffee.html patch | blob | history

diff --git a/TODO.txt b/TODO.txt
index 1c907cf..9003d44 100644 (file)
--- a/TODO.txt
+++ b/TODO.txt
@@ -1,14 +1,18 @@
+TODO ideally should introduce native Mac support (and maybe abandon native windows support in \r
+favior of VM)   \r
+\r
 TODO write some help on the executable.properties within this file! \r
 check that after binaries relocation build tasks point to correct locations!\r
-GET rid of binaries/help directory!\r
-update binaries\r
++ GET rid of binaries/help directory!\r
++ update binaries\r
  + muscle binary version 3.8.31 for win/lin32/lin64 and sources, docs in website/prog_docs\r
  - test Muscle on the cluster\r
  - test Muscle compilation\r
  + probcons up-to-date\r
  + clustal up-to-date \r
- - update tcoffee (8.99 latest)\r
- - update Mafft (6.857 latest)\r
+ + update tcoffee (8.99 latest) source code updated  docs updated \r
+  + tcoffee compilation for IA32 \r
+ + update Mafft (6.857 latest) for win/lin32/lin64 and sources, no docs updates\r
 + make sure conf files are optional!\r
 \r
 TODO: \r
diff --git a/website/prog_docs/tcoffee.html b/website/prog_docs/tcoffee.html
index 2468a40..53c1917 100644 (file)
--- a/website/prog_docs/tcoffee.html
+++ b/website/prog_docs/tcoffee.html
@@ -1,19848 +1,16723 @@
-<html xmlns:v="urn:schemas-microsoft-com:vml"\r
-xmlns:o="urn:schemas-microsoft-com:office:office"\r
-xmlns:w="urn:schemas-microsoft-com:office:word"\r
-xmlns:st1="urn:schemas-microsoft-com:office:smarttags"\r
-xmlns="http://www.w3.org/TR/REC-html40">\r
-\r
-<head>\r
-<meta http-equiv=Content-Type content="text/html; charset=windows-1252">\r
-<meta name=ProgId content=Word.Document>\r
-<meta name=Generator content="Microsoft Word 11">\r
-<meta name=Originator content="Microsoft Word 11">\r
-<link rel=File-List href="t_coffee_technical_files/filelist.xml">\r
-<link rel=Edit-Time-Data href="t_coffee_technical_files/editdata.mso">\r
-<!--[if !mso]>\r
-<style>\r
-v\:* {behavior:url(#default#VML);}\r
-o\:* {behavior:url(#default#VML);}\r
-w\:* {behavior:url(#default#VML);}\r
-.shape {behavior:url(#default#VML);}\r
-</style>\r
-<![endif]-->\r
-<title>Manual</title>\r
-<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"\r
- name="place" downloadurl="http://www.5iantlavalamp.com/"/>\r
-<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"\r
- name="City" downloadurl="http://www.5iamas-microsoft-com:office:smarttags"/>\r
-<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"\r
- name="address"/>\r
-<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"\r
- name="State"/>\r
-<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"\r
- name="Street"/>\r
-<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"\r
- name="country-region" downloadurl="http://www.5iantlavalamp.com/"/>\r
-<!--[if gte mso 9]><xml>\r
- <o:DocumentProperties>\r
-  <o:Author>Notredame</o:Author>\r
-  <o:Template>Normal</o:Template>\r
-  <o:LastAuthor>Notredame</o:LastAuthor>\r
-  <o:Revision>2</o:Revision>\r
-  <o:TotalTime>28339</o:TotalTime>\r
-  <o:LastPrinted>2006-03-05T18:42:00Z</o:LastPrinted>\r
-  <o:Created>2009-07-22T23:43:00Z</o:Created>\r
-  <o:LastSaved>2009-07-22T23:43:00Z</o:LastSaved>\r
-  <o:Pages>1</o:Pages>\r
-  <o:Words>20247</o:Words>\r
-  <o:Characters>111361</o:Characters>\r
-  <o:Company>SIB</o:Company>\r
-  <o:Lines>928</o:Lines>\r
-  <o:Paragraphs>262</o:Paragraphs>\r
-  <o:CharactersWithSpaces>131346</o:CharactersWithSpaces>\r
-  <o:Version>11.6360</o:Version>\r
- </o:DocumentProperties>\r
-</xml><![endif]--><!--[if gte mso 9]><xml>\r
- <w:WordDocument>\r
-  <w:HyphenationZone>21</w:HyphenationZone>\r
-  <w:ValidateAgainstSchemas/>\r
-  <w:SaveIfXMLInvalid>false</w:SaveIfXMLInvalid>\r
-  <w:IgnoreMixedContent>false</w:IgnoreMixedContent>\r
-  <w:AlwaysShowPlaceholderText>false</w:AlwaysShowPlaceholderText>\r
-  <w:Compatibility>\r
-   <w:BreakWrappedTables/>\r
-   <w:SnapToGridInCell/>\r
-   <w:WrapTextWithPunct/>\r
-   <w:UseAsianBreakRules/>\r
-   <w:UseWord2002TableStyleRules/>\r
-  </w:Compatibility>\r
-  <w:BrowserLevel>MicrosoftInternetExplorer4</w:BrowserLevel>\r
- </w:WordDocument>\r
-</xml><![endif]--><!--[if gte mso 9]><xml>\r
- <w:LatentStyles DefLockedState="false" LatentStyleCount="156">\r
- </w:LatentStyles>\r
-</xml><![endif]--><!--[if !mso]><object\r
- classid="clsid:38481807-CA0E-42D2-BF39-B33AF135CC4D" id=ieooui></object>\r
-<style>\r
-st1\:*{behavior:url(#ieooui) }\r
-</style>\r
-<![endif]-->\r
-<style>\r
-<!--\r
- /* Font Definitions */\r
- @font-face\r
-       {font-family:Helvetica;\r
-       panose-1:2 11 6 4 2 2 2 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:Courier;\r
-       panose-1:2 7 4 9 2 2 5 2 4 4;\r
-       mso-font-alt:"Courier New";\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:modern;\r
-       mso-font-format:other;\r
-       mso-font-pitch:fixed;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Tms Rmn";\r
-       panose-1:2 2 6 3 4 5 5 2 3 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-format:other;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:Helv;\r
-       panose-1:2 11 6 4 2 2 2 3 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-format:other;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"New York";\r
-       panose-1:2 2 5 2 6 3 5 6 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:System;\r
-       panose-1:0 0 0 0 0 0 0 0 0 0;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-format:other;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:Wingdings;\r
-       panose-1:5 0 0 0 0 0 0 0 0 0;\r
-       mso-font-charset:2;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:0 268435456 0 0 -2147483648 0;}\r
-@font-face\r
-       {font-family:"MS Mincho";\r
-       panose-1:2 2 6 9 4 2 5 8 3 4;\r
-       mso-font-alt:"\FF2D\FF33 \660E\671D";\r
-       mso-font-charset:128;\r
-       mso-generic-font-family:modern;\r
-       mso-font-pitch:fixed;\r
-       mso-font-signature:-1610612033 1757936891 16 0 131231 0;}\r
-@font-face\r
-       {font-family:Batang;\r
-       panose-1:2 3 6 0 0 1 1 1 1 1;\r
-       mso-font-alt:\BC14\D0D5;\r
-       mso-font-charset:129;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-1342176593 1775729915 48 0 524447 0;}\r
-@font-face\r
-       {font-family:SimSun;\r
-       panose-1:2 1 6 0 3 1 1 1 1 1;\r
-       mso-font-alt:\5B8B\4F53;\r
-       mso-font-charset:134;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 135135232 16 0 262145 0;}\r
-@font-face\r
-       {font-family:PMingLiU;\r
-       panose-1:2 2 3 0 0 0 0 0 0 0;\r
-       mso-font-alt:\65B0\7D30\660E\9AD4;\r
-       mso-font-charset:136;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 137232384 22 0 1048577 0;}\r
-@font-face\r
-       {font-family:"MS Gothic";\r
-       panose-1:2 11 6 9 7 2 5 8 2 4;\r
-       mso-font-alt:"\FF2D\FF33 \30B4\30B7\30C3\30AF";\r
-       mso-font-charset:128;\r
-       mso-generic-font-family:modern;\r
-       mso-font-pitch:fixed;\r
-       mso-font-signature:-1610612033 1757936891 16 0 131231 0;}\r
-@font-face\r
-       {font-family:Dotum;\r
-       panose-1:2 11 6 0 0 1 1 1 1 1;\r
-       mso-font-alt:\B3CB\C6C0;\r
-       mso-font-charset:129;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-1342176593 1775729915 48 0 524447 0;}\r
-@font-face\r
-       {font-family:SimHei;\r
-       panose-1:2 1 6 0 3 1 1 1 1 1;\r
-       mso-font-alt:\9ED1\4F53;\r
-       mso-font-charset:134;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:1 135135232 16 0 262144 0;}\r
-@font-face\r
-       {font-family:MingLiU;\r
-       panose-1:2 2 3 9 0 0 0 0 0 0;\r
-       mso-font-alt:\7D30\660E\9AD4;\r
-       mso-font-charset:136;\r
-       mso-generic-font-family:modern;\r
-       mso-font-pitch:fixed;\r
-       mso-font-signature:3 137232384 22 0 1048577 0;}\r
-@font-face\r
-       {font-family:Mincho;\r
-       panose-1:2 2 6 9 4 3 5 8 3 5;\r
-       mso-font-alt:\660E\671D;\r
-       mso-font-charset:128;\r
-       mso-generic-font-family:roman;\r
-       mso-font-format:other;\r
-       mso-font-pitch:fixed;\r
-       mso-font-signature:1 134676480 16 0 131072 0;}\r
-@font-face\r
-       {font-family:Gulim;\r
-       panose-1:2 11 6 0 0 1 1 1 1 1;\r
-       mso-font-alt:\AD74\B9BC;\r
-       mso-font-charset:129;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-1342176593 1775729915 48 0 524447 0;}\r
-@font-face\r
-       {font-family:Century;\r
-       panose-1:2 4 6 4 5 5 5 2 3 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:647 0 0 0 159 0;}\r
-@font-face\r
-       {font-family:"Angsana New";\r
-       panose-1:2 2 6 3 5 4 5 2 3 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:16777219 0 0 0 65537 0;}\r
-@font-face\r
-       {font-family:"Cordia New";\r
-       panose-1:2 11 3 4 2 2 2 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:16777219 0 0 0 65537 0;}\r
-@font-face\r
-       {font-family:Mangal;\r
-       panose-1:0 0 4 0 0 0 0 0 0 0;\r
-       mso-font-charset:1;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:32768 0 0 0 0 0;}\r
-@font-face\r
-       {font-family:Latha;\r
-       panose-1:2 0 4 0 0 0 0 0 0 0;\r
-       mso-font-charset:1;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:1048576 0 0 0 0 0;}\r
-@font-face\r
-       {font-family:Sylfaen;\r
-       panose-1:1 10 5 2 5 3 6 3 3 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:67110535 0 0 0 159 0;}\r
-@font-face\r
-       {font-family:Vrinda;\r
-       panose-1:1 1 6 0 1 1 1 1 1 1;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:65539 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:Raavi;\r
-       panose-1:2 0 5 0 0 0 0 0 0 0;\r
-       mso-font-charset:1;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:131072 0 0 0 0 0;}\r
-@font-face\r
-       {font-family:Shruti;\r
-       panose-1:2 0 5 0 0 0 0 0 0 0;\r
-       mso-font-charset:1;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:262144 0 0 0 0 0;}\r
-@font-face\r
-       {font-family:Sendnya;\r
-       panose-1:0 0 4 0 0 0 0 0 0 0;\r
-       mso-font-charset:1;\r
-       mso-generic-font-family:roman;\r
-       mso-font-format:other;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:0 0 0 0 0 0;}\r
-@font-face\r
-       {font-family:Gautami;\r
-       panose-1:2 0 5 0 0 0 0 0 0 0;\r
-       mso-font-charset:1;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:2097152 0 0 0 0 0;}\r
-@font-face\r
-       {font-family:Tunga;\r
-       panose-1:0 0 4 0 0 0 0 0 0 0;\r
-       mso-font-charset:1;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:4194304 0 0 0 0 0;}\r
-@font-face\r
-       {font-family:"Estrangelo Edessa";\r
-       panose-1:3 8 6 0 0 0 0 0 0 0;\r
-       mso-font-charset:1;\r
-       mso-generic-font-family:script;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-2147459008 0 128 0 0 0;}\r
-@font-face\r
-       {font-family:Kartika;\r
-       panose-1:2 2 5 3 3 4 4 6 2 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:8388611 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Arial Unicode MS";\r
-       panose-1:2 11 6 4 2 2 2 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-format:other;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:Times;\r
-       panose-1:2 2 6 3 5 4 5 2 3 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:"Comic Sans MS";\r
-       panose-1:3 15 7 2 3 3 2 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:script;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:647 0 0 0 159 0;}\r
-@font-face\r
-       {font-family:Tahoma;\r
-       panose-1:2 11 6 4 3 5 4 4 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:1627421319 -2147483648 8 0 66047 0;}\r
-@font-face\r
-       {font-family:Garamond;\r
-       panose-1:2 2 4 4 3 3 1 1 8 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:647 0 0 0 159 0;}\r
-@font-face\r
-       {font-family:"Arial Black";\r
-       panose-1:2 11 10 4 2 1 2 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:647 0 0 0 159 0;}\r
-@font-face\r
-       {font-family:starbats;\r
-       mso-font-charset:2;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:0 0 0 0 0 0;}\r
-@font-face\r
-       {font-family:SWMacro;\r
-       panose-1:0 0 0 0 0 0 0 0 0 0;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:modern;\r
-       mso-font-format:other;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:Marlett;\r
-       panose-1:0 0 0 0 0 0 0 0 0 0;\r
-       mso-font-charset:2;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:0 268435456 0 0 -2147483648 0;}\r
-@font-face\r
-       {font-family:"Lucida Console";\r
-       panose-1:2 11 6 9 4 5 4 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:modern;\r
-       mso-font-pitch:fixed;\r
-       mso-font-signature:-2147482993 6144 0 0 31 0;}\r
-@font-face\r
-       {font-family:"Lucida Sans Unicode";\r
-       panose-1:2 11 6 2 3 5 4 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-2147476737 14699 0 0 63 0;}\r
-@font-face\r
-       {font-family:Verdana;\r
-       panose-1:2 11 6 4 3 5 4 4 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:536871559 0 0 0 415 0;}\r
-@font-face\r
-       {font-family:Impact;\r
-       panose-1:2 11 8 6 3 9 2 5 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:647 0 0 0 159 0;}\r
-@font-face\r
-       {font-family:Georgia;\r
-       panose-1:2 4 5 2 5 4 5 2 3 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:647 0 0 0 159 0;}\r
-@font-face\r
-       {font-family:"Franklin Gothic Medium";\r
-       panose-1:2 11 6 3 2 1 2 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:647 0 0 0 159 0;}\r
-@font-face\r
-       {font-family:"Palatino Linotype";\r
-       panose-1:2 4 5 2 5 5 5 3 3 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-536870009 1073741843 0 0 415 0;}\r
-@font-face\r
-       {font-family:"Trebuchet MS";\r
-       panose-1:2 11 6 3 2 2 2 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:647 0 0 0 159 0;}\r
-@font-face\r
-       {font-family:Webdings;\r
-       panose-1:5 3 1 2 1 5 9 6 7 3;\r
-       mso-font-charset:2;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:0 268435456 0 0 -2147483648 0;}\r
-@font-face\r
-       {font-family:"MV Boli";\r
-       panose-1:2 0 5 0 3 2 0 9 0 0;\r
-       mso-font-charset:1;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:0 0 256 0 0 0;}\r
-@font-face\r
-       {font-family:"Microsoft Sans Serif";\r
-       panose-1:2 11 6 4 2 2 2 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:1627421663 -2147483648 8 0 66047 0;}\r
-@font-face\r
-       {font-family:AngsanaUPC;\r
-       panose-1:2 2 6 3 5 4 5 2 3 4;\r
-       mso-font-charset:222;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:16777219 0 0 0 65536 0;}\r
-@font-face\r
-       {font-family:BrowalliaUPC;\r
-       panose-1:2 11 6 4 2 2 2 2 2 4;\r
-       mso-font-charset:222;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:16777219 0 0 0 65536 0;}\r
-@font-face\r
-       {font-family:"Browallia New";\r
-       panose-1:2 11 6 4 2 2 2 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:16777219 0 0 0 65537 0;}\r
-@font-face\r
-       {font-family:CordiaUPC;\r
-       panose-1:2 11 3 4 2 2 2 2 2 4;\r
-       mso-font-charset:222;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:16777219 0 0 0 65536 0;}\r
-@font-face\r
-       {font-family:DilleniaUPC;\r
-       panose-1:2 2 6 3 5 4 5 2 3 4;\r
-       mso-font-charset:222;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:16777217 0 0 0 65536 0;}\r
-@font-face\r
-       {font-family:EucrosiaUPC;\r
-       panose-1:2 2 6 3 5 4 5 2 3 4;\r
-       mso-font-charset:222;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:16777217 0 0 0 65536 0;}\r
-@font-face\r
-       {font-family:FreesiaUPC;\r
-       panose-1:2 11 6 4 2 2 2 2 2 4;\r
-       mso-font-charset:222;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:16777217 0 0 0 65536 0;}\r
-@font-face\r
-       {font-family:IrisUPC;\r
-       panose-1:2 11 6 4 2 2 2 2 2 4;\r
-       mso-font-charset:222;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:16777217 0 0 0 65536 0;}\r
-@font-face\r
-       {font-family:JasmineUPC;\r
-       panose-1:2 2 6 3 5 4 5 2 3 4;\r
-       mso-font-charset:222;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:16777217 0 0 0 65536 0;}\r
-@font-face\r
-       {font-family:KodchiangUPC;\r
-       panose-1:2 2 6 3 5 4 5 2 3 4;\r
-       mso-font-charset:222;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:16777217 0 0 0 65536 0;}\r
-@font-face\r
-       {font-family:LilyUPC;\r
-       panose-1:2 11 6 4 2 2 2 2 2 4;\r
-       mso-font-charset:222;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:16777217 0 0 0 65536 0;}\r
-@font-face\r
-       {font-family:Aharoni;\r
-       panose-1:0 0 0 0 0 0 0 0 0 0;\r
-       mso-font-charset:177;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:6145 0 0 0 32 0;}\r
-@font-face\r
-       {font-family:David;\r
-       panose-1:0 0 0 0 0 0 0 0 0 0;\r
-       mso-font-charset:177;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:6145 0 0 0 32 0;}\r
-@font-face\r
-       {font-family:"David Transparent";\r
-       panose-1:0 0 0 0 0 0 0 0 0 0;\r
-       mso-font-charset:177;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:6145 0 0 0 32 0;}\r
-@font-face\r
-       {font-family:FrankRuehl;\r
-       panose-1:0 0 0 0 0 0 0 0 0 0;\r
-       mso-font-charset:177;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:6145 0 0 0 32 0;}\r
-@font-face\r
-       {font-family:"Levenim MT";\r
-       panose-1:0 0 0 0 0 0 0 0 0 0;\r
-       mso-font-charset:177;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:6145 0 0 0 32 0;}\r
-@font-face\r
-       {font-family:Miriam;\r
-       panose-1:0 0 0 0 0 0 0 0 0 0;\r
-       mso-font-charset:177;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:6145 0 0 0 32 0;}\r
-@font-face\r
-       {font-family:"Miriam Transparent";\r
-       panose-1:0 0 0 0 0 0 0 0 0 0;\r
-       mso-font-charset:177;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:6145 0 0 0 32 0;}\r
-@font-face\r
-       {font-family:"Miriam Fixed";\r
-       panose-1:0 0 0 9 0 0 0 0 0 0;\r
-       mso-font-charset:177;\r
-       mso-generic-font-family:modern;\r
-       mso-font-pitch:fixed;\r
-       mso-font-signature:6145 0 0 0 32 0;}\r
-@font-face\r
-       {font-family:"Fixed Miriam Transparent";\r
-       panose-1:0 0 0 9 0 0 0 0 0 0;\r
-       mso-font-charset:177;\r
-       mso-generic-font-family:modern;\r
-       mso-font-pitch:fixed;\r
-       mso-font-signature:6145 0 0 0 32 0;}\r
-@font-face\r
-       {font-family:Narkisim;\r
-       panose-1:0 0 0 0 0 0 0 0 0 0;\r
-       mso-font-charset:177;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:6145 0 0 0 32 0;}\r
-@font-face\r
-       {font-family:Rod;\r
-       panose-1:0 0 0 9 0 0 0 0 0 0;\r
-       mso-font-charset:177;\r
-       mso-generic-font-family:modern;\r
-       mso-font-pitch:fixed;\r
-       mso-font-signature:6145 0 0 0 32 0;}\r
-@font-face\r
-       {font-family:"Rod Transparent";\r
-       panose-1:0 0 0 9 0 0 0 0 0 0;\r
-       mso-font-charset:177;\r
-       mso-generic-font-family:modern;\r
-       mso-font-pitch:fixed;\r
-       mso-font-signature:6145 0 0 0 32 0;}\r
-@font-face\r
-       {font-family:"Traditional Arabic";\r
-       panose-1:2 1 0 0 0 0 0 0 0 0;\r
-       mso-font-charset:178;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:24577 0 0 0 64 0;}\r
-@font-face\r
-       {font-family:"Arabic Transparent";\r
-       panose-1:2 1 0 0 0 0 0 0 0 0;\r
-       mso-font-charset:178;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:8193 0 0 0 64 0;}\r
-@font-face\r
-       {font-family:Andalus;\r
-       panose-1:2 1 0 0 0 0 0 0 0 0;\r
-       mso-font-charset:178;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:24577 0 0 0 64 0;}\r
-@font-face\r
-       {font-family:"Simplified Arabic";\r
-       panose-1:2 1 0 0 0 0 0 0 0 0;\r
-       mso-font-charset:178;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:8193 0 0 0 64 0;}\r
-@font-face\r
-       {font-family:"Simplified Arabic Fixed";\r
-       panose-1:2 1 0 9 0 0 0 0 0 0;\r
-       mso-font-charset:178;\r
-       mso-generic-font-family:modern;\r
-       mso-font-pitch:fixed;\r
-       mso-font-signature:8193 0 0 0 64 0;}\r
-@font-face\r
-       {font-family:Amienne;\r
-       panose-1:4 0 5 8 6 0 0 2 0 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:decorative;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-2147483609 1073741898 0 0 1 0;}\r
-@font-face\r
-       {font-family:Arnprior;\r
-       panose-1:2 0 4 0 0 0 0 0 0 0;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-2147483481 74 0 0 17 0;}\r
-@font-face\r
-       {font-family:Baveuse;\r
-       panose-1:2 0 7 0 0 0 0 0 0 0;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-2147483609 10 0 0 19 0;}\r
-@font-face\r
-       {font-family:Berylium;\r
-       panose-1:2 0 0 0 0 0 0 0 0 0;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-1610612561 74 0 0 403 0;}\r
-@font-face\r
-       {font-family:"Blue Highway";\r
-       panose-1:2 1 6 3 2 2 2 2 3 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-1610612689 10 0 0 403 0;}\r
-@font-face\r
-       {font-family:"Blue Highway Condensed";\r
-       panose-1:2 1 6 3 2 2 2 2 3 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-1610612689 10 0 0 403 0;}\r
-@font-face\r
-       {font-family:"Blue Highway D Type";\r
-       panose-1:0 0 4 0 0 0 0 0 0 0;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Blue Highway Linocut";\r
-       panose-1:0 0 0 0 0 0 0 0 0 0;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-1610612697 0 0 0 403 0;}\r
-@font-face\r
-       {font-family:"Burnstown Dam";\r
-       panose-1:2 0 4 0 0 0 0 0 0 0;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-2147483609 2 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Carbon Block";\r
-       panose-1:0 0 4 0 0 0 0 0 0 0;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-2147483609 2 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Credit Valley";\r
-       panose-1:2 0 4 0 0 0 0 0 0 0;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-2147483601 10 0 0 147 0;}\r
-@font-face\r
-       {font-family:"Earwig Factory";\r
-       panose-1:2 0 4 0 0 0 0 0 0 0;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-2147483609 10 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Hurry Up";\r
-       panose-1:2 0 4 0 0 0 0 0 0 0;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Heavy Heap";\r
-       panose-1:2 0 5 3 0 0 0 2 0 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:Kredit;\r
-       panose-1:2 0 5 6 0 0 0 2 0 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Minya Nouvelle";\r
-       panose-1:0 0 4 0 0 0 0 0 0 0;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-2147483609 2 0 0 1 0;}\r
-@font-face\r
-       {font-family:Neuropol;\r
-       panose-1:2 11 5 0 0 0 0 0 0 0;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-1610612569 268435466 0 0 275 0;}\r
-@font-face\r
-       {font-family:"Planet Benson 2";\r
-       panose-1:2 0 5 3 0 0 0 2 0 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-2147483609 10 0 0 1 0;}\r
-@font-face\r
-       {font-family:Pupcat;\r
-       panose-1:0 0 0 0 0 0 0 0 0 0;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-2147483481 74 0 0 147 0;}\r
-@font-face\r
-       {font-family:Stereofidelic;\r
-       panose-1:2 0 4 0 0 0 0 0 0 0;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-1610612697 10 0 0 273 0;}\r
-@font-face\r
-       {font-family:"Sybil Green";\r
-       panose-1:2 0 5 6 3 0 0 2 0 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-2147483609 2 0 0 1 0;}\r
-@font-face\r
-       {font-family:Teen;\r
-       panose-1:2 0 4 0 0 0 0 0 0 0;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-1610612689 10 0 0 403 0;}\r
-@font-face\r
-       {font-family:"Teen Light";\r
-       panose-1:2 0 4 0 0 0 0 0 0 0;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-1610612689 10 0 0 403 0;}\r
-@font-face\r
-       {font-family:"Velvenda Cooler";\r
-       panose-1:2 0 5 6 0 0 0 2 0 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-1610612697 10 0 0 275 0;}\r
-@font-face\r
-       {font-family:Biondi;\r
-       panose-1:2 0 5 5 3 0 0 2 0 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-2147483601 74 0 0 1 0;}\r
-@font-face\r
-       {font-family:Boopee;\r
-       panose-1:2 0 5 6 2 0 0 2 0 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-2147483609 1342177354 0 0 1 0;}\r
-@font-face\r
-       {font-family:Byington;\r
-       panose-1:2 0 5 5 8 0 0 2 0 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-2147483609 74 0 0 1 0;}\r
-@font-face\r
-       {font-family:Catriel;\r
-       panose-1:2 0 5 3 0 0 0 2 0 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-2147483473 1342177354 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Euphorigenic S";\r
-       panose-1:2 0 4 0 0 0 0 0 0 0;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-2147483601 1073741898 0 0 1 0;}\r
-@font-face\r
-       {font-family:Huxtable;\r
-       panose-1:2 0 5 6 0 0 0 2 0 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-2147483609 1073741898 0 0 1 0;}\r
-@font-face\r
-       {font-family:Ligurino;\r
-       panose-1:2 0 5 3 3 0 0 2 0 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-2147483601 1342177354 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Ligurino Condensed";\r
-       panose-1:2 0 5 6 5 0 0 2 0 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-2147483601 1342177354 0 0 1 0;}\r
-@font-face\r
-       {font-family:Mufferaw;\r
-       panose-1:3 8 6 2 5 3 2 2 2 1;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:script;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-1610612697 72 0 0 275 0;}\r
-@font-face\r
-       {font-family:Tandelle;\r
-       panose-1:2 0 5 8 3 0 0 2 0 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-1610612689 1342177354 0 0 147 0;}\r
-@font-face\r
-       {font-family:Waker;\r
-       panose-1:2 0 4 0 0 0 0 0 0 0;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-2147483645 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Futura Bk";\r
-       panose-1:2 11 5 2 2 2 4 2 3 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:647 0 0 0 159 0;}\r
-@font-face\r
-       {font-family:"Futura Hv";\r
-       panose-1:2 11 7 2 2 2 4 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:647 0 0 0 159 0;}\r
-@font-face\r
-       {font-family:"Futura Lt";\r
-       panose-1:2 11 4 2 2 2 4 2 3 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:647 0 0 0 159 0;}\r
-@font-face\r
-       {font-family:"Futura Md";\r
-       panose-1:2 11 6 2 2 2 4 2 3 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:647 0 0 0 159 0;}\r
-@font-face\r
-       {font-family:"Agency FB";\r
-       panose-1:2 11 5 3 2 2 2 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Albertus Extra Bold";\r
-       panose-1:2 14 8 2 4 3 4 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:"Albertus Medium";\r
-       panose-1:2 14 6 2 3 3 4 2 3 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:"Albertus MT";\r
-       panose-1:2 14 6 2 3 3 4 2 3 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Albertus MT Lt";\r
-       panose-1:2 14 5 2 3 3 4 2 3 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Animals 1";\r
-       panose-1:5 0 0 0 0 0 0 0 0 0;\r
-       mso-font-charset:2;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:0 268435456 0 0 -2147483648 0;}\r
-@font-face\r
-       {font-family:"Animals 2";\r
-       panose-1:5 0 0 0 0 0 0 0 0 0;\r
-       mso-font-charset:2;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:0 268435456 0 0 -2147483648 0;}\r
-@font-face\r
-       {font-family:"Antique Olive";\r
-       panose-1:2 11 6 3 2 2 4 3 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:"Antique Olive CompactPS";\r
-       panose-1:2 11 9 4 3 5 4 3 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:"Antique Olive Roman";\r
-       panose-1:2 11 6 3 2 2 4 3 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:"Apple Chancery";\r
-       panose-1:3 2 7 2 4 5 6 6 5 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:script;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:"Arial Narrow";\r
-       panose-1:2 11 5 6 2 2 2 3 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:647 0 0 0 159 0;}\r
-@font-face\r
-       {font-family:"Arial Rounded MT Bold";\r
-       panose-1:2 15 7 4 3 5 4 3 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:Arrows2;\r
-       panose-1:2 11 6 3 5 3 2 2 2 4;\r
-       mso-font-charset:2;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:0 268435456 0 0 -2147483648 0;}\r
-@font-face\r
-       {font-family:"AvantGarde Bk BT";\r
-       panose-1:2 11 4 2 2 2 2 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:135 0 0 0 27 0;}\r
-@font-face\r
-       {font-family:Balloons;\r
-       panose-1:2 11 6 3 5 3 2 2 2 4;\r
-       mso-font-charset:2;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:0 268435456 0 0 -2147483648 0;}\r
-@font-face\r
-       {font-family:"\@Batang";\r
-       panose-1:2 3 6 0 0 1 1 1 1 1;\r
-       mso-font-charset:129;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-1342176593 1775729915 48 0 524447 0;}\r
-@font-face\r
-       {font-family:BatangChe;\r
-       panose-1:2 3 6 9 0 1 1 1 1 1;\r
-       mso-font-charset:129;\r
-       mso-generic-font-family:modern;\r
-       mso-font-pitch:fixed;\r
-       mso-font-signature:-1342176593 1775729915 48 0 524447 0;}\r
-@font-face\r
-       {font-family:"\@BatangChe";\r
-       panose-1:2 3 6 9 0 1 1 1 1 1;\r
-       mso-font-charset:129;\r
-       mso-generic-font-family:modern;\r
-       mso-font-pitch:fixed;\r
-       mso-font-signature:-1342176593 1775729915 48 0 524447 0;}\r
-@font-face\r
-       {font-family:Gungsuh;\r
-       panose-1:2 3 6 0 0 1 1 1 1 1;\r
-       mso-font-charset:129;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-1342176593 1775729915 48 0 524447 0;}\r
-@font-face\r
-       {font-family:"\@Gungsuh";\r
-       panose-1:2 3 6 0 0 1 1 1 1 1;\r
-       mso-font-charset:129;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-1342176593 1775729915 48 0 524447 0;}\r
-@font-face\r
-       {font-family:GungsuhChe;\r
-       panose-1:2 3 6 9 0 1 1 1 1 1;\r
-       mso-font-charset:129;\r
-       mso-generic-font-family:modern;\r
-       mso-font-pitch:fixed;\r
-       mso-font-signature:-1342176593 1775729915 48 0 524447 0;}\r
-@font-face\r
-       {font-family:"\@GungsuhChe";\r
-       panose-1:2 3 6 9 0 1 1 1 1 1;\r
-       mso-font-charset:129;\r
-       mso-generic-font-family:modern;\r
-       mso-font-pitch:fixed;\r
-       mso-font-signature:-1342176593 1775729915 48 0 524447 0;}\r
-@font-face\r
-       {font-family:"BernhardFashion BT";\r
-       panose-1:4 3 2 5 2 11 2 2 5 2;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:decorative;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:135 0 0 0 27 0;}\r
-@font-face\r
-       {font-family:"Blackadder ITC";\r
-       panose-1:4 2 5 5 5 16 7 2 13 2;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:decorative;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Bodoni MT";\r
-       panose-1:2 7 6 3 8 6 6 2 2 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Bodoni MT Black";\r
-       panose-1:2 7 10 3 8 6 6 2 2 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Bodoni MT Condensed";\r
-       panose-1:2 7 6 6 8 6 6 2 2 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Bodoni Poster";\r
-       panose-1:2 7 10 4 8 9 5 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:"Bodoni PosterCompressed";\r
-       panose-1:2 7 6 8 8 9 5 3 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:BodoniPS;\r
-       panose-1:2 7 6 3 6 7 6 2 3 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:"Boink LET";\r
-       panose-1:0 0 4 0 0 0 0 0 0 0;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:131 0 0 0 9 0;}\r
-@font-face\r
-       {font-family:"Book Antiqua";\r
-       panose-1:2 4 6 2 5 3 5 3 3 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:647 0 0 0 159 0;}\r
-@font-face\r
-       {font-family:"BookmanITC Lt BT";\r
-       panose-1:2 5 6 4 5 5 5 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:135 0 0 0 27 0;}\r
-@font-face\r
-       {font-family:"Bookman Old Style";\r
-       panose-1:2 5 6 4 5 5 5 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:647 0 0 0 159 0;}\r
-@font-face\r
-       {font-family:"Bookshelf Symbol 7";\r
-       panose-1:5 1 1 1 1 1 1 1 1 1;\r
-       mso-font-charset:2;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:0 268435456 0 0 -2147483648 0;}\r
-@font-face\r
-       {font-family:"Bradley Hand ITC";\r
-       panose-1:3 7 4 2 5 3 2 3 2 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:script;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"BrushScript BT";\r
-       panose-1:3 6 8 2 4 4 6 7 3 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:script;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:135 0 0 0 27 0;}\r
-@font-face\r
-       {font-family:Buildings;\r
-       panose-1:2 11 6 3 5 3 2 2 2 4;\r
-       mso-font-charset:2;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:0 268435456 0 0 -2147483648 0;}\r
-@font-face\r
-       {font-family:"Calisto MT";\r
-       panose-1:2 4 6 3 5 5 5 3 3 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:Candid;\r
-       panose-1:5 2 1 2 1 6 7 2 7 5;\r
-       mso-font-charset:2;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:0 268435456 0 0 -2147483648 0;}\r
-@font-face\r
-       {font-family:Castellar;\r
-       panose-1:2 10 4 2 6 4 6 1 3 1;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Century Gothic";\r
-       panose-1:2 11 5 2 2 2 2 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:647 0 0 0 159 0;}\r
-@font-face\r
-       {font-family:"Century Schoolbook";\r
-       panose-1:2 4 6 4 5 5 5 2 3 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:647 0 0 0 159 0;}\r
-@font-face\r
-       {font-family:"CentSchbook BT";\r
-       panose-1:2 4 6 3 5 7 5 2 3 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:135 0 0 0 27 0;}\r
-@font-face\r
-       {font-family:"CG Omega";\r
-       panose-1:2 11 5 2 5 5 8 2 3 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:"CG Times";\r
-       panose-1:2 2 6 3 5 4 5 2 3 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:Chicago;\r
-       panose-1:2 11 8 6 8 6 4 4 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:"Clarendon Condensed";\r
-       panose-1:2 4 7 6 4 7 5 4 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:"Clarendon Light";\r
-       panose-1:2 4 6 4 4 5 5 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:ClarendonPS;\r
-       panose-1:2 4 6 4 4 5 5 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:CommonBullets;\r
-       panose-1:2 11 6 3 5 3 2 2 2 4;\r
-       mso-font-charset:2;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:0 268435456 0 0 -2147483648 0;}\r
-@font-face\r
-       {font-family:"Compacta Blk BT";\r
-       panose-1:2 11 9 4 4 7 2 6 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:135 0 0 0 27 0;}\r
-@font-face\r
-       {font-family:"Compacta Lt BT";\r
-       panose-1:2 11 5 8 3 7 2 6 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:135 0 0 0 27 0;}\r
-@font-face\r
-       {font-family:Computers;\r
-       panose-1:2 11 6 3 5 3 2 2 2 4;\r
-       mso-font-charset:2;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:0 268435456 0 0 -2147483648 0;}\r
-@font-face\r
-       {font-family:"Cooper Black";\r
-       panose-1:2 8 9 4 4 3 11 2 4 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Cooper Md BT";\r
-       panose-1:2 8 6 3 5 3 11 2 4 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:135 0 0 0 27 0;}\r
-@font-face\r
-       {font-family:"Copperplate Gothic Bold";\r
-       panose-1:2 14 7 5 2 2 6 2 4 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"CopprplGoth BT";\r
-       panose-1:2 14 6 5 2 2 3 2 4 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:135 0 0 0 27 0;}\r
-@font-face\r
-       {font-family:"Copperplate Gothic Light";\r
-       panose-1:2 14 5 7 2 2 6 2 4 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:Copperplate32bc;\r
-       panose-1:2 14 6 7 2 2 6 2 4 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:Copperplate33bc;\r
-       panose-1:2 14 9 7 2 2 6 2 4 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:Coronet;\r
-       panose-1:3 3 5 2 4 4 6 7 6 5;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:script;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:CoronetPS;\r
-       panose-1:3 3 5 2 4 4 6 7 6 5;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:script;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:CourierPS;\r
-       panose-1:2 7 6 9 2 2 5 2 4 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:modern;\r
-       mso-font-pitch:fixed;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:"Curlz MT";\r
-       panose-1:4 4 4 4 5 7 2 2 2 2;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:decorative;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:Dauphin;\r
-       panose-1:2 4 5 2 3 3 11 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"DF Calligraphic Ornaments LET";\r
-       panose-1:0 0 4 0 0 0 0 0 0 0;\r
-       mso-font-charset:2;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:0 268435456 0 0 -2147483648 0;}\r
-@font-face\r
-       {font-family:"DF Diversions LET";\r
-       panose-1:0 0 4 0 0 0 0 0 0 0;\r
-       mso-font-charset:2;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:0 268435456 0 0 -2147483648 0;}\r
-@font-face\r
-       {font-family:"DF Diversities LET";\r
-       panose-1:0 0 4 0 0 0 0 0 0 0;\r
-       mso-font-charset:2;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:0 268435456 0 0 -2147483648 0;}\r
-@font-face\r
-       {font-family:"DomBold BT";\r
-       panose-1:3 6 9 2 3 2 2 2 2 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:script;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:135 0 0 0 27 0;}\r
-@font-face\r
-       {font-family:"DomCasual BT";\r
-       panose-1:3 6 9 2 3 3 2 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:script;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:135 0 0 0 27 0;}\r
-@font-face\r
-       {font-family:"Edwardian Script ITC";\r
-       panose-1:3 3 3 2 4 7 7 13 8 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:script;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:Elephant;\r
-       panose-1:2 2 9 4 9 5 5 2 3 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"English111 Presto BT";\r
-       panose-1:3 3 6 2 4 6 7 15 11 5;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:script;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:135 0 0 0 27 0;}\r
-@font-face\r
-       {font-family:"English111 Vivace BT";\r
-       panose-1:3 3 7 2 3 6 7 9 11 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:script;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:135 0 0 0 27 0;}\r
-@font-face\r
-       {font-family:"Engravers MT";\r
-       panose-1:2 9 7 7 8 5 5 2 3 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Eras Bold ITC";\r
-       panose-1:2 11 9 7 3 5 4 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Eras Demi ITC";\r
-       panose-1:2 11 8 5 3 5 4 2 8 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Eras Light ITC";\r
-       panose-1:2 11 4 2 3 5 4 2 8 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Eras Medium ITC";\r
-       panose-1:2 11 6 2 3 5 4 2 8 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:Eurostile;\r
-       panose-1:2 11 5 4 2 2 2 5 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:"Eurostile Bold";\r
-       panose-1:2 11 8 4 2 2 2 5 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:"Eurostile ExtendedTwo";\r
-       panose-1:2 11 5 7 2 2 2 6 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:"EVA Hand 1";\r
-       panose-1:0 0 0 0 0 0 0 0 0 0;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Felix Titling";\r
-       panose-1:4 6 5 5 6 2 2 2 10 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:decorative;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:Festive;\r
-       panose-1:2 11 6 3 5 3 2 2 2 4;\r
-       mso-font-charset:2;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:0 268435456 0 0 -2147483648 0;}\r
-@font-face\r
-       {font-family:FlamencoD;\r
-       panose-1:4 4 8 5 7 16 2 2 13 2;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:decorative;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:Food;\r
-       panose-1:2 11 6 3 5 3 2 2 2 4;\r
-       mso-font-charset:2;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:0 268435456 0 0 -2147483648 0;}\r
-@font-face\r
-       {font-family:Forte;\r
-       panose-1:3 6 9 2 4 5 2 7 2 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:script;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Franklin Gothic Book";\r
-       panose-1:2 11 5 3 2 1 2 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:647 0 0 0 159 0;}\r
-@font-face\r
-       {font-family:"Franklin Gothic Demi";\r
-       panose-1:2 11 7 3 2 1 2 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:647 0 0 0 159 0;}\r
-@font-face\r
-       {font-family:"Franklin Gothic Demi Cond";\r
-       panose-1:2 11 7 6 3 4 2 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:647 0 0 0 159 0;}\r
-@font-face\r
-       {font-family:"Franklin Gothic Heavy";\r
-       panose-1:2 11 9 3 2 1 2 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:647 0 0 0 159 0;}\r
-@font-face\r
-       {font-family:"Franklin Gothic Medium Cond";\r
-       panose-1:2 11 6 6 3 4 2 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:647 0 0 0 159 0;}\r
-@font-face\r
-       {font-family:"French Script MT";\r
-       panose-1:3 2 4 2 4 6 7 4 6 5;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:script;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Futura XBlkCn BT";\r
-       panose-1:2 11 8 6 2 2 4 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:135 0 0 0 27 0;}\r
-@font-face\r
-       {font-family:"Futura Md BT";\r
-       panose-1:2 11 6 2 2 2 4 2 3 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:135 0 0 0 27 0;}\r
-@font-face\r
-       {font-family:Geneva;\r
-       panose-1:2 11 5 3 3 4 4 4 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:Gigi;\r
-       panose-1:4 4 5 4 6 16 7 2 13 2;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:decorative;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Gill Sans MT";\r
-       panose-1:2 11 5 2 2 1 4 2 2 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 3 0;}\r
-@font-face\r
-       {font-family:"Gill Sans MT Condensed";\r
-       panose-1:2 11 5 6 2 1 4 2 2 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 3 0;}\r
-@font-face\r
-       {font-family:"Gill Sans MT Ext Condensed Bold";\r
-       panose-1:2 11 9 2 2 1 4 2 2 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 3 0;}\r
-@font-face\r
-       {font-family:"Gill Sans Ultra Bold";\r
-       panose-1:2 11 10 2 2 1 4 2 2 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 3 0;}\r
-@font-face\r
-       {font-family:"Gill Sans Ultra Bold Condensed";\r
-       panose-1:2 11 10 6 2 1 4 2 2 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 3 0;}\r
-@font-face\r
-       {font-family:GillSans;\r
-       panose-1:2 11 6 2 2 2 4 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:"GillSans Condensed";\r
-       panose-1:2 11 5 6 2 2 4 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:"GillSans ExtraBold";\r
-       panose-1:2 11 9 2 2 2 4 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:"GillSans Light";\r
-       panose-1:2 11 4 2 2 2 4 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:"Gloucester MT Extra Condensed";\r
-       panose-1:2 3 8 8 2 6 1 1 1 1;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:Goudy;\r
-       panose-1:2 2 5 2 5 3 5 2 3 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Goudy ExtraBold";\r
-       panose-1:2 4 7 2 5 3 5 2 3 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Goudy Old Style";\r
-       panose-1:2 2 5 2 5 3 5 2 3 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Goudy Stout";\r
-       panose-1:2 2 9 4 7 3 11 2 4 1;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"\@Gulim";\r
-       panose-1:2 11 6 0 0 1 1 1 1 1;\r
-       mso-font-charset:129;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-1342176593 1775729915 48 0 524447 0;}\r
-@font-face\r
-       {font-family:GulimChe;\r
-       panose-1:2 11 6 9 0 1 1 1 1 1;\r
-       mso-font-charset:129;\r
-       mso-generic-font-family:modern;\r
-       mso-font-pitch:fixed;\r
-       mso-font-signature:-1342176593 1775729915 48 0 524447 0;}\r
-@font-face\r
-       {font-family:"\@GulimChe";\r
-       panose-1:2 11 6 9 0 1 1 1 1 1;\r
-       mso-font-charset:129;\r
-       mso-generic-font-family:modern;\r
-       mso-font-pitch:fixed;\r
-       mso-font-signature:-1342176593 1775729915 48 0 524447 0;}\r
-@font-face\r
-       {font-family:"\@Dotum";\r
-       panose-1:2 11 6 0 0 1 1 1 1 1;\r
-       mso-font-charset:129;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-1342176593 1775729915 48 0 524447 0;}\r
-@font-face\r
-       {font-family:DotumChe;\r
-       panose-1:2 11 6 9 0 1 1 1 1 1;\r
-       mso-font-charset:129;\r
-       mso-generic-font-family:modern;\r
-       mso-font-pitch:fixed;\r
-       mso-font-signature:-1342176593 1775729915 48 0 524447 0;}\r
-@font-face\r
-       {font-family:"\@DotumChe";\r
-       panose-1:2 11 6 9 0 1 1 1 1 1;\r
-       mso-font-charset:129;\r
-       mso-generic-font-family:modern;\r
-       mso-font-pitch:fixed;\r
-       mso-font-signature:-1342176593 1775729915 48 0 524447 0;}\r
-@font-face\r
-       {font-family:Haettenschweiler;\r
-       panose-1:2 11 7 6 4 9 2 6 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:647 0 0 0 159 0;}\r
-@font-face\r
-       {font-family:"Helvetica Condensed";\r
-       panose-1:2 11 6 6 2 2 2 3 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:"Helvetica Narrow";\r
-       panose-1:2 11 6 6 2 2 2 3 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:"Hoefler Text";\r
-       panose-1:2 3 6 2 5 5 6 2 2 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:"Hoefler Text Black";\r
-       panose-1:2 3 8 2 6 7 6 2 2 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:"Hoefler Text Ornaments";\r
-       panose-1:5 9 1 2 1 2 7 2 2 2;\r
-       mso-font-charset:2;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:0 268435456 0 0 -2147483648 0;}\r
-@font-face\r
-       {font-family:Household;\r
-       panose-1:2 11 6 3 5 3 2 2 2 4;\r
-       mso-font-charset:2;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:0 268435456 0 0 -2147483648 0;}\r
-@font-face\r
-       {font-family:"Humanst521 Cn BT";\r
-       panose-1:2 11 5 6 2 2 4 3 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:135 0 0 0 27 0;}\r
-@font-face\r
-       {font-family:Hygiene;\r
-       panose-1:2 11 6 3 5 3 2 2 2 4;\r
-       mso-font-charset:2;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:0 268435456 0 0 -2147483648 0;}\r
-@font-face\r
-       {font-family:"Imprint MT Shadow";\r
-       panose-1:4 2 6 5 6 3 3 3 2 2;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:decorative;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"ITC Avant Garde Gothic Demi";\r
-       panose-1:2 11 8 2 2 2 2 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:"ITC Avant Garde Gothic";\r
-       panose-1:2 11 6 2 2 2 2 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:"ITC Bookman Demi";\r
-       panose-1:2 5 8 4 4 5 5 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:"ITC Bookman Light";\r
-       panose-1:2 5 6 4 5 5 5 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:"ITC Zapf Chancery";\r
-       panose-1:3 2 7 2 4 4 3 8 8 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:script;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:"ITC Zapf Dingbats";\r
-       panose-1:5 2 1 2 1 7 4 2 6 9;\r
-       mso-font-charset:2;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:0 268435456 0 0 -2147483648 0;}\r
-@font-face\r
-       {font-family:"Joanna MT";\r
-       panose-1:2 6 5 2 5 5 5 3 2 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:Kidnap;\r
-       panose-1:5 0 0 0 0 0 0 0 0 0;\r
-       mso-font-charset:2;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:0 268435456 0 0 -2147483648 0;}\r
-@font-face\r
-       {font-family:Kids;\r
-       panose-1:3 5 5 2 4 2 2 2 2 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:script;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Letter Gothic";\r
-       panose-1:2 11 4 9 2 2 2 3 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:modern;\r
-       mso-font-pitch:fixed;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:"Letter GothicPS";\r
-       panose-1:2 11 4 9 2 2 2 3 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:modern;\r
-       mso-font-pitch:fixed;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:Lithograph;\r
-       panose-1:4 11 5 0 0 0 0 0 0 0;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:decorative;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Lubalin Graph";\r
-       panose-1:2 6 5 3 2 2 5 2 4 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:"Lucida Sans";\r
-       panose-1:2 11 6 2 3 5 4 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Lucida Sans Typewriter";\r
-       panose-1:2 11 5 9 3 5 4 3 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:modern;\r
-       mso-font-pitch:fixed;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Maiandra GD";\r
-       panose-1:2 14 5 2 3 3 8 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:Marigold;\r
-       panose-1:3 2 7 2 4 4 2 2 5 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:script;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:MarigoldPS;\r
-       panose-1:3 2 7 2 4 4 2 2 5 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:script;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"\@MingLiU";\r
-       panose-1:2 2 3 9 0 0 0 0 0 0;\r
-       mso-font-charset:136;\r
-       mso-generic-font-family:modern;\r
-       mso-font-pitch:fixed;\r
-       mso-font-signature:3 137232384 22 0 1048577 0;}\r
-@font-face\r
-       {font-family:"\@PMingLiU";\r
-       panose-1:2 2 3 0 0 0 0 0 0 0;\r
-       mso-font-charset:136;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 137232384 22 0 1048577 0;}\r
-@font-face\r
-       {font-family:"Mona Lisa Recut";\r
-       panose-1:4 5 5 4 8 6 3 3 5 2;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:decorative;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:Monaco;\r
-       panose-1:2 11 5 9 3 4 4 4 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:modern;\r
-       mso-font-pitch:fixed;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:"Monotype Corsiva";\r
-       panose-1:3 1 1 1 1 2 1 1 1 1;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:script;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:647 0 0 0 159 0;}\r
-@font-face\r
-       {font-family:"\@MS Gothic";\r
-       panose-1:2 11 6 9 7 2 5 8 2 4;\r
-       mso-font-charset:128;\r
-       mso-generic-font-family:modern;\r
-       mso-font-pitch:fixed;\r
-       mso-font-signature:-1610612033 1757936891 16 0 131231 0;}\r
-@font-face\r
-       {font-family:"MS PGothic";\r
-       panose-1:2 11 6 0 7 2 5 8 2 4;\r
-       mso-font-charset:128;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-1610612033 1757936891 16 0 131231 0;}\r
-@font-face\r
-       {font-family:"\@MS PGothic";\r
-       panose-1:2 11 6 0 7 2 5 8 2 4;\r
-       mso-font-charset:128;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-1610612033 1757936891 16 0 131231 0;}\r
-@font-face\r
-       {font-family:"MS UI Gothic";\r
-       panose-1:2 11 6 0 7 2 5 8 2 4;\r
-       mso-font-charset:128;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-1610612033 1757936891 16 0 131231 0;}\r
-@font-face\r
-       {font-family:"\@MS UI Gothic";\r
-       panose-1:2 11 6 0 7 2 5 8 2 4;\r
-       mso-font-charset:128;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-1610612033 1757936891 16 0 131231 0;}\r
-@font-face\r
-       {font-family:"\@MS Mincho";\r
-       panose-1:2 2 6 9 4 2 5 8 3 4;\r
-       mso-font-charset:128;\r
-       mso-generic-font-family:modern;\r
-       mso-font-pitch:fixed;\r
-       mso-font-signature:-1610612033 1757936891 16 0 131231 0;}\r
-@font-face\r
-       {font-family:"MS PMincho";\r
-       panose-1:2 2 6 0 4 2 5 8 3 4;\r
-       mso-font-charset:128;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-1610612033 1757936891 16 0 131231 0;}\r
-@font-face\r
-       {font-family:"\@MS PMincho";\r
-       panose-1:2 2 6 0 4 2 5 8 3 4;\r
-       mso-font-charset:128;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-1610612033 1757936891 16 0 131231 0;}\r
-@font-face\r
-       {font-family:"MS Outlook";\r
-       panose-1:5 1 1 0 1 0 0 0 0 0;\r
-       mso-font-charset:2;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:0 268435456 0 0 -2147483648 0;}\r
-@font-face\r
-       {font-family:"MS Reference Sans Serif";\r
-       panose-1:2 11 6 4 3 5 4 4 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:536871559 0 0 0 415 0;}\r
-@font-face\r
-       {font-family:"MS Reference Specialty";\r
-       panose-1:5 0 5 0 0 0 0 0 0 0;\r
-       mso-font-charset:2;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:0 268435456 0 0 -2147483648 0;}\r
-@font-face\r
-       {font-family:"MT Extra";\r
-       panose-1:5 5 1 2 1 2 5 2 2 2;\r
-       mso-font-charset:2;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:0 268435456 0 0 -2147483648 0;}\r
-@font-face\r
-       {font-family:Music;\r
-       panose-1:5 0 0 0 0 0 0 0 0 0;\r
-       mso-font-charset:2;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:0 268435456 0 0 -2147483648 0;}\r
-@font-face\r
-       {font-family:"Myriad Condensed Web";\r
-       panose-1:2 11 5 6 3 4 3 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:"Myriad Web";\r
-       panose-1:2 11 5 3 3 4 3 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:"NewBskvll BT";\r
-       panose-1:2 2 6 2 7 5 6 2 3 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:135 0 0 0 27 0;}\r
-@font-face\r
-       {font-family:"New Century Schoolbook";\r
-       panose-1:2 4 6 3 5 7 5 2 3 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:"Nuptial BT";\r
-       panose-1:3 3 6 2 4 4 5 8 11 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:script;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:135 0 0 0 27 0;}\r
-@font-face\r
-       {font-family:"OCR A Extended";\r
-       panose-1:2 1 5 9 2 1 2 1 3 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:modern;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:Optima;\r
-       panose-1:2 11 5 2 5 5 8 2 3 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:Oxford;\r
-       panose-1:3 8 7 2 3 3 2 2 5 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:script;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Palace Script MT";\r
-       panose-1:3 3 3 2 2 6 7 12 11 5;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:script;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:Palatino;\r
-       panose-1:2 4 5 2 5 5 5 3 3 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:Papyrus;\r
-       panose-1:3 7 5 2 6 5 2 3 2 5;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:script;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:Perpetua;\r
-       panose-1:2 2 5 2 6 4 1 2 3 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Perpetua Titling MT";\r
-       panose-1:2 2 5 2 6 5 5 2 8 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:Plants;\r
-       panose-1:2 11 6 3 5 3 2 2 2 4;\r
-       mso-font-charset:2;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:0 268435456 0 0 -2147483648 0;}\r
-@font-face\r
-       {font-family:Pristina;\r
-       panose-1:3 6 4 2 4 4 6 8 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:script;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Rage Italic";\r
-       panose-1:3 7 5 2 4 5 7 7 3 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:script;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:Rockwell;\r
-       panose-1:2 6 6 3 2 2 5 2 4 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Rockwell Condensed";\r
-       panose-1:2 6 6 3 5 4 5 2 1 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Rockwell Extra Bold";\r
-       panose-1:2 6 9 3 4 5 5 2 4 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Script MT Bold";\r
-       panose-1:3 4 6 2 4 6 7 8 9 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:script;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Scruff LET";\r
-       panose-1:0 0 0 0 0 0 0 0 0 0;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:131 0 0 0 9 0;}\r
-@font-face\r
-       {font-family:"\@SimHei";\r
-       panose-1:2 1 6 0 3 1 1 1 1 1;\r
-       mso-font-charset:134;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:1 135135232 16 0 262144 0;}\r
-@font-face\r
-       {font-family:"\@SimSun";\r
-       panose-1:2 1 6 0 3 1 1 1 1 1;\r
-       mso-font-charset:134;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 135135232 16 0 262145 0;}\r
-@font-face\r
-       {font-family:NSimSun;\r
-       panose-1:2 1 6 9 3 1 1 1 1 1;\r
-       mso-font-charset:134;\r
-       mso-generic-font-family:modern;\r
-       mso-font-pitch:fixed;\r
-       mso-font-signature:3 135135232 16 0 262145 0;}\r
-@font-face\r
-       {font-family:"\@NSimSun";\r
-       panose-1:2 1 6 9 3 1 1 1 1 1;\r
-       mso-font-charset:134;\r
-       mso-generic-font-family:modern;\r
-       mso-font-pitch:fixed;\r
-       mso-font-signature:3 135135232 16 0 262145 0;}\r
-@font-face\r
-       {font-family:SimSun-PUA;\r
-       panose-1:2 1 6 0 3 1 1 1 1 1;\r
-       mso-font-charset:134;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:1 403570688 16 0 262144 0;}\r
-@font-face\r
-       {font-family:"\@SimSun-PUA";\r
-       panose-1:2 1 6 0 3 1 1 1 1 1;\r
-       mso-font-charset:134;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:1 403570688 16 0 262144 0;}\r
-@font-face\r
-       {font-family:SportsFigures;\r
-       panose-1:2 11 6 3 5 3 2 2 2 4;\r
-       mso-font-charset:2;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:0 268435456 0 0 -2147483648 0;}\r
-@font-face\r
-       {font-family:"StempelGaramond Roman";\r
-       panose-1:2 2 5 2 5 3 6 2 2 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:SymbolPS;\r
-       panose-1:5 5 1 2 1 6 7 2 6 7;\r
-       mso-font-charset:2;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:0 268435456 0 0 -2147483648 0;}\r
-@font-face\r
-       {font-family:Taffy;\r
-       panose-1:3 5 4 2 3 2 2 3 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:script;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:Technical;\r
-       panose-1:3 5 5 2 4 2 2 2 11 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:script;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:Transportation;\r
-       panose-1:2 11 6 3 5 3 2 2 2 4;\r
-       mso-font-charset:2;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:0 268435456 0 0 -2147483648 0;}\r
-@font-face\r
-       {font-family:"Tw Cen MT";\r
-       panose-1:2 11 6 2 2 1 4 2 6 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 3 0;}\r
-@font-face\r
-       {font-family:"Tw Cen MT Condensed";\r
-       panose-1:2 11 6 6 2 1 4 2 2 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 3 0;}\r
-@font-face\r
-       {font-family:"Tw Cen MT Condensed Extra Bold";\r
-       panose-1:2 11 8 3 2 2 2 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 3 0;}\r
-@font-face\r
-       {font-family:"Univers 45 Light";\r
-       panose-1:2 11 4 3 2 2 2 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:"Univers 47 CondensedLight";\r
-       panose-1:2 11 7 6 3 5 3 5 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:"Univers 55";\r
-       panose-1:2 1 6 3 2 2 2 3 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:"Univers 57 Condensed";\r
-       panose-1:2 11 6 6 2 2 2 6 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:"Univers Condensed";\r
-       panose-1:2 11 6 6 2 2 2 6 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:"Univers ExtendedPS";\r
-       panose-1:2 11 6 5 3 5 2 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:Univers;\r
-       panose-1:2 11 6 3 2 2 2 3 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 147 0;}\r
-@font-face\r
-       {font-family:"VAGRounded BT";\r
-       panose-1:2 15 7 2 2 2 4 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:135 0 0 0 27 0;}\r
-@font-face\r
-       {font-family:"Van Dijk";\r
-       panose-1:3 8 4 2 3 2 2 6 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:script;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:VivaldiD;\r
-       panose-1:3 1 1 1 1 1 1 1 1 1;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:script;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:7 0 0 0 19 0;}\r
-@font-face\r
-       {font-family:Weather;\r
-       panose-1:2 11 6 3 5 3 2 2 2 4;\r
-       mso-font-charset:2;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:0 268435456 0 0 -2147483648 0;}\r
-@font-face\r
-       {font-family:"Wingdings 2";\r
-       panose-1:5 2 1 2 1 5 7 7 7 7;\r
-       mso-font-charset:2;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:0 268435456 0 0 -2147483648 0;}\r
-@font-face\r
-       {font-family:"Wingdings 3";\r
-       panose-1:5 4 1 2 1 8 7 7 7 7;\r
-       mso-font-charset:2;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:0 268435456 0 0 -2147483648 0;}\r
-@font-face\r
-       {font-family:"SWGamekeys MT";\r
-       panose-1:5 1 1 1 1 1 1 1 1 1;\r
-       mso-font-charset:2;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:0 268435456 0 0 -2147483648 0;}\r
-@font-face\r
-       {font-family:"Frutiger SAIN Bd v\.1";\r
-       panose-1:0 0 7 0 0 0 0 0 0 0;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Frutiger SBIN Bd v\.1";\r
-       panose-1:0 0 7 0 0 0 0 0 0 0;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Frutiger SCIN Bd v\.1";\r
-       panose-1:0 0 7 0 0 0 0 0 0 0;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Frutiger SAIN It v\.1";\r
-       panose-1:0 0 4 0 0 0 0 0 0 0;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Frutiger SBIN It v\.1";\r
-       panose-1:0 0 4 0 0 0 0 0 0 0;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Frutiger SCIN It v\.1";\r
-       panose-1:0 0 4 0 0 0 0 0 0 0;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Frutiger SAIN Rm v\.1";\r
-       panose-1:0 0 4 0 0 0 0 0 0 0;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Frutiger SBIN Rm v\.1";\r
-       panose-1:0 0 4 0 0 0 0 0 0 0;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"Frutiger SCIN Rm v\.1";\r
-       panose-1:0 0 4 0 0 0 0 0 0 0;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"StoneSerif SAIN SmBd v\.1";\r
-       panose-1:0 0 4 0 0 0 0 0 0 0;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"StoneSerif SBIN SmBd v\.1";\r
-       panose-1:0 0 4 0 0 0 0 0 0 0;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:"StoneSerif SCIN SmBd v\.1";\r
-       panose-1:0 0 4 0 0 0 0 0 0 0;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:3 0 0 0 1 0;}\r
-@font-face\r
-       {font-family:Calibri;\r
-       panose-1:2 15 5 2 2 2 4 3 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-1610611985 1073750139 0 0 159 0;}\r
-@font-face\r
-       {font-family:Cambria;\r
-       panose-1:2 4 5 3 5 4 6 3 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-1610611985 1073741899 0 0 159 0;}\r
-@font-face\r
-       {font-family:"Cambria Math";\r
-       panose-1:2 4 5 3 5 4 6 3 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-1610611985 1107304683 0 0 159 0;}\r
-@font-face\r
-       {font-family:Candara;\r
-       panose-1:2 14 5 2 3 3 3 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-1610611985 1073750091 0 0 159 0;}\r
-@font-face\r
-       {font-family:Consolas;\r
-       panose-1:2 11 6 9 2 2 4 3 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:modern;\r
-       mso-font-pitch:fixed;\r
-       mso-font-signature:-1610611985 1073750091 0 0 159 0;}\r
-@font-face\r
-       {font-family:Constantia;\r
-       panose-1:2 3 6 2 5 3 6 3 3 3;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-1610611985 1073750091 0 0 159 0;}\r
-@font-face\r
-       {font-family:Corbel;\r
-       panose-1:2 11 5 3 2 2 4 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-1610611985 1073750091 0 0 159 0;}\r
-@font-face\r
-       {font-family:"DejaVu Sans Condensed";\r
-       panose-1:2 11 6 6 3 8 4 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-419422465 1375794687 270369 0 447 0;}\r
-@font-face\r
-       {font-family:"DejaVu Serif";\r
-       panose-1:2 6 6 3 5 6 5 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-469761281 1342206459 262176 0 159 0;}\r
-@font-face\r
-       {font-family:"DejaVu Serif Condensed";\r
-       panose-1:2 6 6 6 5 6 5 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:roman;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-469761281 1342206459 262176 0 159 0;}\r
-@font-face\r
-       {font-family:"DejaVu Sans Mono";\r
-       panose-1:2 11 6 9 3 8 4 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:modern;\r
-       mso-font-pitch:fixed;\r
-       mso-font-signature:-436206849 1342208507 32 0 159 0;}\r
-@font-face\r
-       {font-family:"DejaVu Sans";\r
-       panose-1:2 11 6 3 3 8 4 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-419414273 -771686913 270377 0 -2147483137 0;}\r
-@font-face\r
-       {font-family:"DejaVu Sans Light";\r
-       panose-1:2 11 2 3 3 8 4 2 2 4;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:swiss;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-536860929 1342177403 32 0 415 0;}\r
-@font-face\r
-       {font-family:OpenSymbol;\r
-       panose-1:5 1 0 0 0 0 0 0 0 0;\r
-       mso-font-charset:0;\r
-       mso-generic-font-family:auto;\r
-       mso-font-pitch:variable;\r
-       mso-font-signature:-2147483473 268561642 0 0 1 0;}\r
- /* Style Definitions */\r
- p.MsoNormal, li.MsoNormal, div.MsoNormal\r
-       {mso-style-parent:"";\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-pagination:widow-orphan;\r
-       font-size:8.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-h1\r
-       {mso-style-link:"Heading 1 Char";\r
-       mso-style-next:"Body Text";\r
-       margin-top:12.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:6.0pt;\r
-       margin-left:0mm;\r
-       mso-pagination:widow-orphan;\r
-       page-break-after:avoid;\r
-       mso-outline-level:1;\r
-       font-size:16.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Arial Black";\r
-       color:gray;\r
-       letter-spacing:-1.25pt;\r
-       mso-font-kerning:14.0pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:normal;}\r
-h2\r
-       {mso-style-update:auto;\r
-       mso-style-parent:"Heading 1";\r
-       mso-style-next:"Body Text";\r
-       margin-top:12.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:6.0pt;\r
-       margin-left:0mm;\r
-       mso-line-height-alt:12.0pt;\r
-       mso-pagination:widow-orphan;\r
-       page-break-after:avoid;\r
-       mso-outline-level:2;\r
-       font-size:16.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Arial Black";\r
-       color:gray;\r
-       letter-spacing:-.5pt;\r
-       mso-font-kerning:14.0pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:normal;}\r
-h3\r
-       {mso-style-update:auto;\r
-       mso-style-next:Normal;\r
-       margin-top:6.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:6.0pt;\r
-       margin-left:18.0pt;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       page-break-after:avoid;\r
-       mso-outline-level:3;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:14.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Arial Black";\r
-       mso-hansi-font-family:Symbol;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:normal;}\r
-h4\r
-       {mso-style-update:auto;\r
-       mso-style-parent:MyNormal;\r
-       mso-style-next:Normal;\r
-       margin-top:2.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:12.0pt;\r
-       margin-left:10.0mm;\r
-       mso-pagination:none;\r
-       page-break-after:avoid;\r
-       mso-outline-level:4;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:11.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Courier New";\r
-       text-transform:uppercase;\r
-       letter-spacing:1.5pt;\r
-       mso-ansi-language:AF;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:normal;}\r
-h5\r
-       {mso-style-next:"Body Text";\r
-       margin-top:2.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:12.0pt;\r
-       margin-left:0mm;\r
-       mso-pagination:widow-orphan;\r
-       page-break-after:avoid;\r
-       mso-outline-level:5;\r
-       mso-element:frame;\r
-       mso-element-frame-width:90.0pt;\r
-       mso-element-wrap:around;\r
-       mso-element-anchor-vertical:paragraph;\r
-       mso-element-anchor-horizontal:page;\r
-       mso-element-left:60.05pt;\r
-       mso-element-top:.05pt;\r
-       mso-height-rule:exactly;\r
-       font-size:9.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Arial Black";\r
-       letter-spacing:-.25pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:normal;}\r
-h6\r
-       {mso-style-next:"Body Text";\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-pagination:widow-orphan;\r
-       page-break-after:avoid;\r
-       mso-outline-level:6;\r
-       mso-element:frame;\r
-       mso-element-frame-width:90.0pt;\r
-       mso-element-wrap:around;\r
-       mso-element-anchor-vertical:paragraph;\r
-       mso-element-anchor-horizontal:page;\r
-       mso-element-left:60.05pt;\r
-       mso-element-top:.05pt;\r
-       mso-height-rule:exactly;\r
-       font-size:8.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:normal;}\r
-p.MsoHeading7, li.MsoHeading7, div.MsoHeading7\r
-       {mso-style-next:"Body Text";\r
-       margin-top:3.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-pagination:widow-orphan;\r
-       mso-outline-level:7;\r
-       background:#F2F2F2;\r
-       mso-shading:windowtext;\r
-       mso-pattern:gray-5 auto;\r
-       border:none;\r
-       mso-border-alt:solid white .75pt;\r
-       padding:0mm;\r
-       mso-padding-alt:12.0pt 12.0pt 12.0pt 12.0pt;\r
-       mso-element:frame;\r
-       mso-element-frame-width:189.0pt;\r
-       mso-element-frame-hspace:12.0pt;\r
-       mso-element-wrap:around;\r
-       mso-element-anchor-vertical:paragraph;\r
-       mso-element-anchor-horizontal:page;\r
-       mso-element-left:74.45pt;\r
-       mso-element-top:.05pt;\r
-       mso-height-rule:exactly;\r
-       font-size:14.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       letter-spacing:-.25pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-style:italic;\r
-       mso-bidi-font-style:normal;}\r
-p.MsoHeading8, li.MsoHeading8, div.MsoHeading8\r
-       {mso-style-next:"Body Text";\r
-       margin-top:3.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:0mm;\r
-       margin-bottom:.0001pt;\r
-       text-align:center;\r
-       line-height:16.0pt;\r
-       mso-line-height-rule:exactly;\r
-       mso-pagination:widow-orphan;\r
-       page-break-after:avoid;\r
-       mso-outline-level:8;\r
-       border:none;\r
-       mso-border-top-alt:solid windowtext 3.0pt;\r
-       mso-border-bottom-alt:solid windowtext .75pt;\r
-       padding:0mm;\r
-       mso-padding-alt:0mm 0mm 0mm 0mm;\r
-       mso-element:frame;\r
-       mso-element-frame-width:93.0pt;\r
-       mso-element-wrap:around;\r
-       mso-element-anchor-vertical:paragraph;\r
-       mso-element-anchor-horizontal:page;\r
-       mso-element-left:60.05pt;\r
-       mso-element-top:.05pt;\r
-       mso-height-rule:exactly;\r
-       font-size:7.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Arial Black";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       text-transform:uppercase;\r
-       letter-spacing:3.0pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.MsoHeading9, li.MsoHeading9, div.MsoHeading9\r
-       {mso-style-next:"Body Text";\r
-       margin-top:4.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:3.0pt;\r
-       margin-left:0mm;\r
-       mso-pagination:widow-orphan;\r
-       page-break-after:avoid;\r
-       mso-outline-level:9;\r
-       font-size:8.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       mso-font-kerning:14.0pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;\r
-       font-style:italic;\r
-       mso-bidi-font-style:normal;}\r
-p.MsoIndex1, li.MsoIndex1, div.MsoIndex1\r
-       {mso-style-update:auto;\r
-       mso-style-noshow:yes;\r
-       mso-style-next:Normal;\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:8.0pt;\r
-       margin-bottom:.0001pt;\r
-       text-indent:-8.0pt;\r
-       mso-pagination:widow-orphan;\r
-       font-size:8.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.MsoToc1, li.MsoToc1, div.MsoToc1\r
-       {mso-style-noshow:yes;\r
-       margin-top:6.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-pagination:widow-orphan;\r
-       font-size:14.0pt;\r
-       mso-bidi-font-size:12.0pt;\r
-       font-family:"Arial Black";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       color:black;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-style:italic;}\r
-p.MsoToc2, li.MsoToc2, div.MsoToc2\r
-       {mso-style-noshow:yes;\r
-       mso-style-parent:"TOC 1";\r
-       margin-top:6.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-pagination:widow-orphan;\r
-       font-size:11.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       color:black;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       font-style:italic;\r
-       mso-bidi-font-style:normal;}\r
-p.MsoToc3, li.MsoToc3, div.MsoToc3\r
-       {mso-style-noshow:yes;\r
-       mso-style-next:Normal;\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-pagination:widow-orphan;\r
-       font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.MsoToc4, li.MsoToc4, div.MsoToc4\r
-       {mso-style-noshow:yes;\r
-       mso-style-next:Normal;\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:17.0pt;\r
-       margin-bottom:.0001pt;\r
-       mso-pagination:widow-orphan;\r
-       font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-style:italic;\r
-       mso-bidi-font-style:normal;}\r
-p.MsoToc5, li.MsoToc5, div.MsoToc5\r
-       {mso-style-update:auto;\r
-       mso-style-noshow:yes;\r
-       mso-style-next:Normal;\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:48.0pt;\r
-       margin-bottom:.0001pt;\r
-       mso-pagination:widow-orphan;\r
-       font-size:12.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"MS Mincho";}\r
-p.MsoToc6, li.MsoToc6, div.MsoToc6\r
-       {mso-style-update:auto;\r
-       mso-style-noshow:yes;\r
-       mso-style-next:Normal;\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:60.0pt;\r
-       margin-bottom:.0001pt;\r
-       mso-pagination:widow-orphan;\r
-       font-size:12.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"MS Mincho";}\r
-p.MsoToc7, li.MsoToc7, div.MsoToc7\r
-       {mso-style-update:auto;\r
-       mso-style-noshow:yes;\r
-       mso-style-next:Normal;\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:72.0pt;\r
-       margin-bottom:.0001pt;\r
-       mso-pagination:widow-orphan;\r
-       font-size:12.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"MS Mincho";}\r
-p.MsoToc8, li.MsoToc8, div.MsoToc8\r
-       {mso-style-update:auto;\r
-       mso-style-noshow:yes;\r
-       mso-style-next:Normal;\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:84.0pt;\r
-       margin-bottom:.0001pt;\r
-       mso-pagination:widow-orphan;\r
-       font-size:12.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"MS Mincho";}\r
-p.MsoToc9, li.MsoToc9, div.MsoToc9\r
-       {mso-style-update:auto;\r
-       mso-style-noshow:yes;\r
-       mso-style-next:Normal;\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:96.0pt;\r
-       margin-bottom:.0001pt;\r
-       mso-pagination:widow-orphan;\r
-       font-size:12.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"MS Mincho";}\r
-p.MsoHeader, li.MsoHeader, div.MsoHeader\r
-       {margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-pagination:widow-orphan lines-together;\r
-       tab-stops:center 216.0pt right 432.0pt;\r
-       font-size:7.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Arial Black";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       text-transform:uppercase;\r
-       letter-spacing:3.0pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.MsoFooter, li.MsoFooter, div.MsoFooter\r
-       {margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       text-align:center;\r
-       mso-pagination:widow-orphan lines-together;\r
-       tab-stops:center 216.0pt right 432.0pt;\r
-       border:none;\r
-       mso-border-top-alt:solid windowtext .75pt;\r
-       padding:0mm;\r
-       mso-padding-alt:3.0pt 0mm 0mm 0mm;\r
-       font-size:8.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Arial Black";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.MsoCaption, li.MsoCaption, div.MsoCaption\r
-       {mso-style-noshow:yes;\r
-       mso-style-next:"Body Text";\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:12.0pt;\r
-       margin-left:0mm;\r
-       mso-pagination:widow-orphan;\r
-       font-size:8.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       letter-spacing:-.25pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-span.MsoCommentReference\r
-       {mso-style-noshow:yes;\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:8.0pt;}\r
-span.MsoLineNumber\r
-       {mso-style-parent:"";\r
-       mso-ansi-font-size:9.0pt;\r
-       font-family:Arial;\r
-       mso-ascii-font-family:Arial;\r
-       mso-hansi-font-family:Arial;\r
-       mso-bidi-font-family:Arial;}\r
-span.MsoPageNumber\r
-       {mso-style-parent:"";\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.MsoList, li.MsoList, div.MsoList\r
-       {mso-style-parent:"Body Text";\r
-       mso-style-link:"List Char";\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:12.0pt;\r
-       margin-left:18.0pt;\r
-       text-align:justify;\r
-       mso-pagination:widow-orphan;\r
-       tab-stops:36.0pt;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       letter-spacing:-.25pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.MsoListBullet, li.MsoListBullet, div.MsoListBullet\r
-       {mso-style-parent:List;\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:12.0pt;\r
-       margin-left:18.0pt;\r
-       text-align:justify;\r
-       text-indent:0mm;\r
-       mso-pagination:widow-orphan;\r
-       mso-list:l25 level1 lfo5;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       letter-spacing:-.25pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.MsoListNumber, li.MsoListNumber, div.MsoListNumber\r
-       {mso-style-parent:List;\r
-       margin-top:0mm;\r
-       margin-right:18.0pt;\r
-       margin-bottom:12.0pt;\r
-       margin-left:36.0pt;\r
-       text-align:justify;\r
-       text-indent:-18.0pt;\r
-       mso-pagination:widow-orphan;\r
-       mso-list:l8 level1 lfo7;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       letter-spacing:-.25pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.MsoList2, li.MsoList2, div.MsoList2\r
-       {mso-style-parent:List;\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:12.0pt;\r
-       margin-left:54.0pt;\r
-       text-align:justify;\r
-       mso-pagination:widow-orphan;\r
-       tab-stops:54.0pt;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       letter-spacing:-.25pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.MsoList3, li.MsoList3, div.MsoList3\r
-       {mso-style-parent:List;\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:12.0pt;\r
-       margin-left:72.0pt;\r
-       text-align:justify;\r
-       mso-pagination:widow-orphan;\r
-       tab-stops:72.0pt;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       letter-spacing:-.25pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.MsoList4, li.MsoList4, div.MsoList4\r
-       {mso-style-parent:List;\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:12.0pt;\r
-       margin-left:90.0pt;\r
-       text-align:justify;\r
-       mso-pagination:widow-orphan;\r
-       tab-stops:90.0pt;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       letter-spacing:-.25pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.MsoList5, li.MsoList5, div.MsoList5\r
-       {mso-style-parent:List;\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:12.0pt;\r
-       margin-left:108.0pt;\r
-       text-align:justify;\r
-       mso-pagination:widow-orphan;\r
-       tab-stops:108.0pt;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       letter-spacing:-.25pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.MsoListBullet2, li.MsoListBullet2, div.MsoListBullet2\r
-       {mso-style-parent:"List Bullet";\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:12.0pt;\r
-       margin-left:54.0pt;\r
-       text-align:justify;\r
-       text-indent:0mm;\r
-       mso-pagination:widow-orphan;\r
-       mso-list:l7 level1 lfo8;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       letter-spacing:-.25pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.MsoListBullet3, li.MsoListBullet3, div.MsoListBullet3\r
-       {mso-style-parent:"List Bullet";\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:12.0pt;\r
-       margin-left:72.0pt;\r
-       text-align:justify;\r
-       text-indent:0mm;\r
-       mso-pagination:widow-orphan;\r
-       mso-list:l6 level1 lfo9;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       letter-spacing:-.25pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.MsoListBullet4, li.MsoListBullet4, div.MsoListBullet4\r
-       {mso-style-parent:"List Bullet";\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:12.0pt;\r
-       margin-left:90.0pt;\r
-       text-align:justify;\r
-       text-indent:0mm;\r
-       mso-pagination:widow-orphan;\r
-       mso-list:l5 level1 lfo10;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       letter-spacing:-.25pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.MsoListBullet5, li.MsoListBullet5, div.MsoListBullet5\r
-       {margin-top:0mm;\r
-       margin-right:18.0pt;\r
-       margin-bottom:0mm;\r
-       margin-left:18.0pt;\r
-       margin-bottom:.0001pt;\r
-       text-indent:-18.0pt;\r
-       line-height:16.0pt;\r
-       mso-line-height-rule:exactly;\r
-       mso-pagination:widow-orphan;\r
-       mso-list:l22 level1 lfo12;\r
-       tab-stops:list 18.0pt;\r
-       border:none;\r
-       mso-border-bottom-alt:solid windowtext .75pt;\r
-       padding:0mm;\r
-       mso-padding-alt:0mm 0mm 0mm 0mm;\r
-       mso-element:frame;\r
-       mso-element-frame-width:93.0pt;\r
-       mso-element-wrap:around;\r
-       mso-element-anchor-vertical:paragraph;\r
-       mso-element-anchor-horizontal:page;\r
-       mso-element-left:60.05pt;\r
-       mso-element-top:.05pt;\r
-       mso-height-rule:exactly;\r
-       font-size:9.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.MsoListNumber2, li.MsoListNumber2, div.MsoListNumber2\r
-       {mso-style-parent:"List Number";\r
-       margin-top:0mm;\r
-       margin-right:18.0pt;\r
-       margin-bottom:12.0pt;\r
-       margin-left:54.0pt;\r
-       text-align:justify;\r
-       text-indent:-18.0pt;\r
-       mso-pagination:widow-orphan;\r
-       mso-list:l3 level1 lfo14;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       letter-spacing:-.25pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.MsoListNumber3, li.MsoListNumber3, div.MsoListNumber3\r
-       {mso-style-parent:"List Number";\r
-       margin-top:0mm;\r
-       margin-right:18.0pt;\r
-       margin-bottom:12.0pt;\r
-       margin-left:72.0pt;\r
-       text-align:justify;\r
-       text-indent:-18.0pt;\r
-       mso-pagination:widow-orphan;\r
-       mso-list:l2 level1 lfo15;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       letter-spacing:-.25pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.MsoListNumber4, li.MsoListNumber4, div.MsoListNumber4\r
-       {mso-style-parent:"List Number";\r
-       margin-top:0mm;\r
-       margin-right:18.0pt;\r
-       margin-bottom:12.0pt;\r
-       margin-left:90.0pt;\r
-       text-align:justify;\r
-       text-indent:-18.0pt;\r
-       mso-pagination:widow-orphan;\r
-       mso-list:l1 level1 lfo16;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       letter-spacing:-.25pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.MsoListNumber5, li.MsoListNumber5, div.MsoListNumber5\r
-       {mso-style-parent:"List Number";\r
-       margin-top:0mm;\r
-       margin-right:18.0pt;\r
-       margin-bottom:12.0pt;\r
-       margin-left:108.0pt;\r
-       text-align:justify;\r
-       text-indent:-18.0pt;\r
-       mso-pagination:widow-orphan;\r
-       mso-list:l0 level1 lfo17;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       letter-spacing:-.25pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.MsoTitle, li.MsoTitle, div.MsoTitle\r
-       {mso-style-parent:"Heading Base";\r
-       margin-top:5.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:180.0pt;\r
-       margin-left:0mm;\r
-       text-align:center;\r
-       line-height:30.0pt;\r
-       mso-line-height-rule:exactly;\r
-       mso-pagination:widow-orphan;\r
-       page-break-after:avoid;\r
-       border:none;\r
-       mso-border-bottom-alt:solid gray .75pt;\r
-       padding:0mm;\r
-       mso-padding-alt:0mm 0mm 14.0pt 0mm;\r
-       font-size:24.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Arial Black";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       color:gray;\r
-       letter-spacing:-1.75pt;\r
-       mso-font-kerning:14.0pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.MsoBodyText, li.MsoBodyText, div.MsoBodyText\r
-       {margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:12.0pt;\r
-       margin-left:0mm;\r
-       text-align:justify;\r
-       mso-pagination:widow-orphan;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       letter-spacing:-.25pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.MsoBodyTextIndent, li.MsoBodyTextIndent, div.MsoBodyTextIndent\r
-       {mso-style-parent:"Body Text";\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:12.0pt;\r
-       margin-left:0mm;\r
-       text-align:justify;\r
-       text-indent:18.0pt;\r
-       mso-pagination:widow-orphan;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       letter-spacing:-.25pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.MsoListContinue, li.MsoListContinue, div.MsoListContinue\r
-       {mso-style-parent:List;\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:8.0pt;\r
-       margin-left:18.0pt;\r
-       text-align:justify;\r
-       mso-pagination:widow-orphan;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       letter-spacing:-.25pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.MsoListContinue2, li.MsoListContinue2, div.MsoListContinue2\r
-       {mso-style-parent:"List Continue";\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:8.0pt;\r
-       margin-left:54.0pt;\r
-       text-align:justify;\r
-       mso-pagination:widow-orphan;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       letter-spacing:-.25pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.MsoListContinue3, li.MsoListContinue3, div.MsoListContinue3\r
-       {mso-style-parent:"List Continue";\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:8.0pt;\r
-       margin-left:72.0pt;\r
-       text-align:justify;\r
-       mso-pagination:widow-orphan;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       letter-spacing:-.25pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.MsoListContinue4, li.MsoListContinue4, div.MsoListContinue4\r
-       {mso-style-parent:"List Continue";\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:8.0pt;\r
-       margin-left:90.0pt;\r
-       text-align:justify;\r
-       mso-pagination:widow-orphan;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       letter-spacing:-.25pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.MsoListContinue5, li.MsoListContinue5, div.MsoListContinue5\r
-       {mso-style-parent:"List Continue";\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:8.0pt;\r
-       margin-left:108.0pt;\r
-       text-align:justify;\r
-       mso-pagination:widow-orphan;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       letter-spacing:-.25pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.MsoSubtitle, li.MsoSubtitle, div.MsoSubtitle\r
-       {mso-style-parent:Title;\r
-       mso-style-next:"Body Text";\r
-       margin-top:97.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:0mm;\r
-       margin-bottom:.0001pt;\r
-       text-align:center;\r
-       line-height:10.0pt;\r
-       mso-pagination:widow-orphan;\r
-       page-break-after:avoid;\r
-       border:none;\r
-       mso-border-bottom-alt:solid gray .75pt;\r
-       padding:0mm;\r
-       mso-padding-alt:0mm 0mm 14.0pt 0mm;\r
-       font-size:9.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       color:gray;\r
-       text-transform:uppercase;\r
-       letter-spacing:1.5pt;\r
-       mso-font-kerning:14.0pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       mso-bidi-font-weight:bold;}\r
-p.MsoDate, li.MsoDate, div.MsoDate\r
-       {mso-style-parent:"Body Text";\r
-       margin-top:24.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:8.0pt;\r
-       margin-left:0mm;\r
-       text-align:center;\r
-       mso-pagination:widow-orphan;\r
-       font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-a:link, span.MsoHyperlink\r
-       {color:blue;\r
-       text-decoration:underline;\r
-       text-underline:single;}\r
-a:visited, span.MsoHyperlinkFollowed\r
-       {color:purple;\r
-       text-decoration:underline;\r
-       text-underline:single;}\r
-em\r
-       {mso-style-parent:"";\r
-       mso-ansi-font-size:9.0pt;\r
-       font-family:"Arial Black";\r
-       mso-ascii-font-family:"Arial Black";\r
-       mso-hansi-font-family:"Arial Black";\r
-       font-style:normal;}\r
-p.MsoPlainText, li.MsoPlainText, div.MsoPlainText\r
-       {margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-pagination:widow-orphan;\r
-       font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-fareast-language:FR;}\r
-code\r
-       {font-family:"Courier New";\r
-       mso-ascii-font-family:"Courier New";\r
-       mso-fareast-font-family:"MS Mincho";\r
-       mso-hansi-font-family:"Courier New";\r
-       mso-bidi-font-family:"Courier New";}\r
-span.Heading1Char\r
-       {mso-style-name:"Heading 1 Char";\r
-       mso-style-locked:yes;\r
-       mso-style-link:"Heading 1";\r
-       mso-ansi-font-size:16.0pt;\r
-       font-family:"Arial Black";\r
-       mso-ascii-font-family:"Arial Black";\r
-       mso-hansi-font-family:"Arial Black";\r
-       color:gray;\r
-       letter-spacing:-1.25pt;\r
-       mso-font-kerning:14.0pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       mso-bidi-language:AR-SA;}\r
-p.MyNormal, li.MyNormal, div.MyNormal\r
-       {mso-style-name:MyNormal;\r
-       mso-style-update:auto;\r
-       mso-style-link:"MyNormal Char";\r
-       margin-top:2.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:6.0pt;\r
-       margin-left:42.55pt;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:11.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Courier New";\r
-       mso-ansi-language:AF;\r
-       mso-fareast-language:EN-US;}\r
-span.MyNormalChar\r
-       {mso-style-name:"MyNormal Char";\r
-       mso-style-locked:yes;\r
-       mso-style-parent:"example Char";\r
-       mso-style-link:MyNormal;\r
-       mso-ansi-font-size:11.0pt;\r
-       mso-bidi-font-size:11.0pt;\r
-       font-family:"Courier New";\r
-       mso-bidi-font-family:"Courier New";\r
-       mso-ansi-language:AF;\r
-       mso-fareast-language:EN-US;\r
-       mso-bidi-language:AR-SA;}\r
-span.exampleChar\r
-       {mso-style-name:"example Char";\r
-       mso-style-locked:yes;\r
-       mso-style-link:example;\r
-       mso-ansi-font-size:8.0pt;\r
-       font-family:"Courier New";\r
-       mso-ascii-font-family:"Courier New";\r
-       mso-hansi-font-family:"Courier New";\r
-       mso-bidi-font-family:"Courier New";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       mso-bidi-language:AR-SA;}\r
-p.example, li.example, div.example\r
-       {mso-style-name:example;\r
-       mso-style-update:auto;\r
-       mso-style-link:"example Char";\r
-       margin-top:6.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:6.0pt;\r
-       margin-left:0mm;\r
-       text-indent:36.0pt;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:8.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.FAQ, li.FAQ, div.FAQ\r
-       {mso-style-name:FAQ;\r
-       mso-style-update:auto;\r
-       mso-style-parent:"Heading 3";\r
-       margin-top:12.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:6.0pt;\r
-       margin-left:10.0mm;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       page-break-after:avoid;\r
-       mso-outline-level:3;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:14.0pt;\r
-       font-family:"Comic Sans MS";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-GB;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-span.ListChar\r
-       {mso-style-name:"List Char";\r
-       mso-style-locked:yes;\r
-       mso-style-parent:"Text body Char";\r
-       mso-style-link:List;\r
-       mso-ansi-font-size:12.0pt;\r
-       font-family:Garamond;\r
-       mso-ascii-font-family:Garamond;\r
-       mso-hansi-font-family:Garamond;\r
-       letter-spacing:-.25pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       mso-bidi-language:AR-SA;}\r
-span.TextbodyChar\r
-       {mso-style-name:"Text body Char";\r
-       mso-style-locked:yes;\r
-       mso-style-link:"Text body";\r
-       mso-ansi-font-size:12.0pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       mso-bidi-language:AR-SA;}\r
-p.Textbody, li.Textbody, div.Textbody\r
-       {mso-style-name:"Text body";\r
-       mso-style-link:"Text body Char";\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.HeadingBase, li.HeadingBase, div.HeadingBase\r
-       {mso-style-name:"Heading Base";\r
-       mso-style-next:"Body Text";\r
-       margin-top:12.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:6.0pt;\r
-       margin-left:0mm;\r
-       mso-pagination:widow-orphan;\r
-       page-break-after:avoid;\r
-       font-size:18.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Arial;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       mso-font-kerning:14.0pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.BlockQuotation, li.BlockQuotation, div.BlockQuotation\r
-       {mso-style-name:"Block Quotation";\r
-       mso-style-next:"Body Text";\r
-       margin-top:0mm;\r
-       margin-right:30.0pt;\r
-       margin-bottom:12.0pt;\r
-       margin-left:30.0pt;\r
-       text-align:justify;\r
-       mso-pagination:widow-orphan;\r
-       background:#F9F9F9;\r
-       mso-shading:windowtext;\r
-       mso-pattern:gray-10 gray;\r
-       border:none;\r
-       mso-border-alt:solid white .75pt;\r
-       padding:0mm;\r
-       mso-padding-alt:12.0pt 12.0pt 12.0pt 12.0pt;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       letter-spacing:-.25pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.BlockQuotationFirst, li.BlockQuotationFirst, div.BlockQuotationFirst\r
-       {mso-style-name:"Block Quotation First";\r
-       mso-style-next:"Block Quotation";\r
-       margin-top:0mm;\r
-       margin-right:24.0pt;\r
-       margin-bottom:0mm;\r
-       margin-left:24.0pt;\r
-       margin-bottom:.0001pt;\r
-       text-indent:3.0pt;\r
-       mso-pagination:widow-orphan lines-together;\r
-       background:#E5E5E5;\r
-       mso-shading:windowtext;\r
-       mso-pattern:gray-10 auto;\r
-       border:none;\r
-       mso-border-top-alt:solid white .75pt;\r
-       mso-border-left-alt:solid white .75pt;\r
-       mso-border-right-alt:solid white .75pt;\r
-       padding:0mm;\r
-       mso-padding-alt:6.0pt 6.0pt 0mm 6.0pt;\r
-       font-size:10.5pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Arial Black";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       letter-spacing:-.5pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.BlockQuotationLast, li.BlockQuotationLast, div.BlockQuotationLast\r
-       {mso-style-name:"Block Quotation Last";\r
-       mso-style-parent:"Block Quotation";\r
-       mso-style-next:"Body Text";\r
-       margin-top:0mm;\r
-       margin-right:36.0pt;\r
-       margin-bottom:12.0pt;\r
-       margin-left:36.0pt;\r
-       mso-pagination:widow-orphan lines-together;\r
-       font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-style:italic;\r
-       mso-bidi-font-style:normal;}\r
-p.BodyTextKeep, li.BodyTextKeep, div.BodyTextKeep\r
-       {mso-style-name:"Body Text Keep";\r
-       mso-style-parent:"Body Text";\r
-       mso-style-next:"Body Text";\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:12.0pt;\r
-       margin-left:0mm;\r
-       text-align:justify;\r
-       mso-pagination:widow-orphan;\r
-       page-break-after:avoid;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       letter-spacing:-.25pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.ChapterLabel, li.ChapterLabel, div.ChapterLabel\r
-       {mso-style-name:"Chapter Label";\r
-       mso-style-next:"Body Text";\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:12.0pt;\r
-       margin-left:0mm;\r
-       mso-pagination:widow-orphan;\r
-       page-break-after:avoid;\r
-       border:none;\r
-       mso-border-bottom-alt:solid windowtext .75pt;\r
-       padding:0mm;\r
-       mso-padding-alt:0mm 0mm 3.0pt 0mm;\r
-       font-size:7.5pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Arial Black";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       text-transform:uppercase;\r
-       letter-spacing:3.5pt;\r
-       mso-font-kerning:14.0pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.ChapterSubtitle, li.ChapterSubtitle, div.ChapterSubtitle\r
-       {mso-style-name:"Chapter Subtitle";\r
-       mso-style-next:"Body Text";\r
-       margin-top:0mm;\r
-       margin-right:90.0pt;\r
-       margin-bottom:18.0pt;\r
-       margin-left:0mm;\r
-       mso-line-height-alt:12.0pt;\r
-       mso-pagination:widow-orphan lines-together;\r
-       page-break-after:avoid;\r
-       font-size:14.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       letter-spacing:-1.0pt;\r
-       mso-font-kerning:14.0pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-style:italic;\r
-       mso-bidi-font-style:normal;}\r
-p.ChapterTitle, li.ChapterTitle, div.ChapterTitle\r
-       {mso-style-name:"Chapter Title";\r
-       mso-style-update:auto;\r
-       mso-style-link:"Chapter Title Char";\r
-       mso-style-next:"Chapter Subtitle";\r
-       margin-top:30.0pt;\r
-       margin-right:4.25pt;\r
-       margin-bottom:102.0pt;\r
-       margin-left:0mm;\r
-       text-align:center;\r
-       mso-line-height-alt:22.0pt;\r
-       page-break-before:always;\r
-       mso-pagination:widow-orphan lines-together;\r
-       page-break-after:avoid;\r
-       background:#CCCCCC;\r
-       border:none;\r
-       mso-border-alt:solid windowtext 3.0pt;\r
-       padding:0mm;\r
-       mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;\r
-       font-size:36.0pt;\r
-       mso-bidi-font-size:48.0pt;\r
-       font-family:"Arial Black";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       color:white;\r
-       letter-spacing:-1.75pt;\r
-       mso-font-kerning:14.0pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-span.ChapterTitleChar\r
-       {mso-style-name:"Chapter Title Char";\r
-       mso-style-locked:yes;\r
-       mso-style-link:"Chapter Title";\r
-       mso-ansi-font-size:36.0pt;\r
-       mso-bidi-font-size:48.0pt;\r
-       font-family:"Arial Black";\r
-       mso-ascii-font-family:"Arial Black";\r
-       mso-hansi-font-family:"Arial Black";\r
-       color:white;\r
-       letter-spacing:-1.75pt;\r
-       mso-font-kerning:14.0pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       mso-bidi-language:AR-SA;}\r
-p.CompanyName, li.CompanyName, div.CompanyName\r
-       {mso-style-name:"Company Name";\r
-       mso-style-next:Normal;\r
-       margin-top:21.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:3.0pt;\r
-       margin-left:0mm;\r
-       line-height:16.0pt;\r
-       mso-line-height-rule:exactly;\r
-       mso-pagination:widow-orphan;\r
-       font-size:19.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       text-transform:uppercase;\r
-       mso-font-kerning:18.0pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.DocumentLabel, li.DocumentLabel, div.DocumentLabel\r
-       {mso-style-name:"Document Label";\r
-       margin-top:12.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:18.0pt;\r
-       margin-left:0mm;\r
-       mso-pagination:widow-orphan;\r
-       page-break-after:avoid;\r
-       font-size:18.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       mso-font-kerning:14.0pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.FooterEven, li.FooterEven, div.FooterEven\r
-       {mso-style-name:"Footer Even";\r
-       mso-style-parent:Footer;\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       text-align:center;\r
-       mso-pagination:widow-orphan lines-together;\r
-       tab-stops:center 216.0pt right 432.0pt;\r
-       border:none;\r
-       mso-border-top-alt:solid windowtext .75pt;\r
-       padding:0mm;\r
-       mso-padding-alt:3.0pt 0mm 0mm 0mm;\r
-       font-size:8.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Arial Black";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.FooterFirst, li.FooterFirst, div.FooterFirst\r
-       {mso-style-name:"Footer First";\r
-       mso-style-parent:Footer;\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       text-align:center;\r
-       mso-pagination:widow-orphan lines-together;\r
-       tab-stops:center 216.0pt;\r
-       font-size:8.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Arial Black";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       letter-spacing:-.5pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.FooterOdd, li.FooterOdd, div.FooterOdd\r
-       {mso-style-name:"Footer Odd";\r
-       mso-style-parent:Footer;\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       text-align:center;\r
-       mso-pagination:widow-orphan lines-together;\r
-       tab-stops:right 0mm center 216.0pt right 432.0pt;\r
-       border:none;\r
-       mso-border-top-alt:solid windowtext .75pt;\r
-       padding:0mm;\r
-       mso-padding-alt:3.0pt 0mm 0mm 0mm;\r
-       font-size:8.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Arial Black";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.FootnoteBase, li.FootnoteBase, div.FootnoteBase\r
-       {mso-style-name:"Footnote Base";\r
-       margin-top:12.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-pagination:widow-orphan;\r
-       font-size:9.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.HeaderBase, li.HeaderBase, div.HeaderBase\r
-       {mso-style-name:"Header Base";\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-pagination:widow-orphan lines-together;\r
-       tab-stops:center 216.0pt right 432.0pt;\r
-       font-size:8.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.HeaderEven, li.HeaderEven, div.HeaderEven\r
-       {mso-style-name:"Header Even";\r
-       mso-style-parent:Header;\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-pagination:widow-orphan lines-together;\r
-       tab-stops:center 216.0pt right 432.0pt;\r
-       font-size:7.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Arial Black";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       text-transform:uppercase;\r
-       letter-spacing:3.0pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.HeaderFirst, li.HeaderFirst, div.HeaderFirst\r
-       {mso-style-name:"Header First";\r
-       mso-style-parent:Header;\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-pagination:widow-orphan lines-together;\r
-       tab-stops:center 216.0pt;\r
-       font-size:7.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       text-transform:uppercase;\r
-       letter-spacing:3.0pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.HeaderOdd, li.HeaderOdd, div.HeaderOdd\r
-       {mso-style-name:"Header Odd";\r
-       mso-style-parent:Header;\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       text-align:right;\r
-       mso-pagination:widow-orphan lines-together;\r
-       tab-stops:right 0mm center 216.0pt right 432.0pt;\r
-       font-size:7.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Arial Black";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       text-transform:uppercase;\r
-       letter-spacing:3.0pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.Icon1, li.Icon1, div.Icon1\r
-       {mso-style-name:"Icon 1";\r
-       margin-top:3.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:0mm;\r
-       margin-bottom:.0001pt;\r
-       text-align:center;\r
-       line-height:72.0pt;\r
-       mso-line-height-rule:exactly;\r
-       mso-pagination:widow-orphan;\r
-       background:#E5E5E5;\r
-       mso-shading:windowtext;\r
-       mso-pattern:gray-10 auto;\r
-       mso-element:frame;\r
-       mso-element-frame-width:72.0pt;\r
-       mso-element-frame-hspace:9.35pt;\r
-       mso-element-wrap:around;\r
-       mso-element-anchor-vertical:paragraph;\r
-       mso-element-anchor-horizontal:margin;\r
-       mso-element-top:.05pt;\r
-       mso-height-rule:exactly;\r
-       font-size:80.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Wingdings;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       color:white;\r
-       letter-spacing:-.5pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.IndexBase, li.IndexBase, div.IndexBase\r
-       {mso-style-name:"Index Base";\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       line-height:12.0pt;\r
-       mso-pagination:widow-orphan;\r
-       tab-stops:right 198.0pt;\r
-       font-size:9.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.ListBulletFirst, li.ListBulletFirst, div.ListBulletFirst\r
-       {mso-style-name:"List Bullet First";\r
-       mso-style-parent:"List Bullet";\r
-       mso-style-next:"List Bullet";\r
-       margin-top:4.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:8.0pt;\r
-       margin-left:18.0pt;\r
-       text-indent:0mm;\r
-       mso-pagination:widow-orphan;\r
-       mso-list:l25 level1 lfo5;\r
-       font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.ListBulletLast, li.ListBulletLast, div.ListBulletLast\r
-       {mso-style-name:"List Bullet Last";\r
-       mso-style-parent:"List Bullet";\r
-       mso-style-next:"Body Text";\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:12.0pt;\r
-       margin-left:18.0pt;\r
-       text-indent:0mm;\r
-       mso-pagination:widow-orphan;\r
-       mso-list:l25 level1 lfo5;\r
-       font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.ListFirst, li.ListFirst, div.ListFirst\r
-       {mso-style-name:"List First";\r
-       mso-style-parent:List;\r
-       mso-style-next:List;\r
-       margin-top:4.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:4.0pt;\r
-       margin-left:36.0pt;\r
-       text-indent:-18.0pt;\r
-       mso-pagination:widow-orphan;\r
-       tab-stops:36.0pt;\r
-       font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.ListLast, li.ListLast, div.ListLast\r
-       {mso-style-name:"List Last";\r
-       mso-style-parent:List;\r
-       mso-style-next:"Body Text";\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:12.0pt;\r
-       margin-left:36.0pt;\r
-       text-indent:-18.0pt;\r
-       mso-pagination:widow-orphan;\r
-       tab-stops:36.0pt;\r
-       font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.ListNumberFirst, li.ListNumberFirst, div.ListNumberFirst\r
-       {mso-style-name:"List Number First";\r
-       mso-style-parent:"List Number";\r
-       mso-style-next:"List Number";\r
-       margin-top:4.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:8.0pt;\r
-       margin-left:36.0pt;\r
-       text-indent:-18.0pt;\r
-       mso-pagination:widow-orphan;\r
-       mso-list:l8 level1 lfo7;\r
-       font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.ListNumberLast, li.ListNumberLast, div.ListNumberLast\r
-       {mso-style-name:"List Number Last";\r
-       mso-style-parent:"List Number";\r
-       mso-style-next:"Body Text";\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:12.0pt;\r
-       margin-left:36.0pt;\r
-       text-indent:-18.0pt;\r
-       mso-pagination:widow-orphan;\r
-       mso-list:l8 level1 lfo7;\r
-       font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.PartLabel, li.PartLabel, div.PartLabel\r
-       {mso-style-name:"Part Label";\r
-       mso-style-link:"Part Label Char";\r
-       mso-style-next:Normal;\r
-       margin-top:16.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:0mm;\r
-       margin-bottom:.0001pt;\r
-       text-align:center;\r
-       line-height:78.0pt;\r
-       mso-line-height-rule:exactly;\r
-       mso-pagination:widow-orphan;\r
-       background:#CCCCCC;\r
-       mso-shading:windowtext;\r
-       mso-pattern:gray-20 auto;\r
-       mso-element:frame;\r
-       mso-element-frame-width:102.25pt;\r
-       mso-element-frame-hspace:9.35pt;\r
-       mso-element-frame-vspace:9.35pt;\r
-       mso-element-wrap:no-wrap-beside;\r
-       mso-element-anchor-vertical:page;\r
-       mso-element-anchor-horizontal:margin;\r
-       mso-element-left:right;\r
-       mso-element-top:48.3pt;\r
-       mso-height-rule:exactly;\r
-       font-size:98.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Arial Black";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       color:white;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-span.PartLabelChar\r
-       {mso-style-name:"Part Label Char";\r
-       mso-style-locked:yes;\r
-       mso-style-link:"Part Label";\r
-       mso-ansi-font-size:98.0pt;\r
-       font-family:"Arial Black";\r
-       mso-ascii-font-family:"Arial Black";\r
-       mso-hansi-font-family:"Arial Black";\r
-       color:white;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       mso-bidi-language:AR-SA;}\r
-p.PartSubtitle, li.PartSubtitle, div.PartSubtitle\r
-       {mso-style-name:"Part Subtitle";\r
-       mso-style-next:"Body Text";\r
-       margin-top:18.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:6.0pt;\r
-       margin-left:0mm;\r
-       text-align:center;\r
-       mso-pagination:widow-orphan;\r
-       page-break-after:avoid;\r
-       font-size:16.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Arial;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       mso-font-kerning:14.0pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-style:italic;\r
-       mso-bidi-font-style:normal;}\r
-p.PartTitle, li.PartTitle, div.PartTitle\r
-       {mso-style-name:"Part Title";\r
-       mso-style-next:"Part Label";\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       text-align:center;\r
-       line-height:24.0pt;\r
-       mso-line-height-rule:exactly;\r
-       page-break-before:always;\r
-       mso-pagination:widow-orphan;\r
-       page-break-after:avoid;\r
-       background:#CCCCCC;\r
-       mso-shading:windowtext;\r
-       mso-pattern:gray-20 auto;\r
-       mso-element:frame;\r
-       mso-element-frame-width:102.25pt;\r
-       mso-element-frame-hspace:9.35pt;\r
-       mso-element-frame-vspace:9.35pt;\r
-       mso-element-wrap:no-wrap-beside;\r
-       mso-element-anchor-vertical:page;\r
-       mso-element-anchor-horizontal:margin;\r
-       mso-element-left:right;\r
-       mso-element-top:48.3pt;\r
-       mso-height-rule:exactly;\r
-       font-size:18.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Arial Black";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       letter-spacing:-2.5pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.Picture, li.Picture, div.Picture\r
-       {mso-style-name:Picture;\r
-       mso-style-parent:"Body Text";\r
-       mso-style-next:Caption;\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:12.0pt;\r
-       margin-left:0mm;\r
-       text-align:justify;\r
-       mso-pagination:widow-orphan;\r
-       page-break-after:avoid;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       letter-spacing:-.25pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.ReturnAddress, li.ReturnAddress, div.ReturnAddress\r
-       {mso-style-name:"Return Address";\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       text-align:center;\r
-       mso-pagination:widow-orphan;\r
-       font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       letter-spacing:-.15pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.SectionHeading, li.SectionHeading, div.SectionHeading\r
-       {mso-style-name:"Section Heading";\r
-       mso-style-next:"Body Text";\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       line-height:32.0pt;\r
-       mso-pagination:widow-orphan;\r
-       font-size:7.5pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Arial Black";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       text-transform:uppercase;\r
-       letter-spacing:3.0pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.SectionLabel, li.SectionLabel, div.SectionLabel\r
-       {mso-style-name:"Section Label";\r
-       mso-style-next:Normal;\r
-       margin-top:102.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:18.0pt;\r
-       margin-left:0mm;\r
-       line-height:24.0pt;\r
-       mso-pagination:widow-orphan;\r
-       font-size:24.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Arial Black";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       color:gray;\r
-       letter-spacing:-1.75pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.SubtitleCover, li.SubtitleCover, div.SubtitleCover\r
-       {mso-style-name:"Subtitle Cover";\r
-       mso-style-next:Normal;\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:264.0pt;\r
-       margin-left:0mm;\r
-       line-height:24.0pt;\r
-       mso-line-height-rule:exactly;\r
-       mso-pagination:widow-orphan;\r
-       page-break-after:avoid;\r
-       border:none;\r
-       mso-border-top-alt:solid windowtext .75pt;\r
-       padding:0mm;\r
-       mso-padding-alt:1.0pt 0mm 0mm 0mm;\r
-       font-size:22.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       letter-spacing:-.75pt;\r
-       mso-font-kerning:14.0pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.TitleCover, li.TitleCover, div.TitleCover\r
-       {mso-style-name:"Title Cover";\r
-       mso-style-parent:"Heading Base";\r
-       mso-style-next:"Subtitle Cover";\r
-       margin-top:0mm;\r
-       margin-right:30.0pt;\r
-       margin-bottom:0mm;\r
-       margin-left:30.0pt;\r
-       margin-bottom:.0001pt;\r
-       text-align:right;\r
-       line-height:72.0pt;\r
-       mso-line-height-rule:exactly;\r
-       mso-pagination:widow-orphan;\r
-       background:#E5E5E5;\r
-       mso-shading:windowtext;\r
-       mso-pattern:gray-10 auto;\r
-       border:none;\r
-       mso-border-alt:solid white .75pt;\r
-       padding:0mm;\r
-       mso-padding-alt:31.0pt 31.0pt 31.0pt 31.0pt;\r
-       font-size:72.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       letter-spacing:-3.5pt;\r
-       mso-font-kerning:14.0pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.TOCBase, li.TOCBase, div.TOCBase\r
-       {mso-style-name:"TOC Base";\r
-       mso-style-parent:"TOC 2";\r
-       margin-top:6.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-pagination:widow-orphan;\r
-       font-size:11.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       color:black;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       font-style:italic;\r
-       mso-bidi-font-style:normal;}\r
-span.Lead-inEmphasis\r
-       {mso-style-name:"Lead-in Emphasis";\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:11.0pt;\r
-       text-transform:uppercase;}\r
-span.Superscript\r
-       {mso-style-name:Superscript;\r
-       mso-style-parent:"";\r
-       position:relative;\r
-       top:0pt;\r
-       mso-text-raise:0pt;\r
-       vertical-align:super;}\r
-p.Heading, li.Heading, div.Heading\r
-       {mso-style-name:Heading;\r
-       mso-style-next:Normal;\r
-       margin-top:12.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:6.0pt;\r
-       margin-left:0mm;\r
-       mso-pagination:none;\r
-       page-break-after:avoid;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:14.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Helvetica;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-span.WW-Absatz-Standardschriftart\r
-       {mso-style-name:WW-Absatz-Standardschriftart;\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:12.0pt;}\r
-span.FootnoteSymbol\r
-       {mso-style-name:"Footnote Symbol";\r
-       mso-style-parent:WW-Absatz-Standardschriftart;\r
-       mso-ansi-font-size:12.0pt;\r
-       vertical-align:super;}\r
-span.WW-Absatz-Standardschriftart1\r
-       {mso-style-name:WW-Absatz-Standardschriftart1;\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:12.0pt;}\r
-span.WW-FootnoteSymbol\r
-       {mso-style-name:"WW-Footnote Symbol";\r
-       mso-style-parent:WW-Absatz-Standardschriftart1;\r
-       mso-ansi-font-size:12.0pt;\r
-       vertical-align:super;}\r
-span.WW-Absatz-Standardschriftart11\r
-       {mso-style-name:WW-Absatz-Standardschriftart11;\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:12.0pt;}\r
-span.WW-FootnoteSymbol1\r
-       {mso-style-name:"WW-Footnote Symbol1";\r
-       mso-style-parent:WW-Absatz-Standardschriftart11;\r
-       mso-ansi-font-size:12.0pt;\r
-       vertical-align:super;}\r
-span.WW-Absatz-Standardschriftart111\r
-       {mso-style-name:WW-Absatz-Standardschriftart111;\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:12.0pt;}\r
-span.WW-FootnoteSymbol11\r
-       {mso-style-name:"WW-Footnote Symbol11";\r
-       mso-style-parent:WW-Absatz-Standardschriftart111;\r
-       mso-ansi-font-size:12.0pt;\r
-       vertical-align:super;}\r
-span.WW-Absatz-Standardschriftart1111\r
-       {mso-style-name:WW-Absatz-Standardschriftart1111;\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:12.0pt;}\r
-span.WW-FootnoteSymbol111\r
-       {mso-style-name:"WW-Footnote Symbol111";\r
-       mso-style-parent:WW-Absatz-Standardschriftart1111;\r
-       mso-ansi-font-size:12.0pt;\r
-       vertical-align:super;}\r
-span.WW-Absatz-Standardschriftart11111\r
-       {mso-style-name:WW-Absatz-Standardschriftart11111;\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:12.0pt;}\r
-span.WW-FootnoteSymbol1111\r
-       {mso-style-name:"WW-Footnote Symbol1111";\r
-       mso-style-parent:WW-Absatz-Standardschriftart11111;\r
-       mso-ansi-font-size:12.0pt;\r
-       vertical-align:super;}\r
-span.WW-Absatz-Standardschriftart111111\r
-       {mso-style-name:WW-Absatz-Standardschriftart111111;\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:12.0pt;}\r
-span.WW-FootnoteSymbol11111\r
-       {mso-style-name:"WW-Footnote Symbol11111";\r
-       mso-style-parent:WW-Absatz-Standardschriftart111111;\r
-       mso-ansi-font-size:12.0pt;\r
-       vertical-align:super;}\r
-span.WW-Absatz-Standardschriftart1111111\r
-       {mso-style-name:WW-Absatz-Standardschriftart1111111;\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:12.0pt;}\r
-span.WW-FootnoteSymbol111111\r
-       {mso-style-name:"WW-Footnote Symbol111111";\r
-       mso-style-parent:WW-Absatz-Standardschriftart1111111;\r
-       mso-ansi-font-size:12.0pt;\r
-       vertical-align:super;}\r
-span.WW-Absatz-Standardschriftart11111111\r
-       {mso-style-name:WW-Absatz-Standardschriftart11111111;\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:12.0pt;}\r
-span.WW-FootnoteSymbol1111111\r
-       {mso-style-name:"WW-Footnote Symbol1111111";\r
-       mso-style-parent:WW-Absatz-Standardschriftart11111111;\r
-       mso-ansi-font-size:12.0pt;\r
-       vertical-align:super;}\r
-span.WW-Absatz-Standardschriftart111111111\r
-       {mso-style-name:WW-Absatz-Standardschriftart111111111;\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:12.0pt;}\r
-span.WW-FootnoteSymbol11111111\r
-       {mso-style-name:"WW-Footnote Symbol11111111";\r
-       mso-style-parent:WW-Absatz-Standardschriftart111111111;\r
-       mso-ansi-font-size:12.0pt;\r
-       vertical-align:super;}\r
-span.EndnoteSymbol\r
-       {mso-style-name:"Endnote Symbol";\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:12.0pt;}\r
-span.WW-EndnoteSymbol\r
-       {mso-style-name:"WW-Endnote Symbol";\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:12.0pt;}\r
-span.WW-EndnoteSymbol1\r
-       {mso-style-name:"WW-Endnote Symbol1";\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:12.0pt;}\r
-span.WW-EndnoteSymbol11\r
-       {mso-style-name:"WW-Endnote Symbol11";\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:12.0pt;}\r
-span.WW-EndnoteSymbol111\r
-       {mso-style-name:"WW-Endnote Symbol111";\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:12.0pt;}\r
-span.WW-EndnoteSymbol1111\r
-       {mso-style-name:"WW-Endnote Symbol1111";\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:12.0pt;}\r
-span.WW-EndnoteSymbol11111\r
-       {mso-style-name:"WW-Endnote Symbol11111";\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:12.0pt;}\r
-span.WW-EndnoteSymbol111111\r
-       {mso-style-name:"WW-Endnote Symbol111111";\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:12.0pt;}\r
-span.WW-EndnoteSymbol1111111\r
-       {mso-style-name:"WW-Endnote Symbol1111111";\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:12.0pt;}\r
-span.Internetlink\r
-       {mso-style-name:"Internet link";\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:12.0pt;\r
-       color:navy;\r
-       text-decoration:underline;\r
-       text-underline:single;}\r
-span.WW-Internetlink\r
-       {mso-style-name:"WW-Internet link";\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:12.0pt;\r
-       color:navy;\r
-       text-decoration:underline;\r
-       text-underline:single;}\r
-span.WW-Internetlink1\r
-       {mso-style-name:"WW-Internet link1";\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:12.0pt;\r
-       color:navy;\r
-       text-decoration:underline;\r
-       text-underline:single;}\r
-span.WW-Internetlink11\r
-       {mso-style-name:"WW-Internet link11";\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:12.0pt;\r
-       color:navy;\r
-       text-decoration:underline;\r
-       text-underline:single;}\r
-span.WW-Internetlink111\r
-       {mso-style-name:"WW-Internet link111";\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:12.0pt;\r
-       color:navy;\r
-       text-decoration:underline;\r
-       text-underline:single;}\r
-span.WW-Internetlink1111\r
-       {mso-style-name:"WW-Internet link1111";\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:12.0pt;\r
-       color:navy;\r
-       text-decoration:underline;\r
-       text-underline:single;}\r
-span.WW-Internetlink11111\r
-       {mso-style-name:"WW-Internet link11111";\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:12.0pt;\r
-       color:navy;\r
-       text-decoration:underline;\r
-       text-underline:single;}\r
-span.WW-Internetlink111111\r
-       {mso-style-name:"WW-Internet link111111";\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:12.0pt;\r
-       color:navy;\r
-       text-decoration:underline;\r
-       text-underline:single;}\r
-span.WW-Internetlink1111111\r
-       {mso-style-name:"WW-Internet link1111111";\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:12.0pt;\r
-       color:navy;\r
-       text-decoration:underline;\r
-       text-underline:single;}\r
-span.VisitedInternetLink\r
-       {mso-style-name:"Visited Internet Link";\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:12.0pt;\r
-       color:maroon;\r
-       text-decoration:underline;\r
-       text-underline:single;}\r
-span.WW-VisitedInternetLink\r
-       {mso-style-name:"WW-Visited Internet Link";\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:12.0pt;\r
-       color:maroon;\r
-       text-decoration:underline;\r
-       text-underline:single;}\r
-span.WW-VisitedInternetLink1\r
-       {mso-style-name:"WW-Visited Internet Link1";\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:12.0pt;\r
-       color:maroon;\r
-       text-decoration:underline;\r
-       text-underline:single;}\r
-span.WW-VisitedInternetLink11\r
-       {mso-style-name:"WW-Visited Internet Link11";\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:12.0pt;\r
-       color:maroon;\r
-       text-decoration:underline;\r
-       text-underline:single;}\r
-span.WW-VisitedInternetLink111\r
-       {mso-style-name:"WW-Visited Internet Link111";\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:12.0pt;\r
-       color:maroon;\r
-       text-decoration:underline;\r
-       text-underline:single;}\r
-span.WW-VisitedInternetLink1111\r
-       {mso-style-name:"WW-Visited Internet Link1111";\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:12.0pt;\r
-       color:maroon;\r
-       text-decoration:underline;\r
-       text-underline:single;}\r
-span.WW-VisitedInternetLink11111\r
-       {mso-style-name:"WW-Visited Internet Link11111";\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:12.0pt;\r
-       color:maroon;\r
-       text-decoration:underline;\r
-       text-underline:single;}\r
-span.WW-VisitedInternetLink111111\r
-       {mso-style-name:"WW-Visited Internet Link111111";\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:12.0pt;\r
-       color:maroon;\r
-       text-decoration:underline;\r
-       text-underline:single;}\r
-span.WW-VisitedInternetLink1111111\r
-       {mso-style-name:"WW-Visited Internet Link1111111";\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:12.0pt;\r
-       color:maroon;\r
-       text-decoration:underline;\r
-       text-underline:single;}\r
-span.NumberingSymbols\r
-       {mso-style-name:"Numbering Symbols";\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:12.0pt;}\r
-span.WW-NumberingSymbols\r
-       {mso-style-name:"WW-Numbering Symbols";\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:12.0pt;}\r
-span.WW-NumberingSymbols1\r
-       {mso-style-name:"WW-Numbering Symbols1";\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:12.0pt;}\r
-span.WW-NumberingSymbols11\r
-       {mso-style-name:"WW-Numbering Symbols11";\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:12.0pt;}\r
-span.WW-NumberingSymbols111\r
-       {mso-style-name:"WW-Numbering Symbols111";\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:12.0pt;}\r
-span.WW-NumberingSymbols1111\r
-       {mso-style-name:"WW-Numbering Symbols1111";\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:12.0pt;}\r
-span.WW-NumberingSymbols11111\r
-       {mso-style-name:"WW-Numbering Symbols11111";\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:12.0pt;}\r
-span.BulletSymbols\r
-       {mso-style-name:"Bullet Symbols";\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:9.0pt;\r
-       font-family:starbats;\r
-       mso-ascii-font-family:starbats;\r
-       mso-hansi-font-family:starbats;}\r
-span.WW-BulletSymbols\r
-       {mso-style-name:"WW-Bullet Symbols";\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:9.0pt;\r
-       font-family:starbats;\r
-       mso-ascii-font-family:starbats;\r
-       mso-hansi-font-family:starbats;}\r
-span.WW-BulletSymbols1\r
-       {mso-style-name:"WW-Bullet Symbols1";\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:9.0pt;\r
-       font-family:starbats;\r
-       mso-ascii-font-family:starbats;\r
-       mso-hansi-font-family:starbats;}\r
-span.WW-BulletSymbols11\r
-       {mso-style-name:"WW-Bullet Symbols11";\r
-       mso-style-parent:"";\r
-       mso-ansi-font-size:9.0pt;\r
-       font-family:starbats;\r
-       mso-ascii-font-family:starbats;\r
-       mso-hansi-font-family:starbats;}\r
-p.Index, li.Index, div.Index\r
-       {mso-style-name:Index;\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.ContentsHeading, li.ContentsHeading, div.ContentsHeading\r
-       {mso-style-name:"Contents Heading";\r
-       margin-top:12.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:6.0pt;\r
-       margin-left:0mm;\r
-       mso-pagination:none;\r
-       page-break-after:avoid;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:16.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Helvetica;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.Tableofcontents6, li.Tableofcontents6, div.Tableofcontents6\r
-       {mso-style-name:"Table of contents 6";\r
-       mso-style-parent:Index;\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:70.75pt;\r
-       margin-bottom:.0001pt;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       tab-stops:right dotted 432.0pt;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.Tableofcontents7, li.Tableofcontents7, div.Tableofcontents7\r
-       {mso-style-name:"Table of contents 7";\r
-       mso-style-parent:Index;\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:84.9pt;\r
-       margin-bottom:.0001pt;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       tab-stops:right dotted 432.0pt;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.Tableofcontents8, li.Tableofcontents8, div.Tableofcontents8\r
-       {mso-style-name:"Table of contents 8";\r
-       mso-style-parent:Index;\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:99.05pt;\r
-       margin-bottom:.0001pt;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       tab-stops:right dotted 432.0pt;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.Tableofcontents9, li.Tableofcontents9, div.Tableofcontents9\r
-       {mso-style-name:"Table of contents 9";\r
-       mso-style-parent:Index;\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:113.2pt;\r
-       margin-bottom:.0001pt;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       tab-stops:right dotted 432.0pt;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.Tableofcontents10, li.Tableofcontents10, div.Tableofcontents10\r
-       {mso-style-name:"Table of contents 10";\r
-       mso-style-parent:Index;\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:127.35pt;\r
-       margin-bottom:.0001pt;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       tab-stops:right dotted 432.0pt;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.Textbodyindent, li.Textbodyindent, div.Textbodyindent\r
-       {mso-style-name:"Text body indent";\r
-       mso-style-parent:"Text body";\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:14.15pt;\r
-       margin-bottom:.0001pt;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.ListContents, li.ListContents, div.ListContents\r
-       {mso-style-name:"List Contents";\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:28.3pt;\r
-       margin-bottom:.0001pt;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.FAQexample, li.FAQexample, div.FAQexample\r
-       {mso-style-name:FAQ_example;\r
-       mso-style-parent:example;\r
-       margin-top:12.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:12.0pt;\r
-       margin-left:10.0mm;\r
-       mso-add-space:auto;\r
-       line-height:200%;\r
-       mso-pagination:widow-orphan lines-together;\r
-       page-break-after:avoid;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.FAQexampleCxSpFirst, li.FAQexampleCxSpFirst, div.FAQexampleCxSpFirst\r
-       {mso-style-name:FAQ_exampleCxSpFirst;\r
-       mso-style-parent:example;\r
-       mso-style-type:export-only;\r
-       margin-top:12.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:10.0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-add-space:auto;\r
-       line-height:200%;\r
-       mso-pagination:widow-orphan lines-together;\r
-       page-break-after:avoid;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.FAQexampleCxSpMiddle, li.FAQexampleCxSpMiddle, div.FAQexampleCxSpMiddle\r
-       {mso-style-name:FAQ_exampleCxSpMiddle;\r
-       mso-style-parent:example;\r
-       mso-style-type:export-only;\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:10.0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-add-space:auto;\r
-       line-height:200%;\r
-       mso-pagination:widow-orphan lines-together;\r
-       page-break-after:avoid;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.FAQexampleCxSpLast, li.FAQexampleCxSpLast, div.FAQexampleCxSpLast\r
-       {mso-style-name:FAQ_exampleCxSpLast;\r
-       mso-style-parent:example;\r
-       mso-style-type:export-only;\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:12.0pt;\r
-       margin-left:10.0mm;\r
-       mso-add-space:auto;\r
-       line-height:200%;\r
-       mso-pagination:widow-orphan lines-together;\r
-       page-break-after:avoid;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.Firstlineindent, li.Firstlineindent, div.Firstlineindent\r
-       {mso-style-name:"First line indent";\r
-       mso-style-parent:"Text body";\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       text-align:justify;\r
-       text-indent:14.15pt;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.Hangingindent, li.Hangingindent, div.Hangingindent\r
-       {mso-style-name:"Hanging indent";\r
-       mso-style-parent:"Text body";\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:10.0mm;\r
-       margin-bottom:.0001pt;\r
-       text-align:justify;\r
-       text-indent:-14.15pt;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       tab-stops:10.0mm;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.Numbering3, li.Numbering3, div.Numbering3\r
-       {mso-style-name:"Numbering 3";\r
-       mso-style-parent:List;\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:6.0pt;\r
-       margin-left:42.45pt;\r
-       text-align:justify;\r
-       text-indent:-14.15pt;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.TableContents, li.TableContents, div.TableContents\r
-       {mso-style-name:"Table Contents";\r
-       mso-style-parent:"Text body";\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.TableHeading, li.TableHeading, div.TableHeading\r
-       {mso-style-name:"Table Heading";\r
-       mso-style-parent:"Table Contents";\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       text-align:center;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;\r
-       font-style:italic;\r
-       mso-bidi-font-style:normal;}\r
-p.author, li.author, div.author\r
-       {mso-style-name:author;\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.numberedlist, li.numberedlist, div.numberedlist\r
-       {mso-style-name:"numbered list";\r
-       mso-style-update:auto;\r
-       mso-style-parent:"Heading 4";\r
-       margin-top:3.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:3.0pt;\r
-       margin-left:0mm;\r
-       mso-pagination:none;\r
-       page-break-after:avoid;\r
-       mso-outline-level:4;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       mso-bidi-font-size:12.0pt;\r
-       font-family:"Arial Black";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Courier New";\r
-       letter-spacing:1.0pt;\r
-       mso-ansi-language:AF;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;\r
-       font-style:italic;\r
-       mso-bidi-font-style:normal;}\r
-p.Noteboxtitle, li.Noteboxtitle, div.Noteboxtitle\r
-       {mso-style-name:"Notebox\.title";\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       text-align:center;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:18.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Arial;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;}\r
-p.noteboxexample, li.noteboxexample, div.noteboxexample\r
-       {mso-style-name:"notebox\.example";\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       text-indent:36.0pt;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;}\r
-p.noteboxbody, li.noteboxbody, div.noteboxbody\r
-       {mso-style-name:"notebox\.body";\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-style:italic;}\r
-p.Note, li.Note, div.Note\r
-       {mso-style-name:Note;\r
-       mso-style-update:auto;\r
-       mso-style-link:"Note Char";\r
-       margin-top:6.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:12.0pt;\r
-       margin-left:42.55pt;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       tab-stops:10.0mm;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       mso-bidi-font-size:8.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-GB;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-span.NoteChar\r
-       {mso-style-name:"Note Char";\r
-       mso-style-locked:yes;\r
-       mso-style-link:Note;\r
-       mso-bidi-font-size:8.0pt;\r
-       mso-ansi-language:EN-GB;\r
-       mso-fareast-language:EN-US;\r
-       mso-bidi-language:AR-SA;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.Table, li.Table, div.Table\r
-       {mso-style-name:Table;\r
-       mso-style-parent:Index;\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.flag, li.flag, div.flag\r
-       {mso-style-name:flag;\r
-       mso-style-parent:"Heading 4";\r
-       margin-top:12.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:3.0pt;\r
-       margin-left:10.0mm;\r
-       mso-pagination:none;\r
-       page-break-after:avoid;\r
-       mso-outline-level:4;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:12.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Courier New";\r
-       letter-spacing:1.0pt;\r
-       mso-ansi-language:AF;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;\r
-       font-style:italic;\r
-       mso-bidi-font-style:normal;}\r
-p.flagusage, li.flagusage, div.flagusage\r
-       {mso-style-name:"flag usage";\r
-       mso-style-update:auto;\r
-       mso-style-parent:"Heading 5";\r
-       margin-top:3.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:3.0pt;\r
-       margin-left:42.55pt;\r
-       mso-pagination:none;\r
-       mso-outline-level:5;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:13.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.flagdefault, li.flagdefault, div.flagdefault\r
-       {mso-style-name:"flag default";\r
-       mso-style-parent:"Heading 5";\r
-       margin-top:3.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:3.0pt;\r
-       margin-left:18.0pt;\r
-       mso-pagination:none;\r
-       mso-outline-level:5;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:13.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;}\r
-p.flagdescription, li.flagdescription, div.flagdescription\r
-       {mso-style-name:"flag description";\r
-       mso-style-update:auto;\r
-       mso-style-link:"flag description Char";\r
-       margin-top:6.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:42.55pt;\r
-       margin-bottom:.0001pt;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-span.flagdescriptionChar\r
-       {mso-style-name:"flag description Char";\r
-       mso-style-locked:yes;\r
-       mso-style-link:"flag description";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       mso-bidi-language:AR-SA;}\r
-p.flagNote, li.flagNote, div.flagNote\r
-       {mso-style-name:"flag Note";\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       text-align:justify;\r
-       text-indent:.05pt;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;}\r
-p.flagdescriptionid1, li.flagdescriptionid1, div.flagdescriptionid1\r
-       {mso-style-name:"flag description id1";\r
-       mso-style-parent:"flag description";\r
-       margin-top:6.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:70.9pt;\r
-       margin-bottom:.0001pt;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.output, li.output, div.output\r
-       {mso-style-name:output;\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:18.0pt;\r
-       margin-bottom:.0001pt;\r
-       text-align:justify;\r
-       text-indent:.05pt;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:8.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Courier;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.instruction, li.instruction, div.instruction\r
-       {mso-style-name:instruction;\r
-       mso-style-update:auto;\r
-       mso-style-parent:example;\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:42.55pt;\r
-       margin-bottom:.0001pt;\r
-       line-height:200%;\r
-       mso-pagination:widow-orphan lines-together;\r
-       page-break-after:avoid;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.Format, li.Format, div.Format\r
-       {mso-style-name:Format;\r
-       mso-style-parent:example;\r
-       margin-top:12.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:12.0pt;\r
-       margin-left:10.0mm;\r
-       mso-add-space:auto;\r
-       line-height:200%;\r
-       mso-pagination:widow-orphan lines-together;\r
-       page-break-after:avoid;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-GB;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.FormatCxSpFirst, li.FormatCxSpFirst, div.FormatCxSpFirst\r
-       {mso-style-name:FormatCxSpFirst;\r
-       mso-style-parent:example;\r
-       mso-style-type:export-only;\r
-       margin-top:12.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:10.0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-add-space:auto;\r
-       line-height:200%;\r
-       mso-pagination:widow-orphan lines-together;\r
-       page-break-after:avoid;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-GB;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.FormatCxSpMiddle, li.FormatCxSpMiddle, div.FormatCxSpMiddle\r
-       {mso-style-name:FormatCxSpMiddle;\r
-       mso-style-parent:example;\r
-       mso-style-type:export-only;\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:10.0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-add-space:auto;\r
-       line-height:200%;\r
-       mso-pagination:widow-orphan lines-together;\r
-       page-break-after:avoid;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-GB;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.FormatCxSpLast, li.FormatCxSpLast, div.FormatCxSpLast\r
-       {mso-style-name:FormatCxSpLast;\r
-       mso-style-parent:example;\r
-       mso-style-type:export-only;\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:12.0pt;\r
-       margin-left:10.0mm;\r
-       mso-add-space:auto;\r
-       line-height:200%;\r
-       mso-pagination:widow-orphan lines-together;\r
-       page-break-after:avoid;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-GB;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.ListinFlag, li.ListinFlag, div.ListinFlag\r
-       {mso-style-name:"List in Flag";\r
-       mso-style-parent:List;\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.example2, li.example2, div.example2\r
-       {mso-style-name:example2;\r
-       mso-style-parent:example;\r
-       margin-top:12.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:12.0pt;\r
-       margin-left:20.0mm;\r
-       mso-add-space:auto;\r
-       line-height:200%;\r
-       mso-pagination:widow-orphan lines-together;\r
-       page-break-after:avoid;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.example2CxSpFirst, li.example2CxSpFirst, div.example2CxSpFirst\r
-       {mso-style-name:example2CxSpFirst;\r
-       mso-style-parent:example;\r
-       mso-style-type:export-only;\r
-       margin-top:12.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:20.0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-add-space:auto;\r
-       line-height:200%;\r
-       mso-pagination:widow-orphan lines-together;\r
-       page-break-after:avoid;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.example2CxSpMiddle, li.example2CxSpMiddle, div.example2CxSpMiddle\r
-       {mso-style-name:example2CxSpMiddle;\r
-       mso-style-parent:example;\r
-       mso-style-type:export-only;\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:20.0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-add-space:auto;\r
-       line-height:200%;\r
-       mso-pagination:widow-orphan lines-together;\r
-       page-break-after:avoid;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.example2CxSpLast, li.example2CxSpLast, div.example2CxSpLast\r
-       {mso-style-name:example2CxSpLast;\r
-       mso-style-parent:example;\r
-       mso-style-type:export-only;\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:12.0pt;\r
-       margin-left:20.0mm;\r
-       mso-add-space:auto;\r
-       line-height:200%;\r
-       mso-pagination:widow-orphan lines-together;\r
-       page-break-after:avoid;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.StyleNote, li.StyleNote, div.StyleNote\r
-       {mso-style-name:"Style Note";\r
-       mso-style-parent:Note;\r
-       margin-top:6.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:12.0pt;\r
-       margin-left:-35.45pt;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       tab-stops:10.0mm;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       mso-bidi-font-size:8.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-GB;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;}\r
-p.examplefile, li.examplefile, div.examplefile\r
-       {mso-style-name:example_file;\r
-       mso-style-update:auto;\r
-       margin-top:6.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:6.0pt;\r
-       margin-left:0mm;\r
-       mso-add-space:auto;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       background:#E6E6E6;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       border:none;\r
-       mso-border-alt:solid windowtext .5pt;\r
-       padding:0mm;\r
-       mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;\r
-       font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.examplefileCxSpFirst, li.examplefileCxSpFirst, div.examplefileCxSpFirst\r
-       {mso-style-name:example_fileCxSpFirst;\r
-       mso-style-update:auto;\r
-       mso-style-type:export-only;\r
-       margin-top:6.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-add-space:auto;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       background:#E6E6E6;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       border:none;\r
-       mso-border-alt:solid windowtext .5pt;\r
-       padding:0mm;\r
-       mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;\r
-       font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.examplefileCxSpMiddle, li.examplefileCxSpMiddle, div.examplefileCxSpMiddle\r
-       {mso-style-name:example_fileCxSpMiddle;\r
-       mso-style-update:auto;\r
-       mso-style-type:export-only;\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-add-space:auto;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       background:#E6E6E6;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       border:none;\r
-       mso-border-alt:solid windowtext .5pt;\r
-       padding:0mm;\r
-       mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;\r
-       font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.examplefileCxSpLast, li.examplefileCxSpLast, div.examplefileCxSpLast\r
-       {mso-style-name:example_fileCxSpLast;\r
-       mso-style-update:auto;\r
-       mso-style-type:export-only;\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:6.0pt;\r
-       margin-left:0mm;\r
-       mso-add-space:auto;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       background:#E6E6E6;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       border:none;\r
-       mso-border-alt:solid windowtext .5pt;\r
-       padding:0mm;\r
-       mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;\r
-       font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.Warning, li.Warning, div.Warning\r
-       {mso-style-name:Warning;\r
-       mso-style-update:auto;\r
-       mso-style-link:"Warning Char";\r
-       mso-margin-top-alt:auto;\r
-       margin-right:0mm;\r
-       mso-margin-bottom-alt:auto;\r
-       margin-left:0mm;\r
-       mso-pagination:widow-orphan;\r
-       background:#F7CBB7;\r
-       border:none;\r
-       mso-border-alt:solid windowtext 1.5pt;\r
-       padding:0mm;\r
-       mso-padding-alt:0mm 0mm 0mm 0mm;\r
-       font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-span.WarningChar\r
-       {mso-style-name:"Warning Char";\r
-       mso-style-locked:yes;\r
-       mso-style-parent:"Note Char";\r
-       mso-style-link:Warning;\r
-       mso-bidi-font-size:8.0pt;\r
-       font-family:Garamond;\r
-       mso-ascii-font-family:Garamond;\r
-       mso-hansi-font-family:Garamond;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       mso-bidi-language:AR-SA;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.Heaing3, li.Heaing3, div.Heaing3\r
-       {mso-style-name:"Heaing 3";\r
-       mso-style-parent:Note;\r
-       margin-top:6.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:12.0pt;\r
-       margin-left:42.55pt;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       tab-stops:10.0mm;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       mso-bidi-font-size:8.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-GB;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.NormalJustified, li.NormalJustified, div.NormalJustified\r
-       {mso-style-name:"Normal + Justified";\r
-       mso-style-link:"Normal + Justified Char";\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-GB;\r
-       mso-fareast-language:EN-US;}\r
-span.NormalJustifiedChar\r
-       {mso-style-name:"Normal + Justified Char";\r
-       mso-style-locked:yes;\r
-       mso-style-link:"Normal + Justified";\r
-       mso-ansi-font-size:12.0pt;\r
-       mso-ansi-language:EN-GB;\r
-       mso-fareast-language:EN-US;\r
-       mso-bidi-language:AR-SA;}\r
-p.MyNormalID, li.MyNormalID, div.MyNormalID\r
-       {mso-style-name:MyNormalID;\r
-       mso-style-update:auto;\r
-       mso-style-parent:"List Bullet";\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:31.2pt;\r
-       margin-bottom:.0001pt;\r
-       text-indent:0mm;\r
-       mso-pagination:none;\r
-       mso-list:l8 level1 lfo7;\r
-       mso-hyphenate:none;\r
-       tab-stops:list 18.0pt;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.MyExample, li.MyExample, div.MyExample\r
-       {mso-style-name:MyExample;\r
-       mso-style-update:auto;\r
-       mso-margin-top-alt:auto;\r
-       margin-right:0mm;\r
-       mso-margin-bottom-alt:auto;\r
-       margin-left:20.0mm;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       background:#FFFFCC;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       border:none;\r
-       mso-border-top-alt:solid black .25pt;\r
-       mso-border-bottom-alt:solid black .25pt;\r
-       padding:0mm;\r
-       mso-padding-alt:10.0pt 0mm 10.0pt 0mm;\r
-       font-size:9.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.Style1, li.Style1, div.Style1\r
-       {mso-style-name:Style1;\r
-       mso-style-update:auto;\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-pagination:widow-orphan;\r
-       font-size:8.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-GB;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.StyleHeading6Bold, li.StyleHeading6Bold, div.StyleHeading6Bold\r
-       {mso-style-name:"Style Heading 6 + Bold";\r
-       mso-style-update:auto;\r
-       mso-style-link:"Style Heading 6 + Bold Char";\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-pagination:widow-orphan;\r
-       font-size:8.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;}\r
-span.StyleHeading6BoldChar\r
-       {mso-style-name:"Style Heading 6 + Bold Char";\r
-       mso-style-locked:yes;\r
-       mso-style-link:"Style Heading 6 + Bold";\r
-       mso-ansi-font-size:8.0pt;\r
-       font-family:Garamond;\r
-       mso-ascii-font-family:Garamond;\r
-       mso-hansi-font-family:Garamond;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       mso-bidi-language:AR-SA;\r
-       font-weight:bold;}\r
-p.MyNormaBoldl, li.MyNormaBoldl, div.MyNormaBoldl\r
-       {mso-style-name:MyNormaBoldl;\r
-       mso-style-parent:MyNormal;\r
-       mso-style-link:"MyNormaBoldl Char";\r
-       margin-top:2.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:6.0pt;\r
-       margin-left:42.55pt;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:11.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Courier New";\r
-       mso-ansi-language:AF;\r
-       mso-fareast-language:EN-US;}\r
-p.Mylist, li.Mylist, div.Mylist\r
-       {mso-style-name:Mylist;\r
-       mso-style-parent:MyNormal;\r
-       margin-top:2.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:6.0pt;\r
-       margin-left:128.7pt;\r
-       text-align:justify;\r
-       text-indent:-72.0pt;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:11.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Courier New";\r
-       mso-ansi-language:AF;\r
-       mso-fareast-language:EN-US;\r
-       font-style:italic;\r
-       mso-bidi-font-style:normal;}\r
-p.MyNormalBold, li.MyNormalBold, div.MyNormalBold\r
-       {mso-style-name:MyNormalBold;\r
-       mso-style-parent:MyNormalID;\r
-       margin-top:6.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:12.0pt;\r
-       margin-left:31.2pt;\r
-       text-indent:0mm;\r
-       mso-pagination:lines-together;\r
-       mso-list:l8 level1 lfo7;\r
-       tab-stops:list 18.0pt;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.StyleflagdescriptionBoldItalic, li.StyleflagdescriptionBoldItalic, div.StyleflagdescriptionBoldItalic\r
-       {mso-style-name:"Style flag description + Bold Italic";\r
-       mso-style-update:auto;\r
-       mso-style-parent:"flag description";\r
-       mso-style-link:"Style flag description + Bold Italic Char";\r
-       margin-top:3.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:3.0pt;\r
-       margin-left:42.55pt;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       font-style:italic;}\r
-span.StyleflagdescriptionBoldItalicChar\r
-       {mso-style-name:"Style flag description + Bold Italic Char";\r
-       mso-style-locked:yes;\r
-       mso-style-parent:"flag description Char";\r
-       mso-style-link:"Style flag description + Bold Italic";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       mso-bidi-language:AR-SA;\r
-       font-weight:bold;\r
-       font-style:italic;}\r
-p.Formula, li.Formula, div.Formula\r
-       {mso-style-name:Formula;\r
-       mso-style-parent:"flag description";\r
-       margin-top:6.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:42.55pt;\r
-       margin-bottom:.0001pt;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.examplefilesmall, li.examplefilesmall, div.examplefilesmall\r
-       {mso-style-name:example_file_small;\r
-       mso-style-parent:example_file;\r
-       margin-top:6.0pt;\r
-       margin-right:10.0mm;\r
-       margin-bottom:6.0pt;\r
-       margin-left:0mm;\r
-       mso-add-space:auto;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       background:#E6E6E6;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       border:none;\r
-       mso-border-alt:solid windowtext .5pt;\r
-       padding:0mm;\r
-       mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;\r
-       font-size:8.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.examplefilesmallCxSpFirst, li.examplefilesmallCxSpFirst, div.examplefilesmallCxSpFirst\r
-       {mso-style-name:example_file_smallCxSpFirst;\r
-       mso-style-parent:example_file;\r
-       mso-style-type:export-only;\r
-       margin-top:6.0pt;\r
-       margin-right:10.0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-add-space:auto;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       background:#E6E6E6;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       border:none;\r
-       mso-border-alt:solid windowtext .5pt;\r
-       padding:0mm;\r
-       mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;\r
-       font-size:8.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.examplefilesmallCxSpMiddle, li.examplefilesmallCxSpMiddle, div.examplefilesmallCxSpMiddle\r
-       {mso-style-name:example_file_smallCxSpMiddle;\r
-       mso-style-parent:example_file;\r
-       mso-style-type:export-only;\r
-       margin-top:0mm;\r
-       margin-right:10.0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-add-space:auto;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       background:#E6E6E6;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       border:none;\r
-       mso-border-alt:solid windowtext .5pt;\r
-       padding:0mm;\r
-       mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;\r
-       font-size:8.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.examplefilesmallCxSpLast, li.examplefilesmallCxSpLast, div.examplefilesmallCxSpLast\r
-       {mso-style-name:example_file_smallCxSpLast;\r
-       mso-style-parent:example_file;\r
-       mso-style-type:export-only;\r
-       margin-top:0mm;\r
-       margin-right:10.0mm;\r
-       margin-bottom:6.0pt;\r
-       margin-left:0mm;\r
-       mso-add-space:auto;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       background:#E6E6E6;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       border:none;\r
-       mso-border-alt:solid windowtext .5pt;\r
-       padding:0mm;\r
-       mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;\r
-       font-size:8.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut, li.StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut, div.StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut\r
-       {mso-style-name:"Style notebox\.body + Bold Not Italic Box\: \(Single solid line Aut\.\.\.";\r
-       mso-style-parent:"notebox\.body";\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       background:#FFFF89;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       border:none;\r
-       mso-border-alt:solid windowtext 1.5pt;\r
-       padding:0mm;\r
-       mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;}\r
-p.MyNormalJustified, li.MyNormalJustified, div.MyNormalJustified\r
-       {mso-style-name:MyNormalJustified;\r
-       mso-style-parent:MyNormal;\r
-       margin-top:2.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:6.0pt;\r
-       margin-left:42.55pt;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:11.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Courier New";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.flagheading2, li.flagheading2, div.flagheading2\r
-       {mso-style-name:"flag heading 2";\r
-       mso-style-update:auto;\r
-       mso-style-parent:"flag description";\r
-       margin-top:6.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:45.0pt;\r
-       margin-bottom:.0001pt;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;\r
-       font-style:italic;\r
-       mso-bidi-font-style:normal;\r
-       text-decoration:underline;\r
-       text-underline:single;}\r
-p.example1, li.example1, div.example1\r
-       {mso-style-name:example1;\r
-       mso-style-parent:example2;\r
-       margin-top:12.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:12.0pt;\r
-       margin-left:20.0mm;\r
-       mso-add-space:auto;\r
-       line-height:200%;\r
-       mso-pagination:widow-orphan lines-together;\r
-       page-break-after:avoid;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.example1CxSpFirst, li.example1CxSpFirst, div.example1CxSpFirst\r
-       {mso-style-name:example1CxSpFirst;\r
-       mso-style-parent:example2;\r
-       mso-style-type:export-only;\r
-       margin-top:12.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:20.0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-add-space:auto;\r
-       line-height:200%;\r
-       mso-pagination:widow-orphan lines-together;\r
-       page-break-after:avoid;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.example1CxSpMiddle, li.example1CxSpMiddle, div.example1CxSpMiddle\r
-       {mso-style-name:example1CxSpMiddle;\r
-       mso-style-parent:example2;\r
-       mso-style-type:export-only;\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:20.0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-add-space:auto;\r
-       line-height:200%;\r
-       mso-pagination:widow-orphan lines-together;\r
-       page-break-after:avoid;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.example1CxSpLast, li.example1CxSpLast, div.example1CxSpLast\r
-       {mso-style-name:example1CxSpLast;\r
-       mso-style-parent:example2;\r
-       mso-style-type:export-only;\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:12.0pt;\r
-       margin-left:20.0mm;\r
-       mso-add-space:auto;\r
-       line-height:200%;\r
-       mso-pagination:widow-orphan lines-together;\r
-       page-break-after:avoid;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-span.MyNormaBoldlChar\r
-       {mso-style-name:"MyNormaBoldl Char";\r
-       mso-style-locked:yes;\r
-       mso-style-parent:"MyNormal Char";\r
-       mso-style-link:MyNormaBoldl;\r
-       mso-ansi-font-size:11.0pt;\r
-       mso-bidi-font-size:11.0pt;\r
-       font-family:"Courier New";\r
-       mso-bidi-font-family:"Courier New";\r
-       mso-ansi-language:AF;\r
-       mso-fareast-language:EN-US;\r
-       mso-bidi-language:AR-SA;}\r
-p.MyNormall, li.MyNormall, div.MyNormall\r
-       {mso-style-name:MyNormall;\r
-       mso-style-parent:"Heading 2";\r
-       margin-top:12.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:6.0pt;\r
-       margin-left:0mm;\r
-       mso-line-height-alt:12.0pt;\r
-       mso-pagination:widow-orphan;\r
-       page-break-after:avoid;\r
-       mso-outline-level:2;\r
-       font-size:16.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Arial Black";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       color:gray;\r
-       letter-spacing:-.5pt;\r
-       mso-font-kerning:14.0pt;\r
-       mso-ansi-language:AF;\r
-       mso-fareast-language:EN-US;}\r
-ins\r
-       {mso-style-type:export-only;\r
-       text-decoration:none;}\r
-span.msoDel\r
-       {mso-style-type:export-only;\r
-       mso-style-name:"";\r
-       text-decoration:line-through;\r
-       display:none;\r
-       color:red;}\r
- /* Page Definitions */\r
- @page\r
-       {mso-footnote-separator:url("t_coffee_technical_files/header.htm") fs;\r
-       mso-footnote-continuation-separator:url("t_coffee_technical_files/header.htm") fcs;\r
-       mso-endnote-separator:url("t_coffee_technical_files/header.htm") es;\r
-       mso-endnote-continuation-separator:url("t_coffee_technical_files/header.htm") ecs;}\r
-@page Section1\r
-       {size:210.0mm 842.0pt;\r
-       margin:48.0pt 48.0pt 48.0pt 48.0pt;\r
-       mso-header-margin:0mm;\r
-       mso-footer-margin:0mm;\r
-       mso-page-numbers:0;\r
-       mso-title-page:yes;\r
-       mso-footer:url("t_coffee_technical_files/header.htm") f1;\r
-       mso-paper-source:0;}\r
-div.Section1\r
-       {page:Section1;}\r
-@page Section2\r
-       {size:210.0mm 842.0pt;\r
-       margin:90.0pt 60.0pt 90.0pt 60.0pt;\r
-       mso-header-margin:48.0pt;\r
-       mso-footer-margin:48.0pt;\r
-       mso-page-numbers:roman-lower 1;\r
-       mso-title-page:yes;\r
-       mso-footer:url("t_coffee_technical_files/header.htm") f1;\r
-       mso-first-footer:url("t_coffee_technical_files/header.htm") ff2;\r
-       mso-paper-source:0;}\r
-div.Section2\r
-       {page:Section2;}\r
-@page Section3\r
-       {size:210.0mm 842.0pt;\r
-       margin:90.0pt 60.0pt 90.0pt 60.0pt;\r
-       mso-header-margin:48.0pt;\r
-       mso-footer-margin:48.0pt;\r
-       mso-page-numbers:1;\r
-       mso-header:url("t_coffee_technical_files/header.htm") h3;\r
-       mso-footer:url("t_coffee_technical_files/header.htm") f3;\r
-       mso-first-header:url("t_coffee_technical_files/header.htm") fh3;\r
-       mso-first-footer:url("t_coffee_technical_files/header.htm") ff3;\r
-       mso-paper-source:0;}\r
-div.Section3\r
-       {page:Section3;}\r
-@page Section4\r
-       {size:210.0mm 842.0pt;\r
-       margin:72.0pt 90.0pt 72.0pt 90.0pt;\r
-       mso-header-margin:36.0pt;\r
-       mso-footer-margin:36.0pt;\r
-       mso-header:url("t_coffee_technical_files/header.htm") h4;\r
-       mso-footer:url("t_coffee_technical_files/header.htm") f4;\r
-       mso-first-header:url("t_coffee_technical_files/header.htm") fh4;\r
-       mso-first-footer:url("t_coffee_technical_files/header.htm") ff3;\r
-       mso-paper-source:0;}\r
-div.Section4\r
-       {page:Section4;}\r
- /* List Definitions */\r
- @list l0\r
-       {mso-list-id:-132;\r
-       mso-list-type:simple;\r
-       mso-list-template-ids:243462170;}\r
-@list l0:level1\r
-       {mso-level-style-link:"List Number 3";\r
-       mso-level-tab-stop:90.0pt;\r
-       mso-level-number-position:left;\r
-       margin-left:90.0pt;\r
-       text-indent:-18.0pt;}\r
-@list l1\r
-       {mso-list-id:-131;\r
-       mso-list-type:simple;\r
-       mso-list-template-ids:579796312;}\r
-@list l1:level1\r
-       {mso-level-style-link:"List Number 2";\r
-       mso-level-tab-stop:72.0pt;\r
-       mso-level-number-position:left;\r
-       margin-left:72.0pt;\r
-       text-indent:-18.0pt;}\r
-@list l2\r
-       {mso-list-id:-130;\r
-       mso-list-type:simple;\r
-       mso-list-template-ids:-525153058;}\r
-@list l2:level1\r
-       {mso-level-style-link:"List Bullet 5";\r
-       mso-level-tab-stop:54.0pt;\r
-       mso-level-number-position:left;\r
-       margin-left:54.0pt;\r
-       text-indent:-18.0pt;}\r
-@list l3\r
-       {mso-list-id:-129;\r
-       mso-list-type:simple;\r
-       mso-list-template-ids:1970563230;}\r
-@list l3:level1\r
-       {mso-level-style-link:"List Bullet 4";\r
-       mso-level-tab-stop:36.0pt;\r
-       mso-level-number-position:left;\r
-       text-indent:-18.0pt;}\r
-@list l4\r
-       {mso-list-id:-128;\r
-       mso-list-type:simple;\r
-       mso-list-template-ids:-118980482;}\r
-@list l4:level1\r
-       {mso-level-number-format:bullet;\r
-       mso-level-style-link:"List Bullet 3";\r
-       mso-level-text:\F0B7;\r
-       mso-level-tab-stop:90.0pt;\r
-       mso-level-number-position:left;\r
-       margin-left:90.0pt;\r
-       text-indent:-18.0pt;\r
-       font-family:Symbol;}\r
-@list l5\r
-       {mso-list-id:-127;\r
-       mso-list-type:simple;\r
-       mso-list-template-ids:-1465100272;}\r
-@list l5:level1\r
-       {mso-level-number-format:bullet;\r
-       mso-level-style-link:"List Bullet 2";\r
-       mso-level-text:\F0B7;\r
-       mso-level-tab-stop:72.0pt;\r
-       mso-level-number-position:left;\r
-       margin-left:72.0pt;\r
-       text-indent:-18.0pt;\r
-       font-family:Symbol;}\r
-@list l6\r
-       {mso-list-id:-126;\r
-       mso-list-type:simple;\r
-       mso-list-template-ids:-368430812;}\r
-@list l6:level1\r
-       {mso-level-number-format:bullet;\r
-       mso-level-style-link:"List 5";\r
-       mso-level-text:\F0B7;\r
-       mso-level-tab-stop:54.0pt;\r
-       mso-level-number-position:left;\r
-       margin-left:54.0pt;\r
-       text-indent:-18.0pt;\r
-       font-family:Symbol;}\r
-@list l7\r
-       {mso-list-id:-125;\r
-       mso-list-type:simple;\r
-       mso-list-template-ids:-706941758;}\r
-@list l7:level1\r
-       {mso-level-number-format:bullet;\r
-       mso-level-style-link:"List 4";\r
-       mso-level-text:\F0B7;\r
-       mso-level-tab-stop:36.0pt;\r
-       mso-level-number-position:left;\r
-       text-indent:-18.0pt;\r
-       font-family:Symbol;}\r
-@list l8\r
-       {mso-list-id:-120;\r
-       mso-list-type:simple;\r
-       mso-list-template-ids:1576020400;}\r
-@list l8:level1\r
-       {mso-level-style-link:"Plain Text";\r
-       mso-level-tab-stop:18.0pt;\r
-       mso-level-number-position:left;\r
-       margin-left:18.0pt;\r
-       text-indent:-18.0pt;}\r
-@list l9\r
-       {mso-list-id:-119;\r
-       mso-list-type:simple;\r
-       mso-list-template-ids:96769246;}\r
-@list l9:level1\r
-       {mso-level-number-format:bullet;\r
-       mso-level-style-link:"Text body Char";\r
-       mso-level-text:\F0B7;\r
-       mso-level-tab-stop:18.0pt;\r
-       mso-level-number-position:left;\r
-       margin-left:18.0pt;\r
-       text-indent:-18.0pt;\r
-       font-family:Symbol;}\r
-@list l10\r
-       {mso-list-id:-5;\r
-       mso-list-template-ids:-1557078836;}\r
-@list l10:level1\r
-       {mso-level-number-format:none;\r
-       mso-level-suffix:none;\r
-       mso-level-text:"";\r
-       mso-level-tab-stop:none;\r
-       mso-level-number-position:left;\r
-       margin-left:0mm;\r
-       text-indent:0mm;}\r
-@list l10:level2\r
-       {mso-level-number-format:none;\r
-       mso-level-text:"";\r
-       mso-level-tab-stop:none;\r
-       mso-level-number-position:left;\r
-       mso-level-legacy:yes;\r
-       mso-level-legacy-indent:0mm;\r
-       mso-level-legacy-space:0mm;\r
-       margin-left:0mm;\r
-       text-indent:0mm;}\r
-@list l10:level3\r
-       {mso-level-number-format:none;\r
-       mso-level-text:"";\r
-       mso-level-tab-stop:none;\r
-       mso-level-number-position:left;\r
-       mso-level-legacy:yes;\r
-       mso-level-legacy-indent:0mm;\r
-       mso-level-legacy-space:0mm;\r
-       margin-left:0mm;\r
-       text-indent:0mm;}\r
-@list l10:level4\r
-       {mso-level-number-format:none;\r
-       mso-level-text:"";\r
-       mso-level-tab-stop:none;\r
-       mso-level-number-position:left;\r
-       mso-level-legacy:yes;\r
-       mso-level-legacy-indent:0mm;\r
-       mso-level-legacy-space:0mm;\r
-       margin-left:0mm;\r
-       text-indent:0mm;\r
-       mso-ansi-language:EN-GB;}\r
-@list l10:level5\r
-       {mso-level-start-at:0;\r
-       mso-level-number-format:none;\r
-       mso-level-text:"";\r
-       mso-level-tab-stop:none;\r
-       mso-level-number-position:left;\r
-       margin-left:0mm;\r
-       text-indent:0mm;}\r
-@list l10:level6\r
-       {mso-level-start-at:0;\r
-       mso-level-number-format:none;\r
-       mso-level-text:"";\r
-       mso-level-tab-stop:none;\r
-       mso-level-number-position:left;\r
-       margin-left:0mm;\r
-       text-indent:0mm;}\r
-@list l10:level7\r
-       {mso-level-start-at:0;\r
-       mso-level-number-format:none;\r
-       mso-level-text:"";\r
-       mso-level-tab-stop:none;\r
-       mso-level-number-position:left;\r
-       margin-left:0mm;\r
-       text-indent:0mm;}\r
-@list l10:level8\r
-       {mso-level-start-at:0;\r
-       mso-level-number-format:none;\r
-       mso-level-text:"";\r
-       mso-level-tab-stop:none;\r
-       mso-level-number-position:left;\r
-       margin-left:0mm;\r
-       text-indent:0mm;}\r
-@list l10:level9\r
-       {mso-level-start-at:0;\r
-       mso-level-number-format:none;\r
-       mso-level-text:"";\r
-       mso-level-tab-stop:none;\r
-       mso-level-number-position:left;\r
-       margin-left:0mm;\r
-       text-indent:0mm;}\r
-@list l11\r
-       {mso-list-id:-2;\r
-       mso-list-type:simple;\r
-       mso-list-template-ids:-1;}\r
-@list l11:level1\r
-       {mso-level-start-at:0;\r
-       mso-level-text:*;\r
-       mso-level-tab-stop:none;\r
-       mso-level-number-position:left;\r
-       margin-left:0mm;\r
-       text-indent:0mm;}\r
-@list l12\r
-       {mso-list-id:16198800;\r
-       mso-list-type:hybrid;\r
-       mso-list-template-ids:-1589361750 67895311 67895321 67895323 67895311 67895321 67895323 67895311 67895321 67895323;}\r
-@list l12:level1\r
-       {mso-level-tab-stop:78.55pt;\r
-       mso-level-number-position:left;\r
-       margin-left:78.55pt;\r
-       text-indent:-18.0pt;}\r
-@list l12:level2\r
-       {mso-level-number-format:alpha-lower;\r
-       mso-level-tab-stop:114.55pt;\r
-       mso-level-number-position:left;\r
-       margin-left:114.55pt;\r
-       text-indent:-18.0pt;}\r
-@list l13\r
-       {mso-list-id:31855817;\r
-       mso-list-type:hybrid;\r
-       mso-list-template-ids:1137623166 -1 -1 -1 -1 -1 -1 -1 -1 -1;}\r
-@list l13:level1\r
-       {mso-level-number-format:bullet;\r
-       mso-level-text:\F0A7;\r
-       mso-level-tab-stop:108.0pt;\r
-       mso-level-number-position:left;\r
-       margin-left:108.0pt;\r
-       text-indent:-18.0pt;\r
-       font-family:Wingdings;}\r
-@list l14\r
-       {mso-list-id:351080084;\r
-       mso-list-template-ids:1670832864;}\r
-@list l14:level1\r
-       {mso-level-number-format:bullet;\r
-       mso-level-text:\F0B7;\r
-       mso-level-tab-stop:36.0pt;\r
-       mso-level-number-position:left;\r
-       text-indent:-18.0pt;\r
-       mso-ansi-font-size:10.0pt;\r
-       font-family:Symbol;}\r
-@list l14:level2\r
-       {mso-level-tab-stop:72.0pt;\r
-       mso-level-number-position:left;\r
-       text-indent:-18.0pt;}\r
-@list l15\r
-       {mso-list-id:429860257;\r
-       mso-list-type:simple;\r
-       mso-list-template-ids:-1193904264;}\r
-@list l15:level1\r
-       {mso-level-tab-stop:none;\r
-       mso-level-number-position:left;\r
-       mso-level-legacy:yes;\r
-       mso-level-legacy-indent:18.0pt;\r
-       mso-level-legacy-space:0mm;\r
-       margin-right:36.0pt;\r
-       text-indent:-18.0pt;\r
-       mso-ansi-font-size:10.0pt;\r
-       mso-ascii-font-family:"Arial Black";\r
-       mso-hansi-font-family:"Arial Black";}\r
-@list l16\r
-       {mso-list-id:873344605;\r
-       mso-list-template-ids:1828727762;}\r
-@list l16:level1\r
-       {mso-level-number-format:bullet;\r
-       mso-level-text:\F0A7;\r
-       mso-level-tab-stop:18.0pt;\r
-       mso-level-number-position:left;\r
-       margin-left:18.0pt;\r
-       text-indent:-18.0pt;\r
-       font-family:Wingdings;}\r
-@list l16:level2\r
-       {mso-level-number-format:none;\r
-       mso-level-text:"";\r
-       mso-level-tab-stop:none;\r
-       mso-level-number-position:left;\r
-       mso-level-legacy:yes;\r
-       mso-level-legacy-indent:0mm;\r
-       mso-level-legacy-space:0mm;\r
-       margin-left:0mm;\r
-       text-indent:0mm;}\r
-@list l16:level3\r
-       {mso-level-number-format:none;\r
-       mso-level-text:"";\r
-       mso-level-tab-stop:none;\r
-       mso-level-number-position:left;\r
-       mso-level-legacy:yes;\r
-       mso-level-legacy-indent:0mm;\r
-       mso-level-legacy-space:0mm;\r
-       margin-left:0mm;\r
-       text-indent:0mm;}\r
-@list l16:level4\r
-       {mso-level-number-format:none;\r
-       mso-level-text:"";\r
-       mso-level-tab-stop:none;\r
-       mso-level-number-position:left;\r
-       mso-level-legacy:yes;\r
-       mso-level-legacy-indent:0mm;\r
-       mso-level-legacy-space:0mm;\r
-       margin-left:0mm;\r
-       text-indent:0mm;}\r
-@list l16:level5\r
-       {mso-level-start-at:0;\r
-       mso-level-number-format:none;\r
-       mso-level-text:"";\r
-       mso-level-tab-stop:none;\r
-       mso-level-number-position:left;\r
-       margin-left:0mm;\r
-       text-indent:0mm;}\r
-@list l16:level6\r
-       {mso-level-start-at:0;\r
-       mso-level-number-format:none;\r
-       mso-level-text:"";\r
-       mso-level-tab-stop:none;\r
-       mso-level-number-position:left;\r
-       margin-left:0mm;\r
-       text-indent:0mm;}\r
-@list l16:level7\r
-       {mso-level-start-at:0;\r
-       mso-level-number-format:none;\r
-       mso-level-text:"";\r
-       mso-level-tab-stop:none;\r
-       mso-level-number-position:left;\r
-       margin-left:0mm;\r
-       text-indent:0mm;}\r
-@list l16:level8\r
-       {mso-level-start-at:0;\r
-       mso-level-number-format:none;\r
-       mso-level-text:"";\r
-       mso-level-tab-stop:none;\r
-       mso-level-number-position:left;\r
-       margin-left:0mm;\r
-       text-indent:0mm;}\r
-@list l16:level9\r
-       {mso-level-start-at:0;\r
-       mso-level-number-format:none;\r
-       mso-level-text:"";\r
-       mso-level-tab-stop:none;\r
-       mso-level-number-position:left;\r
-       margin-left:0mm;\r
-       text-indent:0mm;}\r
-@list l17\r
-       {mso-list-id:934939961;\r
-       mso-list-type:hybrid;\r
-       mso-list-template-ids:-467735746 67895311 67895321 67895323 67895311 67895321 67895323 67895311 67895321 67895323;}\r
-@list l17:level1\r
-       {mso-level-tab-stop:78.55pt;\r
-       mso-level-number-position:left;\r
-       margin-left:78.55pt;\r
-       text-indent:-18.0pt;}\r
-@list l18\r
-       {mso-list-id:941451051;\r
-       mso-list-type:hybrid;\r
-       mso-list-template-ids:1232603580 67895311 67895321 67895323 67895311 67895321 67895323 67895311 67895321 67895323;}\r
-@list l18:level1\r
-       {mso-level-tab-stop:78.55pt;\r
-       mso-level-number-position:left;\r
-       margin-left:78.55pt;\r
-       text-indent:-18.0pt;}\r
-@list l19\r
-       {mso-list-id:964848167;\r
-       mso-list-template-ids:1912510992;}\r
-@list l19:level1\r
-       {mso-level-number-format:bullet;\r
-       mso-level-text:\F0B7;\r
-       mso-level-tab-stop:36.0pt;\r
-       mso-level-number-position:left;\r
-       text-indent:-18.0pt;\r
-       mso-ansi-font-size:10.0pt;\r
-       font-family:Symbol;}\r
-@list l19:level2\r
-       {mso-level-number-format:bullet;\r
-       mso-level-text:o;\r
-       mso-level-tab-stop:72.0pt;\r
-       mso-level-number-position:left;\r
-       text-indent:-18.0pt;\r
-       mso-ansi-font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-bidi-font-family:"Times New Roman";}\r
-@list l19:level3\r
-       {mso-level-number-format:bullet;\r
-       mso-level-text:\F0A7;\r
-       mso-level-tab-stop:108.0pt;\r
-       mso-level-number-position:left;\r
-       text-indent:-18.0pt;\r
-       mso-ansi-font-size:10.0pt;\r
-       font-family:Wingdings;}\r
-@list l20\r
-       {mso-list-id:976836001;\r
-       mso-list-type:hybrid;\r
-       mso-list-template-ids:-1213013906 67895311 67895321 67895323 67895311 67895321 67895323 67895311 67895321 67895323;}\r
-@list l20:level1\r
-       {mso-level-tab-stop:78.55pt;\r
-       mso-level-number-position:left;\r
-       margin-left:78.55pt;\r
-       text-indent:-18.0pt;}\r
-@list l21\r
-       {mso-list-id:1112475268;\r
-       mso-list-type:hybrid;\r
-       mso-list-template-ids:1170372944 67895311 67895321 67895323 67895311 67895321 67895323 67895311 67895321 67895323;}\r
-@list l21:level1\r
-       {mso-level-tab-stop:78.55pt;\r
-       mso-level-number-position:left;\r
-       margin-left:78.55pt;\r
-       text-indent:-18.0pt;}\r
-@list l22\r
-       {mso-list-id:1280378370;\r
-       mso-list-type:simple;\r
-       mso-list-template-ids:-247183560;}\r
-@list l22:level1\r
-       {mso-level-number-format:bullet;\r
-       mso-level-style-link:"List Bullet 3";\r
-       mso-level-text:\F0A7;\r
-       mso-level-tab-stop:18.0pt;\r
-       mso-level-number-position:left;\r
-       margin-top:0mm;\r
-       margin-right:18.0pt;\r
-       margin-bottom:0mm;\r
-       margin-left:18.0pt;\r
-       margin-bottom:.0001pt;\r
-       text-indent:-18.0pt;\r
-       font-family:Wingdings;}\r
-@list l23\r
-       {mso-list-id:1469779017;\r
-       mso-list-type:simple;\r
-       mso-list-template-ids:-1193904264;}\r
-@list l23:level1\r
-       {mso-level-tab-stop:none;\r
-       mso-level-number-position:left;\r
-       mso-level-legacy:yes;\r
-       mso-level-legacy-indent:18.0pt;\r
-       mso-level-legacy-space:0mm;\r
-       margin-right:36.0pt;\r
-       text-indent:-18.0pt;\r
-       mso-ansi-font-size:10.0pt;\r
-       mso-ascii-font-family:"Arial Black";\r
-       mso-hansi-font-family:"Arial Black";}\r
-@list l24\r
-       {mso-list-id:1589343465;\r
-       mso-list-template-ids:1670832864;}\r
-@list l24:level1\r
-       {mso-level-number-format:bullet;\r
-       mso-level-text:\F0B7;\r
-       mso-level-tab-stop:36.0pt;\r
-       mso-level-number-position:left;\r
-       text-indent:-18.0pt;\r
-       mso-ansi-font-size:10.0pt;\r
-       font-family:Symbol;}\r
-@list l24:level2\r
-       {mso-level-tab-stop:72.0pt;\r
-       mso-level-number-position:left;\r
-       text-indent:-18.0pt;}\r
-@list l25\r
-       {mso-list-id:1598251408;\r
-       mso-list-type:simple;\r
-       mso-list-template-ids:-674336410;}\r
-@list l25:level1\r
-       {mso-level-number-format:bullet;\r
-       mso-level-style-link:"Text body Char";\r
-       mso-level-text:\F0A7;\r
-       mso-level-tab-stop:18.0pt;\r
-       mso-level-number-position:left;\r
-       margin-top:0mm;\r
-       margin-right:18.0pt;\r
-       margin-bottom:0mm;\r
-       margin-left:18.0pt;\r
-       margin-bottom:.0001pt;\r
-       text-indent:-18.0pt;\r
-       font-family:Wingdings;}\r
-@list l26\r
-       {mso-list-id:1649675689;\r
-       mso-list-type:simple;\r
-       mso-list-template-ids:-1193904264;}\r
-@list l26:level1\r
-       {mso-level-tab-stop:none;\r
-       mso-level-number-position:left;\r
-       mso-level-legacy:yes;\r
-       mso-level-legacy-indent:18.0pt;\r
-       mso-level-legacy-space:0mm;\r
-       margin-right:36.0pt;\r
-       text-indent:-18.0pt;\r
-       mso-ansi-font-size:10.0pt;\r
-       mso-ascii-font-family:"Arial Black";\r
-       mso-hansi-font-family:"Arial Black";}\r
-@list l27\r
-       {mso-list-id:2072076493;\r
-       mso-list-type:hybrid;\r
-       mso-list-template-ids:-1431952502 67895311 67895321 67895323 67895311 67895321 67895323 67895311 67895321 67895323;}\r
-@list l27:level1\r
-       {mso-level-tab-stop:78.55pt;\r
-       mso-level-number-position:left;\r
-       margin-left:78.55pt;\r
-       text-indent:-18.0pt;}\r
-@list l11:level1 lfo19\r
-       {mso-level-number-format:bullet;\r
-       mso-level-numbering:continue;\r
-       mso-level-text:\F031;\r
-       mso-level-tab-stop:none;\r
-       mso-level-number-position:left;\r
-       mso-level-legacy:yes;\r
-       mso-level-legacy-indent:18.0pt;\r
-       mso-level-legacy-space:0mm;\r
-       margin-top:0mm;\r
-       margin-right:18.0pt;\r
-       margin-bottom:0mm;\r
-       margin-left:18.0pt;\r
-       margin-bottom:.0001pt;\r
-       text-indent:-18.0pt;\r
-       mso-ansi-font-size:11.0pt;\r
-       mso-ascii-font-family:Wingdings;\r
-       mso-hansi-font-family:Wingdings;}\r
-@list l11:level1 lfo20\r
-       {mso-level-number-format:bullet;\r
-       mso-level-numbering:continue;\r
-       mso-level-text:\F021;\r
-       mso-level-tab-stop:none;\r
-       mso-level-number-position:left;\r
-       mso-level-legacy:yes;\r
-       mso-level-legacy-indent:18.0pt;\r
-       mso-level-legacy-space:0mm;\r
-       margin-top:0mm;\r
-       margin-right:18.0pt;\r
-       margin-bottom:0mm;\r
-       margin-left:18.0pt;\r
-       margin-bottom:.0001pt;\r
-       text-indent:-18.0pt;\r
-       mso-ansi-font-size:12.0pt;\r
-       mso-ascii-font-family:Wingdings;\r
-       mso-hansi-font-family:Wingdings;}\r
-@list l11:level1 lfo21\r
-       {mso-level-number-format:bullet;\r
-       mso-level-numbering:continue;\r
-       mso-level-text:\F03A;\r
-       mso-level-tab-stop:none;\r
-       mso-level-number-position:left;\r
-       mso-level-legacy:yes;\r
-       mso-level-legacy-indent:18.0pt;\r
-       mso-level-legacy-space:0mm;\r
-       margin-top:0mm;\r
-       margin-right:18.0pt;\r
-       margin-bottom:0mm;\r
-       margin-left:18.0pt;\r
-       margin-bottom:.0001pt;\r
-       text-indent:-18.0pt;\r
-       mso-ansi-font-size:11.0pt;\r
-       mso-ascii-font-family:Wingdings;\r
-       mso-hansi-font-family:Wingdings;}\r
-@list l11:level1 lfo22\r
-       {mso-level-number-format:bullet;\r
-       mso-level-numbering:continue;\r
-       mso-level-text:\F026;\r
-       mso-level-tab-stop:none;\r
-       mso-level-number-position:left;\r
-       mso-level-legacy:yes;\r
-       mso-level-legacy-indent:18.0pt;\r
-       mso-level-legacy-space:0mm;\r
-       margin-top:0mm;\r
-       margin-right:18.0pt;\r
-       margin-bottom:0mm;\r
-       margin-left:18.0pt;\r
-       margin-bottom:.0001pt;\r
-       text-indent:-18.0pt;\r
-       mso-ansi-font-size:10.0pt;\r
-       mso-ascii-font-family:Wingdings;\r
-       mso-hansi-font-family:Wingdings;}\r
-@list l11:level1 lfo23\r
-       {mso-level-number-format:bullet;\r
-       mso-level-numbering:continue;\r
-       mso-level-text:\F0B7;\r
-       mso-level-tab-stop:none;\r
-       mso-level-number-position:left;\r
-       mso-level-legacy:yes;\r
-       mso-level-legacy-indent:18.0pt;\r
-       mso-level-legacy-space:0mm;\r
-       margin-top:0mm;\r
-       margin-right:36.0pt;\r
-       margin-bottom:0mm;\r
-       margin-left:0mm;\r
-       margin-bottom:.0001pt;\r
-       text-indent:-18.0pt;\r
-       mso-ansi-font-size:14.0pt;\r
-       mso-ascii-font-family:Symbol;\r
-       mso-hansi-font-family:Symbol;}\r
-@list l11:level1 lfo24\r
-       {mso-level-number-format:bullet;\r
-       mso-level-numbering:continue;\r
-       mso-level-text:\F0B7;\r
-       mso-level-tab-stop:none;\r
-       mso-level-number-position:left;\r
-       mso-level-legacy:yes;\r
-       mso-level-legacy-indent:18.0pt;\r
-       mso-level-legacy-space:0mm;\r
-       margin-top:0mm;\r
-       margin-right:36.0pt;\r
-       margin-bottom:0mm;\r
-       margin-left:0mm;\r
-       margin-bottom:.0001pt;\r
-       text-indent:-18.0pt;\r
-       mso-ansi-font-size:14.0pt;\r
-       mso-ascii-font-family:Symbol;\r
-       mso-hansi-font-family:Symbol;}\r
-ol\r
-       {margin-bottom:0mm;}\r
-ul\r
-       {margin-bottom:0mm;}\r
--->\r
-</style>\r
-<!--[if gte mso 10]>\r
-<style>\r
- /* Style Definitions */\r
- table.MsoNormalTable\r
-       {mso-style-name:"Table Normal";\r
-       mso-tstyle-rowband-size:0;\r
-       mso-tstyle-colband-size:0;\r
-       mso-style-noshow:yes;\r
-       mso-style-parent:"";\r
-       mso-padding-alt:0mm 5.4pt 0mm 5.4pt;\r
-       mso-para-margin:0mm;\r
-       mso-para-margin-bottom:.0001pt;\r
-       mso-pagination:widow-orphan;\r
-       font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-ansi-language:#0400;\r
-       mso-fareast-language:#0400;\r
-       mso-bidi-language:#0400;}\r
-</style>\r
-<![endif]--><!--[if gte mso 9]><xml>\r
- <o:shapedefaults v:ext="edit" spidmax="2050"/>\r
-</xml><![endif]--><!--[if gte mso 9]><xml>\r
- <o:shapelayout v:ext="edit">\r
-  <o:idmap v:ext="edit" data="1"/>\r
- </o:shapelayout></xml><![endif]-->\r
-</head>\r
-\r
-<body lang=FR link=blue vlink=purple style='tab-interval:35.4pt'>\r
-\r
-<div class=Section1>\r
-\r
-<div style='mso-element:frame;mso-element-wrap:no-wrap-beside;mso-height-rule:\r
-exactly'>\r
-\r
-<table cellspacing=0 cellpadding=0 hspace=0 vspace=0 width=149 align=right>\r
- <tr>\r
-  <td valign=top align=left style='padding-top:9.35pt;padding-right:9.35pt;\r
-  padding-bottom:9.35pt;padding-left:9.35pt'>\r
-  <p class=PartTitle><span lang=EN-US>Technical</span></p>\r
-  </td>\r
- </tr>\r
-</table>\r
-\r
-</div>\r
-\r
-<![if !supportTextWrap]><br clear=ALL>\r
-<![endif]>\r
-\r
-<p class=CompanyName><span lang=EN-US style='font-size:14.0pt'>Centre National\r
-De LA Recherche scientifique (France)<br>\r
-CeNTRO De REGULACIO GENOMICA (<st1:place w:st="on"><st1:country-region w:st="on">SPAIN</st1:country-region></st1:place>)<o:p></o:p></span></p>\r
-\r
-<div style='mso-element:para-border-div;border:none;border-top:solid windowtext 1.0pt;\r
-mso-border-top-alt:solid windowtext .75pt;padding:1.0pt 0mm 0mm 0mm'>\r
-\r
-<p class=SubtitleCover><span lang=EN-US>Cédric Notredame<br>\r
-www.tcoffee.org</span></p>\r
-\r
-</div>\r
-\r
-<div style='mso-element:para-border-div;border:solid white 1.0pt;mso-border-alt:\r
-solid white .75pt;padding:31.0pt 31.0pt 31.0pt 31.0pt;background:#E5E5E5;\r
-mso-shading:windowtext;mso-pattern:gray-10 auto'>\r
-\r
-<p class=TitleCover style='margin:0mm;margin-bottom:.0001pt;background:#E5E5E5;\r
-mso-shading:windowtext;mso-pattern:gray-10 auto'><span lang=EN-US>T-Coffee:<br>\r
-Technical Documentation</span></p>\r
-\r
-</div>\r
-\r
-<div style='mso-element:para-border-div;border:none;border-top:solid windowtext 1.0pt;\r
-mso-border-top-alt:solid windowtext .75pt;padding:1.0pt 0mm 0mm 0mm'>\r
-\r
-<p class=SubtitleCover><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-</div>\r
-\r
-</div>\r
-\r
-<span lang=EN-US style='font-size:72.0pt;mso-bidi-font-size:10.0pt;font-family:\r
-Garamond;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman";\r
-letter-spacing:-3.5pt;mso-font-kerning:14.0pt;mso-ansi-language:EN-US;\r
-mso-fareast-language:EN-US;mso-bidi-language:AR-SA'><br clear=all\r
-style='page-break-before:always;mso-break-type:section-break'>\r
-</span>\r
-\r
-<div class=Section2>\r
-\r
-<div style='mso-element:para-border-div;border:none;border-bottom:solid gray 1.0pt;\r
-mso-border-bottom-alt:solid gray .75pt;padding:0mm 0mm 14.0pt 0mm'>\r
-\r
-<p class=MsoTitle><span lang=EN-US>T-Coffee Technical Documentation<br>\r
-(Version 8.01, July 2009)<br>\r
-www.tcoffee.org<br>\r
-<br>\r
-T-Coffee, seq_reformat<br>\r
-<span style='mso-spacerun:yes'> </span>PSI-Coffee, 3D-Coffee, M-Coffee, R-Coffee,\r
-APDB, iRMSD, T-RMSD</span></p>\r
-\r
-</div>\r
-\r
-<p class=ReturnAddress><span lang=EN-US style='font-family:Symbol;mso-ascii-font-family:\r
-Garamond;mso-hansi-font-family:Garamond;mso-char-type:symbol;mso-symbol-font-family:\r
-Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:Symbol'>ã</span></span><span\r
-lang=EN-US> Cédric Notredame, Centro de Regulacio Genomica, Centre National de\r
-la Recherche <st1:place w:st="on"><st1:City w:st="on">Scientifique</st1:City>, <st1:country-region\r
- w:st="on">France</st1:country-region></st1:place></span><span lang=EN-US\r
-style='letter-spacing:0pt'><o:p></o:p></span></p>\r
-\r
-</div>\r
-\r
-<span lang=EN-US style='font-size:8.0pt;mso-bidi-font-size:10.0pt;font-family:\r
-Garamond;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman";\r
-mso-ansi-language:EN-US;mso-fareast-language:EN-US;mso-bidi-language:AR-SA'><br\r
-clear=all style='page-break-before:always;mso-break-type:section-break'>\r
-</span>\r
-\r
-<div class=Section3>\r
-\r
-<p class=MsoToc1 style='tab-stops:right dotted 474.85pt'><!--[if supportFields]><i\r
-style='mso-bidi-font-style:normal'><span lang=EN-US style='font-size:11.0pt;\r
-font-family:"Times New Roman"'><span style='mso-element:field-begin'></span><span\r
-style='mso-spacerun:yes'> </span>TOC \h \z \t &quot;Heading 1;2;Heading\r
-2;3;Heading 3;4;Chapter Title;1;flag;4;FAQ;4&quot; <span style='mso-element:\r
-field-separator'></span></span></i><![endif]--><span class=MsoHyperlink><span\r
-lang=EN-US style='mso-no-proof:yes'><a href="#_Toc235958452">License and Terms\r
-of Use<span style='color:black;display:none;mso-hide:screen;text-decoration:\r
-none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958452 \h </span><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>6</span><span style='color:black;display:none;mso-hide:\r
-screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400350032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:\r
-"MS Mincho";color:windowtext;mso-ansi-language:FR;mso-fareast-language:JA;\r
-font-weight:normal;mso-bidi-font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958453">T-Coffee is distributed under the Gnu Public License<span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958453 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>6</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400350033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958454">T-Coffee code can be re-used freely<span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958454 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>6</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400350034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958455">T-Coffee can be incorporated in most pipelines:\r
-Plug-in/Plug-out\85<span style='color:windowtext;display:none;mso-hide:screen;\r
-text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>... </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958455 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>6</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400350035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc1 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958456">Addresses and Contacts<span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958456 \h </span><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>7</span><span style='color:black;display:none;mso-hide:\r
-screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400350036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:\r
-"MS Mincho";color:windowtext;mso-ansi-language:FR;mso-fareast-language:JA;\r
-font-weight:normal;mso-bidi-font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958457">Contributors<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958457 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>7</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400350037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958458">Addresses<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958458 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>7</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400350038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc1 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958459">Citations<span style='color:black;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958459 \h </span><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>8</span><span style='color:black;display:none;mso-hide:\r
-screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400350039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:\r
-"MS Mincho";color:windowtext;mso-ansi-language:FR;mso-fareast-language:JA;\r
-font-weight:normal;mso-bidi-font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958460">T-Coffee<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958460 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>8</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400360030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958461">Mocca<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958461 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>9</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400360031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958462">CORE<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958462 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>10</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400360032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958463">Other Contributions<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958463 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>10</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400360033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958464">Bug Reports and Feedback<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958464 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>10</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400360034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc1 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958465">Installation of The T-Coffee Packages<span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958465 \h </span><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>11</span><span style='color:black;display:none;mso-hide:\r
-screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400360035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:\r
-"MS Mincho";color:windowtext;mso-ansi-language:FR;mso-fareast-language:JA;\r
-font-weight:normal;mso-bidi-font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958466">Third Party Packages and On Demand Installations<span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958466 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>11</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400360036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958467">Standard Installation of T-Coffee<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958467 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>11</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400360037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958468">Unix<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958468 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>11</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400360038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958469">Microsoft Windows/Cygwin<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958469 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>13</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400360039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958470">MAC osX, Linux<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958470 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>13</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400370030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958471">CLUSTER Installation<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958471 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>13</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400370031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958472">If you have PDB installed:<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958472 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>13</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400370032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958473">Installing BLAST for T-Coffee<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958473 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>14</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400370033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958474">Why Do I need BLAST with T-Coffee?<span style='color:\r
-windowtext;display:none;mso-hide:screen;text-decoration:none;text-underline:\r
-none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958474 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>14</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400370034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958475">Using the EBI BLAST Client<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958475 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>14</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400370035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958476">Using the NCBI BLAST Client<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958476 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>15</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400370036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958477">Using another Client<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958477 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>15</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400370037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958478">Using a BLAST local version on UNIX<span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958478 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>16</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400370038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958479">Using a BLAST local version on Windows/cygwin<span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958479 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>16</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400370039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958480">Installing Other Companion Packages<span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958480 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>17</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400380030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958481">Installation of PSI-Coffee and Expresso<span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958481 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>18</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400380031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958482">Installation of M-Coffee<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958482 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>19</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400380032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958483">Automated Installation<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958483 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>19</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400380033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958484">Manual Installation<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958484 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>20</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400380034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958485">Installation of APDB and iRMSD<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958485 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>21</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400380035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958486">Installation of tRMSD<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958486 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>21</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400380036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958487">Installation of seq_reformat<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958487 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>22</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400380037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958488">Installation of extract_from_pdb<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958488 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>22</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400380038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958489">Installation of 3D-Coffee/Expresso<span style='color:\r
-windowtext;display:none;mso-hide:screen;text-decoration:none;text-underline:\r
-none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958489 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>22</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400380039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958490">Automated Installation<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958490 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>22</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400390030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958491">Manual Installation<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958491 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>23</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400390031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958492">Installing Fugue for T-Coffee<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958492 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>23</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400390032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958493">Installation of R-Coffee<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958493 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>23</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400390033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958494">Automated Installation<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958494 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>24</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400390034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958495">Manual Installation<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958495 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>24</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400390035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958496">Installing ProbbonsRNA for R-Coffee<span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958496 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>24</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400390036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958497">Installing Consan for R-Coffee<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958497 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>24</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400390037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc1 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958498">Quick Start<span style='color:black;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958498 \h </span><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>25</span><span style='color:black;display:none;mso-hide:\r
-screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400390038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:\r
-"MS Mincho";color:windowtext;mso-ansi-language:FR;mso-fareast-language:JA;\r
-font-weight:normal;mso-bidi-font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958499">T-COFFEE<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958499 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>25</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400390039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958500">M-Coffee<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958500 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>25</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500300030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958501">Expresso<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958501 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>26</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500300031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958502">R-Coffee<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958502 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>26</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500300032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958503">iRMSD and APDB<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958503 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>27</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500300033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958504">tRMSD<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958504 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>27</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500300034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958505">MOCCA<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958505 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>28</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500300035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc1 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958506">Recent Modifications<span style='color:black;display:\r
-none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958506 \h </span><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>29</span><span style='color:black;display:none;mso-hide:\r
-screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500300036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:\r
-"MS Mincho";color:windowtext;mso-ansi-language:FR;mso-fareast-language:JA;\r
-font-weight:normal;mso-bidi-font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc1 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958507">Reference Manual<span style='color:black;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958507 \h </span><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>30</span><span style='color:black;display:none;mso-hide:\r
-screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500300037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:\r
-"MS Mincho";color:windowtext;mso-ansi-language:FR;mso-fareast-language:JA;\r
-font-weight:normal;mso-bidi-font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958508">Environment Variables<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958508 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>30</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500300038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958509">http_proxy_4_TCOFFEE<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958509 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>30</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500300039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958510">email_4_TCOFFEE<span style='color:windowtext;display:\r
-none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958510 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>31</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500310030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958511">DIR_4_TCOFFEE<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958511 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>31</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500310031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958512">TMP_4_TCOFFEE<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958512 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>31</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500310032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958513">CACHE_4_TCOFFEE<span style='color:windowtext;display:\r
-none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958513 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>31</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500310033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958514">NO_ERROR_REPORT_4_TCOFFEE<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958514 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>31</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500310034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958515">PDB_DIR<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958515 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>31</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500310035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958516">NO_WARNING_4_TCOFFEE<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958516 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>31</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500310036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958517">Setting up the T-Coffee environment variables<span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958517 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>31</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500310037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958518">Well Behaved Parameters<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958518 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>32</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500310038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958519">Separation<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958519 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>32</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500310039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958520">Posix<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958520 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>32</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500320030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958521">Entering the right parameters<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958521 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>32</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500320031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958522">Parameters Syntax<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958522 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>32</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500320032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958523">No Flag<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958523 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>32</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500320033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958524">-parameters<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958524 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>33</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500320034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958525">-t_coffee_defaults<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958525 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>33</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500320035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958526">-mode<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958526 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>33</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500320036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958527">-score [Deprecated]<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958527 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>34</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500320037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958528">-evaluate<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958528 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>34</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500320038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958529">-convert [cw]<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958529 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>34</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500320039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958530">-do_align [cw]<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958530 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>34</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500330030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958531">Special Parameters<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958531 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>35</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500330031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958532">-version<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958532 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>35</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500330032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958533">-proxy<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958533 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>35</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500330033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958534">-email<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958534 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>35</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500330034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958535">-check_configuration<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958535 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>35</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500330035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958536">-cache<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958536 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>35</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500330036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958537">-update<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958537 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>35</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500330037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958538">-full_log<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958538 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>35</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500330038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958539">-other_pg<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958539 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>36</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500330039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958540">Input<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958540 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>36</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500340030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958541">Sequence Input<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958541 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>36</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500340031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958542">-infile [cw]<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958542 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>36</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500340032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958543">-in (Cf \96in from the Method and Library Input section)<span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958543 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>36</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500340033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958544">-get_type<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958544 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>36</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500340034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958545">-type [cw]<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958545 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>36</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500340035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958546">-seq<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958546 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>37</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500340036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958547">-seq_source<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958547 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>37</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500340037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958548">Structure Input<span style='color:windowtext;display:\r
-none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958548 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>37</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500340038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958549">-pdb<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958549 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>37</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500340039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958550">Tree Input<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958550 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>37</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500350030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958551">-usetree<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958551 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>37</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500350031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958552">Structures, Sequences Methods and Library Input via the\r
-&#61590;in Flag<span style='color:windowtext;display:none;mso-hide:screen;\r
-text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958552 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>38</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500350032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958553">-in<span style='color:windowtext;display:none;mso-hide:\r
-screen;text-decoration:none;text-underline:none'><span style='mso-tab-count:\r
-1 dotted'>. </span></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-begin'></span></span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'> PAGEREF\r
-_Toc235958553 \h </span><span style='color:windowtext;display:none;mso-hide:\r
-screen;text-decoration:none;text-underline:none'><span style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>38</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500350033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958554">Profile Input<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958554 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>40</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500350034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958555">-profile<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958555 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>40</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500350035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958556">-profile1 [cw]<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958556 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>40</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500350036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958557">-profile2 [cw]<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958557 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>40</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500350037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958558">Alignment Computation<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958558 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>40</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500350038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958559">Library Computation: Methods<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958559 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>40</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500350039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958560">-lalign_n_top<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958560 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>40</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500360030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958561">-align_pdb_param_file<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958561 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>41</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500360031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958562">-align_pdb_hasch_mode<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958562 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>41</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500360032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958563">Library Computation: Extension<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958563 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>41</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500360033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958564">-lib_list [Unsupported]<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958564 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>41</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500360034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958565">-do_normalise<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958565 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>41</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500360035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958566">-extend<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958566 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>41</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500360036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958567">-extend_mode<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958567 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>41</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500360037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958568">-max_n_pair<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958568 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>42</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500360038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958569">-seq_name_for_quadruplet<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958569 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>42</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500360039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958570">-compact<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958570 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>42</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500370030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958571">-clean<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958571 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>42</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500370031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958572">-maximise<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958572 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>42</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500370032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958573">-do_self<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958573 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>42</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500370033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958574">-seq_name_for_quadruplet<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958574 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>42</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500370034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958575">-weight<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958575 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>43</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500370035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958576">Tree Computation<span style='color:windowtext;display:\r
-none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958576 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>43</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500370036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958577">-distance_matrix_mode<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958577 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>43</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500370037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958578">-quicktree [CW]<span style='color:windowtext;display:\r
-none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958578 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>44</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500370038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958579">Pair-wise Alignment Computation<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958579 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>44</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500370039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958580">-dp_mode<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958580 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>44</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500380030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958581">-ktuple<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958581 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>45</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500380031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958582">-ndiag<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958582 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>45</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500380032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958583">-diag_mode<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958583 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>45</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500380033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958584">-diag_threshold<span style='color:windowtext;display:\r
-none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958584 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>46</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500380034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958585">-sim_matrix<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958585 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>46</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500380035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958586">-matrix [CW]<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958586 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>46</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500380036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958587">-nomatch<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958587 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>46</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500380037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958588">-gapopen<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958588 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>46</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500380038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958589">-gapext<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958589 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>47</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500380039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958590">-fgapopen<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958590 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>47</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500390030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958591">-fgapext<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958591 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>47</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500390031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958592">-cosmetic_penalty<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958592 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>47</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500390032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958593">-tg_mode<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958593 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>47</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500390033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958594">Weighting Schemes<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958594 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>47</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500390034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958595">-seq_weight<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958595 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>47</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500390035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958596">Multiple Alignment Computation<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958596 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>48</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500390036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958597">-msa_mode<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958597 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>48</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500390037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958598">-one2all<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958598 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>48</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500390038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958599">-profile_comparison<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958599 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>48</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500390039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958600">-profile_mode<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958600 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>49</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600300030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958601">Alignment Post-Processing<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958601 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>49</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600300031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958602">-clean_aln<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958602 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>49</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600300032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958603">-clean_threshold<span style='color:windowtext;display:\r
-none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958603 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>49</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600300033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958604">-clean_iteration<span style='color:windowtext;display:\r
-none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958604 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>49</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600300034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958605">-clean_evaluation_mode<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958605 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>49</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600300035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958606">-iterate<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958606 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>49</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600300036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958607">CPU Control<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958607 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>50</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600300037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958608">Multithreading<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958608 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>50</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600300038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958609">-multi_thread [NOT Supported]<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958609 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>50</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600300039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958610">Limits<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958610 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>50</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600310030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958611">-mem_mode<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958611 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>50</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600310031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958612">-ulimit<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958612 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>50</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600310032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958613">-maxlen<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958613 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>50</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600310033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958614">Aligning more than 100 sequences with DPA<span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958614 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>50</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600310034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958615">-maxnseq<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958615 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>50</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600310035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958616">-dpa_master_aln<span style='color:windowtext;display:\r
-none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958616 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>50</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600310036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958617">-dpa_maxnseq<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958617 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>51</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600310037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958618">-dpa_min_score1<span style='color:windowtext;display:\r
-none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958618 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>51</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600310038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958619">-dpa_min_score2<span style='color:windowtext;display:\r
-none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958619 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>51</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600310039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958620">-dap_tree [NOT IMPLEMENTED]<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958620 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>51</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600320030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958621">Using Structures<span style='color:windowtext;display:\r
-none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958621 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>51</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600320031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958622">Generic<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958622 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>51</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600320032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958623">-mode<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958623 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>51</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600320033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958624">-check_pdb_status<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958624 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>52</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600320034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958625">3D Coffee: Using SAP<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958625 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>52</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600320035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958626">Using/finding PDB templates for the Sequences<span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958626 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>52</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600320036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958627">-template_file<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958627 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>52</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600320037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958628">-struc_to_use<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958628 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>54</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600320038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958629">Multiple Local Alignments<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958629 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>54</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600320039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958630">-domain/-mocca<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958630 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>55</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600330030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958631">-start<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958631 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>55</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600330031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958632">-len<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958632 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>55</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600330032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958633">-scale<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958633 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>55</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600330033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958634">-domain_interactive [Examples]<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958634 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>56</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600330034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958635">Output Control<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958635 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>57</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600330035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958636">Generic<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958636 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>57</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600330036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958637">Conventions Regarding Filenames<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958637 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>57</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600330037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958638">Identifying the Output files automatically<span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958638 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>57</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600330038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958639">-no_warning<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958639 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>57</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600330039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958640">Alignments<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958640 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>57</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600340030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958641">-outfile<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958641 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>57</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600340031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958642">-output<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958642 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>57</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600340032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958643">-outseqweight<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958643 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>58</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600340033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958644">-case<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958644 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>58</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600340034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958645">-cpu<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958645 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>58</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600340035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958646">-outseqweight<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958646 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>58</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600340036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958647">-outorder [cw]<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958647 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>59</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600340037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958648">-inorder [cw]<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958648 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>59</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600340038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958649">-seqnos<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958649 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>59</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600340039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958650">Libraries<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958650 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>59</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600350030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958651">-out_lib<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958651 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>59</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600350031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958652">-lib_only<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958652 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>59</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600350032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958653">Trees<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958653 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>60</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600350033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958654">-newtree<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958654 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>60</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600350034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958655">Reliability Estimation<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958655 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>60</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600350035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958656">CORE Computation<span style='color:windowtext;display:\r
-none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958656 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>60</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600350036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958657">-evaluate_mode<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958657 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>60</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600350037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958658">Generic Output<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958658 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>61</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600350038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958659">-run_name<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958659 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>61</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600350039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958660">-quiet<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958660 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>61</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600360030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958661">-align [CW]<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958661 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>61</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600360031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958662">APDB, iRMSD and tRMSD Parameters<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958662 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>61</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600360032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958663">-quiet [Same as T-Coffee]<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958663 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>61</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600360033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958664">-run_name [Same as T-Coffee]<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958664 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>61</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600360034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958665">-aln<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958665 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>61</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600360035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958666">-n_excluded_nb<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958666 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>62</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600360036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958667">-maximum_distance<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958667 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>62</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600360037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958668">-similarity_threshold<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958668 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>62</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600360038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958669">-local_mode<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958669 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>62</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600360039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958670">-filter<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958670 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>62</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600370030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958671">-print_rapdb [Unsupported]<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958671 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>63</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600370031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958672">-outfile [Same as T-Coffee]<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958672 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>63</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600370032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958673">-color_mode<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958673 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>63</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600370033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc1 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958674">Building a Server<span style='color:black;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958674 \h </span><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>64</span><span style='color:black;display:none;mso-hide:\r
-screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600370034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:\r
-"MS Mincho";color:windowtext;mso-ansi-language:FR;mso-fareast-language:JA;\r
-font-weight:normal;mso-bidi-font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958675">Environment Variables<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958675 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>64</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600370035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958676">Output of the .dnd file.<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958676 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>65</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600370036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958677">Permissions<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958677 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>65</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600370037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958678">Other Programs<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958678 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>65</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600370038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc1 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958679">Formats<span style='color:black;display:none;mso-hide:\r
-screen;text-decoration:none;text-underline:none'><span style='mso-tab-count:\r
-1 dotted'>. </span></span><!--[if supportFields]><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-begin'></span></span><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'> PAGEREF\r
-_Toc235958679 \h </span><span style='color:black;display:none;mso-hide:screen;\r
-text-decoration:none;text-underline:none'><span style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>66</span><span style='color:black;display:none;mso-hide:\r
-screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600370039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:\r
-"MS Mincho";color:windowtext;mso-ansi-language:FR;mso-fareast-language:JA;\r
-font-weight:normal;mso-bidi-font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958680">Parameter files<span style='color:windowtext;display:\r
-none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958680 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>66</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600380030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958681">Sequence Name Handling<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958681 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>66</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600380031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958682">Automatic Format Recognition<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958682 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>67</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600380032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958683">Structures<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958683 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>67</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600380033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958684">RNA Structures<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958684 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>67</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600380034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958685">Sequences<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958685 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>67</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600380035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958686">Alignments<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958686 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>67</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600380036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958687">Libraries<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958687 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>68</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600380037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958688">T-COFFEE_LIB_FORMAT_01<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958688 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>68</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600380038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958689">T-COFFEE_LIB_FORMAT_02<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958689 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>69</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600380039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958690">Library List<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958690 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>69</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600390030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958691">Substitution matrices.<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958691 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>69</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600390031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958692">ClustalW Style [Deprecated]<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958692 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>69</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600390032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958693">BLAST Format [Recommended]<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958693 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>70</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600390033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958694">Sequences Weights<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958694 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>70</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600390034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc1 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958695">Known Problems<span style='color:black;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958695 \h </span><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>71</span><span style='color:black;display:none;mso-hide:\r
-screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600390035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:\r
-"MS Mincho";color:windowtext;mso-ansi-language:FR;mso-fareast-language:JA;\r
-font-weight:normal;mso-bidi-font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc1 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958696">Technical Notes<span style='color:black;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958696 \h </span><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>72</span><span style='color:black;display:none;mso-hide:\r
-screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600390036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:\r
-"MS Mincho";color:windowtext;mso-ansi-language:FR;mso-fareast-language:JA;\r
-font-weight:normal;mso-bidi-font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958697">Development<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958697 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>72</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600390037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958698">Command Line List<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958698 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>72</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600390038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc1 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958699">To Do\85<span style='color:black;display:none;mso-hide:\r
-screen;text-decoration:none;text-underline:none'><span style='mso-tab-count:\r
-1 dotted'>.. </span></span><!--[if supportFields]><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-begin'></span></span><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'> PAGEREF\r
-_Toc235958699 \h </span><span style='color:black;display:none;mso-hide:screen;\r
-text-decoration:none;text-underline:none'><span style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>74</span><span style='color:black;display:none;mso-hide:\r
-screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600390039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:\r
-"MS Mincho";color:windowtext;mso-ansi-language:FR;mso-fareast-language:JA;\r
-font-weight:normal;mso-bidi-font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoNormal><!--[if supportFields]><i><span lang=EN-US style='font-size:\r
-11.0pt;font-family:"Times New Roman"'><span style='mso-element:field-end'></span></span></i><![endif]--></p>\r
-\r
-</div>\r
-\r
-<span lang=EN-US style='font-size:8.0pt;mso-bidi-font-size:10.0pt;font-family:\r
-Garamond;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman";\r
-mso-ansi-language:EN-US;mso-fareast-language:EN-US;mso-bidi-language:AR-SA'><br\r
-clear=all style='page-break-before:auto;mso-break-type:section-break'>\r
-</span>\r
-\r
-<div class=Section4>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 3.0pt;\r
-padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0mm;margin-right:\r
-4.25pt'>\r
-\r
-<p class=ChapterTitle><a name="_Toc235958452"></a><a name="_Toc102494650"></a><a\r
-name="_Toc101065185"><span style='mso-bookmark:_Toc102494650'><span\r
-style='mso-bookmark:_Toc235958452'><span lang=EN-US>License and Terms of Use</span></span></span></a></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<h2><a name="_Toc235958453"></a><a name="_Toc102494651"></a><a\r
-name="_Toc102494275"><span style='mso-bookmark:_Toc102494651'><span\r
-style='mso-bookmark:_Toc235958453'><span lang=EN-US>T-Coffee is distributed\r
-under the Gnu Public License</span></span></span></a></h2>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MyNormal><span lang=AF>Please make sure you have agreed with the terms\r
-of the license attached to the package before using the T-Coffee package or its\r
-documentation. T-Coffee is a freeware open source distributed under a GPL license.\r
-This means that there are very little restrictions to its use, either in an\r
-academic or a non academic environment.</span></p>\r
-\r
-<h2><a name="_Toc235958454"></a><a name="_Toc102494652"></a><a\r
-name="_Toc102494276"><span style='mso-bookmark:_Toc102494652'><span\r
-style='mso-bookmark:_Toc235958454'><span lang=EN-US>T-Coffee code can be\r
-re-used freely</span></span></span></a></h2>\r
-\r
-<p class=MyNormal><span lang=AF>Our philosophy is that code is meant to be re-used,\r
-including ours. No permission is needed for the cut and paste of a few\r
-functions, although we are always happy to receive pieces of improved code.</span></p>\r
-\r
-<h2><a name="_Toc102494653"></a><a name="_Toc101065186"></a><a\r
-name="_Toc235958455"><span style='mso-bookmark:_Toc101065186'><span\r
-style='mso-bookmark:_Toc102494653'><span lang=EN-US>T-Coffee can be\r
-incorporated in most pipelines: Plug-in/Plug-out\85</span></span></span></a><span\r
-style='mso-bookmark:_Toc101065186'><span style='mso-bookmark:_Toc102494653'></span></span></h2>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065186'><span\r
-style='mso-bookmark:_Toc102494653'><span lang=AF>Our philosophy is to insure\r
-that as many methods as possible can be used as plug-ins within T-Coffee.\r
-Likewise, we will give as much support as possible to anyone wishing to turn\r
-T-Coffee into a plug-in for another method. For more details on how to do this,\r
-see the plug-in and the plug-out sections of the Tutorial Manual.</span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065186'><span\r
-style='mso-bookmark:_Toc102494653'><span lang=AF>Again, you do not need our\r
-permission to either use T-Coffee (or your method as a plug-in/out) but if you\r
-let us know, we will insure the stability of T-Coffee within your system\r
-through future releases. </span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065186'><span\r
-style='mso-bookmark:_Toc102494653'><span lang=AF>The current license only\r
-allows for the incorporation of T-Coffee in non-commercial pipelines (i.e.\r
-where you do not sell the pipeline, or access to it). If your pipeline is\r
-commercial, please get in touch with us. </span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065186'><span\r
-style='mso-bookmark:_Toc102494653'><span lang=AF><o:p>&nbsp;</o:p></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 3.0pt;\r
-padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0mm;margin-right:\r
-4.25pt'>\r
-\r
-<p class=ChapterTitle><span style='mso-bookmark:_Toc101065186'><span\r
-style='mso-bookmark:_Toc102494653'><a name="_Toc235958456"><span lang=EN-US>Addresses\r
-and Contacts</span></a></span></span><span style='mso-bookmark:_Toc235958456'></span><span\r
-style='mso-bookmark:_Toc102494653'></span><span style='mso-bookmark:_Toc101065186'></span><span\r
-lang=EN-US style='font-size:98.0pt;mso-bidi-font-size:48.0pt'><o:p></o:p></span></p>\r
-\r
-</div>\r
-\r
-<h2><a name="_Toc235958457"><span lang=EN-US>Contributors</span></a></h2>\r
-\r
-<p class=MsoBodyText><span lang=EN-US>T-coffee is developed, maintained,\r
-monitored, used and debugged by a dedicated team that include or have included:</span></p>\r
-\r
-<p class=MsoBodyText><span lang=EN-US><span style='mso-tab-count:1'>            </span>Cédric\r
-Notredame, Fabrice Armougom, Des Higgins, Sebastien Moretti, Orla O\92Sullivan. Eamon\r
-O\92Toole, Olivier Poirot, Karsten Suhre, Iain Wallace, Andreas Wilm</span></p>\r
-\r
-<h2><a name="_Toc235958458"><span lang=EN-US>Addresses</span></a></h2>\r
-\r
-<p class=MyNormal><span lang=AF>We are always very eager to get some user\r
-feedback. Please do not hesitate to drop us a line<span\r
-style='mso-spacerun:yes'>  </span>at: <a\r
-href="mailto:cedric.notredame@europe.com"><span lang=EN-US style='mso-ansi-language:\r
-EN-US'>cedric.notredame@europe.com</span></a> The latest updates of T-Coffee\r
-are always available<span style='mso-spacerun:yes'>  </span>on: www.tcoffee.org\r
-. On this address you will also find a link to some of the online T-Coffee\r
-servers, including Tcoffee@igs </span></p>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MyNormal><span lang=AF>T-Coffee can be used to automatically check if\r
-an updated version is available, however the program will not update\r
-automatically, as this can cause endless reproducibility problems.</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee \96update</span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 3.0pt;\r
-padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0mm;margin-right:\r
-4.25pt'>\r
-\r
-<p class=ChapterTitle><a name="_Toc235958459"></a><a name="_Toc102494654"></a><a\r
-name="_Toc101065187"><span style='mso-bookmark:_Toc102494654'><span\r
-style='mso-bookmark:_Toc235958459'><span lang=EN-US>Citations</span></span></span></a></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF>It is important that you cite T-Coffee when you\r
-use it. Citing us is (almost) like giving us money: it helps us convincing our\r
-institutions that what we do is useful and that they should keep paying our\r
-salaries and deliver Donuts to our offices from time to time (Not that they\r
-ever did it, but it would be nice anyway). </span></p>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MyNormal><span lang=AF>Cite the server if you used it, otherwise, cite\r
-the original paper from 2000 (No, it was never named &quot;T-Coffee 2000&quot;).</span></p>\r
-\r
-<table class=MsoNormalTable border=0 cellspacing=5 cellpadding=0 width="81%"\r
- style='width:81.78%;mso-cellspacing:3.7pt;mso-padding-alt:0mm 0mm 0mm 0mm'>\r
- <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>\r
-  <td width="53%" style='width:53.48%;padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US><a\r
-  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=10964570">Notredame\r
-  C, Higgins DG, Heringa J.</a></span><span lang=EN-US style='mso-bidi-font-size:\r
-  12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width="43%" nowrap valign=top style='width:43.3%;padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US><a\r
-  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Display&amp;dopt=pubmed_pubmed&amp;from_uid=10964570"><span\r
-  style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <script language="JavaScript1.2">\r
+<html xmlns:v="urn:schemas-microsoft-com:vml"
+xmlns:o="urn:schemas-microsoft-com:office:office"
+xmlns:w="urn:schemas-microsoft-com:office:word"
+xmlns:m="http://schemas.microsoft.com/office/2004/12/omml"
+xmlns:css="http://macVmlSchemaUri" xmlns="http://www.w3.org/TR/REC-html40">
+
+<head>
+<meta name=Title content=Manual>
+<meta name=Keywords content="">
+<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
+<meta name=ProgId content=Word.Document>
+<meta name=Generator content="Microsoft Word 2008">
+<meta name=Originator content="Microsoft Word 2008">
+<link rel=File-List href="t_coffee_technical_files/filelist.xml">
+<link rel=Edit-Time-Data href="t_coffee_technical_files/editdata.mso">
+<!--[if !mso]>
+<style>
+v\:* {behavior:url(#default#VML);}
+o\:* {behavior:url(#default#VML);}
+w\:* {behavior:url(#default#VML);}
+.shape {behavior:url(#default#VML);}
+</style>
+<![endif]-->
+<title>Manual</title>
+<!--[if gte mso 9]><xml>
+ <o:DocumentProperties>
+  <o:Author>Notredame</o:Author>
+  <o:Template>Normal.dotm</o:Template>
+  <o:LastAuthor>Notredame Cédric</o:LastAuthor>
+  <o:Revision>2</o:Revision>
+  <o:TotalTime>28629</o:TotalTime>
+  <o:LastPrinted>2006-03-05T19:42:00Z</o:LastPrinted>
+  <o:Created>2010-11-18T19:37:00Z</o:Created>
+  <o:LastSaved>2010-11-18T19:37:00Z</o:LastSaved>
+  <o:Pages>9</o:Pages>
+  <o:Words>18210</o:Words>
+  <o:Characters>103800</o:Characters>
+  <o:Company>SIB</o:Company>
+  <o:Lines>865</o:Lines>
+  <o:Paragraphs>207</o:Paragraphs>
+  <o:CharactersWithSpaces>127473</o:CharactersWithSpaces>
+  <o:Version>12.0</o:Version>
+ </o:DocumentProperties>
+ <o:OfficeDocumentSettings>
+  <o:PixelsPerInch>96</o:PixelsPerInch>
+  <o:TargetScreenSize>800x600</o:TargetScreenSize>
+ </o:OfficeDocumentSettings>
+</xml><![endif]--><!--[if gte mso 9]><xml>
+ <w:WordDocument>
+  <w:TrackMoves>false</w:TrackMoves>
+  <w:TrackFormatting/>
+  <w:HyphenationZone>21</w:HyphenationZone>
+  <w:ValidateAgainstSchemas/>
+  <w:SaveIfXMLInvalid>false</w:SaveIfXMLInvalid>
+  <w:IgnoreMixedContent>false</w:IgnoreMixedContent>
+  <w:AlwaysShowPlaceholderText>false</w:AlwaysShowPlaceholderText>
+  <w:Compatibility>
+   <w:BreakWrappedTables/>
+   <w:UseNormalStyleForList/>
+   <w:DontUseIndentAsNumberingTabStop/>
+   <w:FELineBreak11/>
+   <w:WW11IndentRules/>
+   <w:DontAutofitConstrainedTables/>
+   <w:AutofitLikeWW11/>
+   <w:HangulWidthLikeWW11/>
+  </w:Compatibility>
+ </w:WordDocument>
+</xml><![endif]--><!--[if gte mso 9]><xml>
+ <w:LatentStyles DefLockedState="false" LatentStyleCount="276">
+ </w:LatentStyles>
+</xml><![endif]-->
+<style>
 <!--
-var PopUpMenu2_LocalConfig_jsmenu3Config = [
-  ["ShowCloseIcon","yes"],
-  ["Help","window.open('/entrez/query/static/popup.html','Links_Help','resizable=no,scrollbars=yes,toolbar=no,location=no,directories=no,status=no,menubar=no,copyhistory=no,alwaysRaised=no,depend=no,width=400,height=500');"],
-  ["TitleText"," Links "]
-]
-//-->\r
-  </script><script language="JavaScript1.2">\r
-<!--
-var Menu10964570 = [
-  ["UseLocalConfig","jsmenu3Config","",""],
-  ["Cited in PMC","window.top.location='http://www.pubmedcentral.gov/tocrender.fcgi?action=cited&tool=pubmed&pubmedid=10964570'","",""],
-  ["Cited in Books","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Display&dopt=pubmed_books_refs&from_uid=10964570'","",""],
-  ["Books","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=10964570&dopt=Books'","",""],
-  ["LinkOut","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=10964570&dopt=ExternalLink'","",""]
-]
-//-->\r
-  </script><a href="javascript:PopUpMenu2_Set(Menu10964570);" target="_self"><span\r
-  style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></a> </span><span\r
-  lang=EN-US style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>\r
-  <td width="97%" colspan=2 style='width:97.86%;padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US>T-Coffee: A novel method for fast\r
-  and accurate multiple sequence alignment.<br>\r
-  J Mol Biol. 2000 Sep 8;302(1):205-17. <br>\r
-  PMID: 10964570 [PubMed - indexed for MEDLINE]</span><span lang=EN-US\r
-  style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
- </tr>\r
-</table>\r
-\r
-<p class=MyNormal><span lang=AF>Other useful publications include:</span></p>\r
-\r
-<h2><a name="_Toc235958460"></a><a name="_Toc102494655"></a><a\r
-name="_Toc102494277"></a><a name="_Toc101065188"><span style='mso-bookmark:\r
-_Toc102494277'><span style='mso-bookmark:_Toc102494655'><span style='mso-bookmark:\r
-_Toc235958460'><span lang=EN-US>T-Coffee</span></span></span></span></a></h2>\r
-\r
-<table class=MsoNormalTable border=0 cellspacing=5 cellpadding=0 width="81%"\r
- style='width:81.78%;mso-cellspacing:3.7pt;mso-padding-alt:0mm 0mm 0mm 0mm'>\r
- <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>\r
-  <td width="53%" style='width:53.48%;padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US><a\r
-  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=15215460">Claude\r
-  JB, Suhre K, Notredame C, Claverie JM, Abergel C.</a></span><span lang=EN-US\r
-  style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width="43%" nowrap valign=top style='width:43.3%;padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US><a\r
-  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Display&amp;dopt=pubmed_pubmed&amp;from_uid=15215460"><span\r
-  style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <script language="JavaScript1.2">\r
-<!--
-var PopUpMenu2_LocalConfig_jsmenu3Config = [
-  ["ShowCloseIcon","yes"],
-  ["Help","window.open('/entrez/query/static/popup.html','Links_Help','resizable=no,scrollbars=yes,toolbar=no,location=no,directories=no,status=no,menubar=no,copyhistory=no,alwaysRaised=no,depend=no,width=400,height=500');"],
-  ["TitleText"," Links "]
-]
-//-->\r
-  </script><script language="JavaScript1.2">\r
-<!--
-var Menu15215460 = [
-  ["UseLocalConfig","jsmenu3Config","",""],
-  ["Free in PMC","window.top.location='http://www.pubmedcentral.gov/articlerender.fcgi?tool=pubmed&pubmedid=15215460'","",""],
-  ["Books","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=15215460&dopt=Books'","",""],
-  ["LinkOut","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=15215460&dopt=ExternalLink'","",""]
-]
-//-->\r
-  </script><a href="javascript:PopUpMenu2_Set(Menu15215460);" target="_self"><span\r
-  style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></a> </span><span\r
-  lang=EN-US style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>\r
-  <td width="97%" colspan=2 style='width:97.86%;padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US>CaspR: a web server for automated\r
-  molecular replacement using homology modelling.<br>\r
-  Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W606-9. <br>\r
-  PMID: 15215460 [PubMed - indexed for MEDLINE]</span><span lang=EN-US\r
-  style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
- </tr>\r
-</table>\r
-\r
-<p class=MyNormalJustified><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<table class=MsoNormalTable border=0 cellspacing=5 cellpadding=0 width="81%"\r
- style='width:81.98%;mso-cellspacing:3.7pt;mso-padding-alt:0mm 0mm 0mm 0mm'>\r
- <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>\r
-  <td width="53%" style='width:53.5%;padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US><a\r
-  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=15215345">Poirot\r
-  O, Suhre K, Abergel C, O'Toole E, Notredame C.</a></span><span lang=EN-US\r
-  style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
-  <td nowrap valign=top style='padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US><a\r
-  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Display&amp;dopt=pubmed_pubmed&amp;from_uid=15215345"><span\r
-  style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <script language="JavaScript1.2">\r
-<!--
-var Menu15215345 = [
-  ["UseLocalConfig","jsmenu3Config","",""],
-  ["Free in PMC","window.top.location='http://www.pubmedcentral.gov/articlerender.fcgi?tool=pubmed&pubmedid=15215345'","",""],
-  ["Cited in PMC","window.top.location='http://www.pubmedcentral.gov/tocrender.fcgi?action=cited&tool=pubmed&pubmedid=15215345'","",""],
-  ["Books","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=15215345&dopt=Books'","",""],
-  ["LinkOut","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=15215345&dopt=ExternalLink'","",""]
-]
-//-->\r
-  </script><a href="javascript:PopUpMenu2_Set(Menu15215345);" target="_self"><span\r
-  style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></a> </span><span\r
-  lang=EN-US style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>\r
-  <td colspan=2 style='padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US>3DCoffee@igs: a web server for\r
-  combining sequences and structures into a multiple sequence alignment.<br>\r
-  Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W37-40. <br>\r
-  PMID: 15215345 [PubMed - indexed for MEDLINE]</span><span lang=EN-US\r
-  style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
- </tr>\r
-</table>\r
-\r
-<p class=MyNormalJustified><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<table class=MsoNormalTable border=0 cellspacing=5 cellpadding=0 width="81%"\r
- style='width:81.98%;mso-cellspacing:3.7pt;mso-padding-alt:0mm 0mm 0mm 0mm'>\r
- <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>\r
-  <td width="53%" style='width:53.5%;padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US><a\r
-  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=15201059">O'Sullivan\r
-  O, Suhre K, Abergel C, Higgins DG, Notredame C.</a></span><span lang=EN-US\r
-  style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
-  <td nowrap valign=top style='padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US><a\r
-  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Display&amp;dopt=pubmed_pubmed&amp;from_uid=15201059"><span\r
-  style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <script language="JavaScript1.2">\r
-<!--
-var Menu15201059 = [
-  ["UseLocalConfig","jsmenu3Config","",""],
-  ["Cited in PMC","window.top.location='http://www.pubmedcentral.gov/tocrender.fcgi?action=cited&tool=pubmed&pubmedid=15201059'","",""],
-  ["Books","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=15201059&dopt=Books'","",""],
-  ["LinkOut","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=15201059&dopt=ExternalLink'","",""]
-]
-//-->\r
-  </script><a href="javascript:PopUpMenu2_Set(Menu15201059);" target="_self"><span\r
-  style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></a> </span><span\r
-  lang=EN-US style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>\r
-  <td colspan=2 style='padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US>3DCoffee: combining protein\r
-  sequences and structures within multiple sequence alignments.<br>\r
-  J Mol Biol. 2004 Jul 2;340(2):385-95. <br>\r
-  PMID: 15201059 [PubMed - indexed for MEDLINE]</span><span lang=EN-US\r
-  style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
- </tr>\r
-</table>\r
-\r
-<p class=MyNormalJustified><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<table class=MsoNormalTable border=0 cellspacing=5 cellpadding=0 width="81%"\r
- style='width:81.98%;mso-cellspacing:3.7pt;mso-padding-alt:0mm 0mm 0mm 0mm'>\r
- <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>\r
-  <td width="53%" style='width:53.5%;padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US><a\r
-  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=12824354">Poirot\r
-  O, O'Toole E, Notredame C.</a></span><span lang=EN-US style='mso-bidi-font-size:\r
-  12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
-  <td nowrap valign=top style='padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US><a\r
-  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Display&amp;dopt=pubmed_pubmed&amp;from_uid=12824354"><span\r
-  style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <script language="JavaScript1.2">\r
-<!--
-var Menu12824354 = [
-  ["UseLocalConfig","jsmenu3Config","",""],
-  ["Free in PMC","window.top.location='http://www.pubmedcentral.gov/articlerender.fcgi?tool=pubmed&pubmedid=12824354'","",""],
-  ["Cited in PMC","window.top.location='http://www.pubmedcentral.gov/tocrender.fcgi?action=cited&tool=pubmed&pubmedid=12824354'","",""],
-  ["Books","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=12824354&dopt=Books'","",""],
-  ["LinkOut","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=12824354&dopt=ExternalLink'","",""]
-]
-//-->\r
-  </script><a href="javascript:PopUpMenu2_Set(Menu12824354);" target="_self"><span\r
-  style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></a> </span><span\r
-  lang=EN-US style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>\r
-  <td colspan=2 style='padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US>Tcoffee@igs: A web server for\r
-  computing, evaluating and combining multiple sequence alignments.<br>\r
-  Nucleic Acids Res. 2003 Jul 1;31(13):3503-6. <br>\r
-  PMID: 12824354 [PubMed - indexed for MEDLINE]</span><span lang=EN-US\r
-  style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
- </tr>\r
-</table>\r
-\r
-<p class=MyNormalJustified><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<table class=MsoNormalTable border=0 cellspacing=5 cellpadding=0 width="81%"\r
- style='width:81.98%;mso-cellspacing:3.7pt;mso-padding-alt:0mm 0mm 0mm 0mm'>\r
- <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>\r
-  <td width="53%" style='width:53.5%;padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US><a\r
-  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=11301309">Notredame\r
-  C.</a></span><span lang=EN-US style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
-  <td nowrap valign=top style='padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US><a\r
-  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Display&amp;dopt=pubmed_pubmed&amp;from_uid=11301309"><span\r
-  style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <script language="JavaScript1.2">\r
-<!--
-var Menu11301309 = [
-  ["UseLocalConfig","jsmenu3Config","",""],
-  ["Cited in PMC","window.top.location='http://www.pubmedcentral.gov/tocrender.fcgi?action=cited&tool=pubmed&pubmedid=11301309'","",""],
-  ["Books","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=11301309&dopt=Books'","",""],
-  ["LinkOut","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=11301309&dopt=ExternalLink'","",""]
-]
-//-->\r
-  </script><a href="javascript:PopUpMenu2_Set(Menu11301309);" target="_self"><span\r
-  style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></a> </span><span\r
-  lang=EN-US style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>\r
-  <td colspan=2 style='padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US>Mocca: semi-automatic method for\r
-  domain hunting.<br>\r
-  Bioinformatics. 2001 Apr;17(4):373-4. <br>\r
-  PMID: 11301309 [PubMed - indexed for MEDLINE]</span><span lang=EN-US\r
-  style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
- </tr>\r
-</table>\r
-\r
-<p class=MyNormalJustified><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<table class=MsoNormalTable border=0 cellspacing=5 cellpadding=0 width="81%"\r
- style='width:81.98%;mso-cellspacing:3.7pt;mso-padding-alt:0mm 0mm 0mm 0mm'>\r
- <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>\r
-  <td width="53%" style='width:53.5%;padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US><a\r
-  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=10964570">Notredame\r
-  C, Higgins DG, Heringa J.</a></span><span lang=EN-US style='mso-bidi-font-size:\r
-  12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
-  <td nowrap valign=top style='padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US><a\r
-  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Display&amp;dopt=pubmed_pubmed&amp;from_uid=10964570"><span\r
-  style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <script language="JavaScript1.2">\r
-<!--
-var Menu10964570 = [
-  ["UseLocalConfig","jsmenu3Config","",""],
-  ["Cited in PMC","window.top.location='http://www.pubmedcentral.gov/tocrender.fcgi?action=cited&tool=pubmed&pubmedid=10964570'","",""],
-  ["Cited in Books","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Display&dopt=pubmed_books_refs&from_uid=10964570'","",""],
-  ["Books","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=10964570&dopt=Books'","",""],
-  ["LinkOut","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=10964570&dopt=ExternalLink'","",""]
-]
-//-->\r
-  </script><a href="javascript:PopUpMenu2_Set(Menu10964570);" target="_self"><span\r
-  style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></a> </span><span\r
-  lang=EN-US style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>\r
-  <td colspan=2 style='padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US>T-Coffee: A novel method for fast\r
-  and accurate multiple sequence alignment.<br>\r
-  J Mol Biol. 2000 Sep 8;302(1):205-17. <br>\r
-  PMID: 10964570 [PubMed - indexed for MEDLINE]</span><span lang=EN-US\r
-  style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
- </tr>\r
-</table>\r
-\r
-<p class=MyNormalJustified><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<table class=MsoNormalTable border=0 cellspacing=5 cellpadding=0 width="81%"\r
- style='width:81.98%;mso-cellspacing:3.7pt;mso-padding-alt:0mm 0mm 0mm 0mm'>\r
- <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>\r
-  <td width="53%" style='width:53.5%;padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US><a\r
-  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=9682054">Notredame\r
-  C, Holm L, Higgins DG.</a></span><span lang=EN-US style='mso-bidi-font-size:\r
-  12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
-  <td nowrap valign=top style='padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US><a\r
-  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Display&amp;dopt=pubmed_pubmed&amp;from_uid=9682054"><span\r
-  style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <script language="JavaScript1.2">\r
-<!--
-var Menu9682054 = [
-  ["UseLocalConfig","jsmenu3Config","",""],
-  ["Cited in PMC","window.top.location='http://www.pubmedcentral.gov/tocrender.fcgi?action=cited&tool=pubmed&pubmedid=9682054'","",""],
-  ["Books","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=9682054&dopt=Books'","",""],
-  ["LinkOut","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=9682054&dopt=ExternalLink'","",""]
-]
-//-->\r
-  </script><a href="javascript:PopUpMenu2_Set(Menu9682054);" target="_self"><span\r
-  style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></a> </span><span\r
-  lang=EN-US style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>\r
-  <td colspan=2 style='padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US>COFFEE: an objective function for\r
-  multiple sequence alignments.<br>\r
-  Bioinformatics. 1998 Jun;14(5):407-22. <br>\r
-  PMID: 9682054 [PubMed - indexed for MEDLINE]</span><span lang=EN-US\r
-  style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
- </tr>\r
-</table>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<h2><a name="_Toc235958461"></a><a name="_Toc102494656"></a><a\r
-name="_Toc102494278"></a><a name="_Toc101065189"><span style='mso-bookmark:\r
-_Toc102494278'><span style='mso-bookmark:_Toc102494656'><span style='mso-bookmark:\r
-_Toc235958461'><span lang=EN-US>Mocca</span></span></span></span></a></h2>\r
-\r
-<table class=MsoNormalTable border=0 cellspacing=5 cellpadding=0 width="81%"\r
- style='width:81.98%;mso-cellspacing:3.7pt;mso-padding-alt:0mm 0mm 0mm 0mm'>\r
- <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>\r
-  <td width="53%" style='width:53.5%;padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormal><span lang=AF><a\r
-  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=11301309"><span\r
-  lang=EN-US style='mso-ansi-language:EN-US'>Notredame C.</span></a></span><span\r
-  lang=AF style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
-  <td nowrap valign=top style='padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormal><span lang=AF><a\r
-  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Display&amp;dopt=pubmed_pubmed&amp;from_uid=11301309&amp;tool=ExternalSearch"><span\r
-  lang=EN-US style='mso-bidi-font-size:9.0pt;color:#336699;mso-ansi-language:\r
-  EN-US'>Related Articles,</span></a> <script language="JavaScript1.2">\r
-<!--
-var Menu11301309 = [
-  ["UseLocalConfig","jsmenu3Config","",""],
-  ["Cited in PMC","window.top.location='http://www.pubmedcentral.gov/tocrender.fcgi?action=cited&tool=pubmed&pubmedid=11301309'","",""],
-  ["Books","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=11301309&dopt=Books'","",""],
-  ["LinkOut","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=11301309&dopt=ExternalLink'","",""]
-]
-//-->\r
-  </script><a href="javascript:PopUpMenu2_Set(Menu11301309);" target="_self"><span\r
-  lang=EN-US style='mso-bidi-font-size:9.0pt;color:#336699;mso-ansi-language:\r
-  EN-US'>Links</span></a> </span><span lang=AF style='mso-bidi-font-size:12.0pt;\r
-  color:black'><o:p></o:p></span></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>\r
-  <td colspan=2 style='padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormal><span lang=AF>Mocca: semi-automatic method for domain\r
-  hunting.<br>\r
-  Bioinformatics. 2001 Apr;17(4):373-4. <br>\r
-  PMID: 11301309 [PubMed - indexed for MEDLINE]</span><span lang=AF\r
-  style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
- </tr>\r
-</table>\r
-\r
-<h2><a name="_Toc235958462"></a><a name="_Toc102494657"></a><a\r
-name="_Toc102494279"><span style='mso-bookmark:_Toc102494657'><span\r
-style='mso-bookmark:_Toc235958462'><span lang=EN-US>CORE</span></span></span></a></h2>\r
-\r
-<p class=MyNormal><span lang=AF><a\r
-href="http://www.tcoffee.org/Publications/Pdf/core.pp.pdf"><span lang=EN-US\r
-style='mso-ansi-language:EN-US'>http://www.tcoffee.org/Publications/Pdf/core.pp.pdf<o:p></o:p></span></a></span></p>\r
-\r
-<h2><a name="_Toc102494658"></a><a name="_Toc102494280"></a><a\r
-name="_Toc101065367"><span style='mso-bookmark:_Toc102494280'><span\r
-style='mso-bookmark:_Toc102494658'></span></span></a><a name="_Toc235958463"><span\r
-style='mso-bookmark:_Toc102494658'><span style='mso-bookmark:_Toc102494280'><span\r
-style='mso-bookmark:_Toc101065367'><span lang=EN-US>Other Contributions</span></span></span></span></a></h2>\r
-\r
-<p class=MyNormal><span lang=AF>We do not mean to steal code, but we will always\r
-try to re-use pre-existing code whenever that code exists, free of copyright,\r
-just like we expect people to do with our code. However, whenever this happens,\r
-we make a point at properly citing the source of the original contribution. If\r
-ever you recognize a piece of your code improperly cited, please drop us a note\r
-and we will be happy to correct that.</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>In the mean time, here are some important pieces\r
-of code from other packages that have been incorporated within the T-Coffee\r
-package. These include: </span></p>\r
-\r
-<p class=MyNormal><span lang=AF><span style='mso-tab-count:1'>         </span>-The\r
-Sim algorithm of Huang and Miller that given two sequences computes the N best\r
-scoring local alignments.</span></p>\r
-\r
-<p class=MyNormal><span lang=AF><span style='mso-tab-count:1'>         </span>-The\r
-tree reading/computing routines are taken from the ClustalW Package, courtesy\r
-of Julie Thompson, Des Higgins and Toby Gibson (Thompson, Higgins, Gibson,\r
-1994, 4673-4680,vol. 22, Nucleic Acid Research).</span></p>\r
-\r
-<p class=MyNormal><span lang=AF><span style='mso-tab-count:1'>         </span>-The\r
-implementation of the algorithm for aligning two sequences in linear space was\r
-adapted from Myers and Miller, in CABIOS, 1988, 11-17, vol. 1)</span></p>\r
-\r
-<p class=MyNormal><span lang=AF><span style='mso-spacerun:yes'> </span><span\r
-style='mso-tab-count:1'>        </span>-Various techniques and algorithms have\r
-been implemented. Whenever relevant, the source of the code/algorithm/idea is\r
-indicated in the corresponding function.</span></p>\r
-\r
-<p class=MyNormal><span lang=AF><span style='mso-tab-count:1'>         </span>-64\r
-Bits compliance was implemented by Benjamin Sohn, Performance Computing Center\r
-Stuttgart (HLRS), <st1:place w:st="on"><st1:country-region w:st="on">Germany</st1:country-region></st1:place></span></p>\r
-\r
-<p class=MyNormal><span lang=AF><span style='mso-tab-count:1'>         </span>-David\r
-Mathog (Caltech) provided many fixes and useful feedback for improving the code\r
-and making the whole soft behaving more rationally</span></p>\r
-\r
-<h2><a name="_Toc235958464"><span lang=EN-US>Bug Reports and Feedback</span></a></h2>\r
-\r
-<p class=MyNormal><span lang=AF><span style='mso-tab-count:1'>         </span>-Prof\r
-David Jones (UCL) reported and corrected the PDB1K bug (now t_coffee/sap can\r
-align PDB sequences longer than 1000 AA).</span></p>\r
-\r
-<p class=MyNormal><span lang=AF><span style='mso-tab-count:1'>         </span>-Johan\r
-Leckner reported several bugs related to the treatment of PDB structures,\r
-insuring a consistent behavior between version 1.37 and current ones.</span></p>\r
-\r
-<p class=MyNormal><span lang=AF><span style='mso-spacerun:yes'> </span></span></p>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 3.0pt;\r
-padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0mm;margin-right:\r
-4.25pt'>\r
-\r
-<p class=ChapterTitle><a name="_Toc235958465"></a><a name="_Toc102494673"></a><a\r
-name="_Toc101065204"><span style='mso-bookmark:_Toc102494673'><span\r
-style='mso-bookmark:_Toc235958465'><span lang=EN-US>I</span></span></span></a><span\r
-style='mso-bookmark:_Toc235958465'><span lang=EN-US>nstallation of The T-Coffee\r
-Packages</span></span></p>\r
-\r
-</div>\r
-\r
-<h2><a name="_Toc102494674"></a><a name="_Toc102494294"></a><a\r
-name="_Toc101065205"></a><a name="_Toc235958466"><span style='mso-bookmark:\r
-_Toc101065205'><span style='mso-bookmark:_Toc102494294'><span style='mso-bookmark:\r
-_Toc102494674'><span lang=EN-US>Third Party Packages and On Demand\r
-Installations</span></span></span></span></a><span style='mso-bookmark:_Toc101065205'><span\r
-style='mso-bookmark:_Toc102494294'><span style='mso-bookmark:_Toc102494674'></span></span></span></h2>\r
-\r
-<p class=MyNormaBoldl><span style='mso-bookmark:_Toc101065205'><span\r
-style='mso-bookmark:_Toc102494294'><span style='mso-bookmark:_Toc102494674'><span\r
-lang=AF>T-Coffee is a complex package that interacts with many other third part\r
-software. If you only want a standalone version of T-Coffee, you may install\r
-that package on its own. If you want to use a most sophisticated flavor\r
-(3dcoffee, expresso, rcofeee, etc...), the installer will try to install all\r
-the third paparty packages required.</span></span></span></span></p>\r
-\r
-<p class=MyNormaBoldl><span style='mso-bookmark:_Toc101065205'><span\r
-style='mso-bookmark:_Toc102494294'><span style='mso-bookmark:_Toc102494674'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<p class=MyNormaBoldl><span style='mso-bookmark:_Toc101065205'><span\r
-style='mso-bookmark:_Toc102494294'><span style='mso-bookmark:_Toc102494674'><span\r
-lang=AF>Note that since version 7.56, T-Coffee will use 'on demand'\r
-installation and install the third party packages it needs *when* it needs\r
-them. This only works for packages not requiring specific licenses and that can\r
-be installed by the regular installer. Please let us know if you would like\r
-another third party package to be included. </span></span></span></span></p>\r
-\r
-<p class=MyNormaBoldl><span style='mso-bookmark:_Toc101065205'><span\r
-style='mso-bookmark:_Toc102494294'><span style='mso-bookmark:_Toc102494674'><span\r
-lang=AF>Whenver on-demand installation or automated installation fails because\r
-of unforessen system specificities, users should install the third party\r
-package manually. In this documentation gives some tips we have found useful,\r
-but users are encouraged to check the original documentation.</span></span></span></span></p>\r
-\r
-<h2><span style='mso-bookmark:_Toc101065205'><span style='mso-bookmark:_Toc102494294'><span\r
-style='mso-bookmark:_Toc102494674'><a name="_Toc235958467"><span lang=EN-US>Standard\r
-Installation</span></a></span></span></span><span style='mso-bookmark:_Toc235958467'><span\r
-lang=EN-US> of T-Coffee</span></span></h2>\r
-\r
-<h3><a name="_Toc235958468"><span lang=EN-US>Unix</span></a></h3>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>You need to have: gcc, g77, CPAN and an internet\r
-connection and your root password (to install SOAP). If you cannot log as root,\r
-ask (kindly) your system manager to install <a\r
-href="http://search.cpan.org/%7Ebyrne/SOAP-Lite-0.60a/"><span lang=EN-US\r
-style='mso-ansi-language:EN-US'>SOAP::Lite</span></a> for you. You may do this\r
-before or after the installation of T-Coffee. Even without SOAP you will still\r
-be able to use the basic functions of T-Coffee (simplest usage).</span></p>\r
-\r
-<p class=MsoNormal style='margin-left:72.0pt'><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;\r
-margin-left:72.0pt;text-indent:-18.0pt;mso-list:l24 level2 lfo39;tab-stops:\r
-list 72.0pt'><![if !supportLists]><span lang=EN-US style='font-family:Arial;\r
-mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>1.<span\r
-style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;\r
-</span></span></span><![endif]><span dir=LTR><code><span lang=EN-US\r
-style='font-size:10.0pt'>gunzip t_coffee.tar.gz</span></code></span><span\r
-lang=EN-US style='font-family:Arial'><o:p></o:p></span></p>\r
-\r
-<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;\r
-margin-left:72.0pt;text-indent:-18.0pt;mso-list:l24 level2 lfo39;tab-stops:\r
-list 72.0pt'><![if !supportLists]><span lang=EN-US style='font-family:Arial;\r
-mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2.<span\r
-style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;\r
-</span></span></span><![endif]><span dir=LTR><code><span lang=EN-US\r
-style='font-size:10.0pt'>tar -xvf t_coffee.tar</span></code></span><span\r
-lang=EN-US style='font-family:Arial'><o:p></o:p></span></p>\r
-\r
-<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;\r
-margin-left:72.0pt;text-indent:-18.0pt;mso-list:l24 level2 lfo39;tab-stops:\r
-list 72.0pt'><![if !supportLists]><span lang=EN-US style='font-family:Arial;\r
-mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>3.<span\r
-style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;\r
-</span></span></span><![endif]><span dir=LTR><code><span lang=EN-US\r
-style='font-size:10.0pt'>cd t_coffee</span></code></span><span lang=EN-US\r
-style='font-family:Arial'><o:p></o:p></span></p>\r
-\r
-<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;\r
-margin-left:72.0pt;text-indent:-18.0pt;mso-list:l24 level2 lfo39;tab-stops:\r
-list 72.0pt'><![if !supportLists]><span lang=EN-US style='font-family:Arial;\r
-mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>4.<span\r
-style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;\r
-</span></span></span><![endif]><span dir=LTR><code><span lang=EN-US\r
-style='font-size:10.0pt'>./install t_coffee</span></code></span><span\r
-lang=EN-US style='font-family:Arial'><o:p></o:p></span></p>\r
-\r
-<p class=MyNormal><span lang=AF>This installation will try to install EVERY\r
-flavor of T-Coffee along with the packages it requires. It will not re-install\r
-the packages that are already on your computer.</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>If you want a more specific installation, you\r
-can try:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US><span\r
-style='mso-tab-count:1'>   </span>./install t_coffee</span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US><span\r
-style='mso-tab-count:1'>   </span>./install mcoffee</span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US><span\r
-style='mso-tab-count:1'>   </span>./install 3dcoffee</span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US><span\r
-style='mso-tab-count:1'>   </span>./install rcoffee</span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US><span\r
-style='mso-tab-count:1'>   </span>./install psicoffee</span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MyNormal><span lang=AF>Or even</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US><span\r
-style='mso-tab-count:1'>   </span>./install all</span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MyNormal><span lang=AF>-All the corresponding executables will be\r
-downloaded automatically and installed in</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US><span\r
-style='mso-tab-count:1'>   </span>$HOME/.t_coffee/plugins</span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MyNormal><span lang=AF>-if you executables are in a different\r
-location, give it to T-Coffee using the -plugins flag.</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>-If the installation of any of the companion\r
-package fails, you should install it yourself using the provided link (see\r
-below) and following the authors instructions.<span style='mso-tab-count:1'>      </span></span></p>\r
-\r
-<p class=MyNormal><span lang=AF>-If you have not managed to install SOAP::Lite,\r
-you can re-install it later (from anywhere) following steps 1-2.</span></p>\r
-\r
-<p class=MsoNormal style='margin-left:72.0pt'><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>-This procedure attempts 3 things:\r
-installing and Compiling T-Coffee (C program), Installing and compiling <a\r
-href="http://zhang.bioinformatics.ku.edu/TM-align/"><span lang=EN-US\r
-style='mso-ansi-language:EN-US'>TMalign</span></a> (Fortran), Installing and\r
-compiling <a href="http://search.cpan.org/%7Ebyrne/SOAP-Lite-0.60a/"><span\r
-lang=EN-US style='mso-ansi-language:EN-US'>SOAP::Lite</span></a>(Perl Module).</span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>-If you have never installed SOAP::Lite,\r
-CPAN will ask you many questions: say Yes to all </span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>-If everything went well, the procedure has\r
-created in the <b>bin</b> directory two executables: t_coffee and TMalign (<b>Make\r
-sure these executables are on your $PATH!</b>)</span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<h3><a name="_Toc235958469"><span lang=EN-US>Microsoft Windows/Cygwin</span></a></h3>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>Install <a href="http://www.cygwin.com"><span\r
-lang=EN-US style='color:windowtext;mso-ansi-language:EN-US;text-decoration:\r
-none;text-underline:none'>Cygwin</span></a></span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>Download The Installer (NOT Cygwin/X)</span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>Click on view to list ALL the packages</span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>Select: gcc-core, make, wget</span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>Optional: ssh, xemacs, nano</span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>Run mkpasswd in Cywin (as requested when\r
-you start cygwin)</span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>Install T-Coffee within Cygwin using the\r
-Unix procedure</span></p>\r
-\r
-<h3><a name="_Toc235958470"><span lang=EN-US>MAC osX, Linux</span></a></h3>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>Make sure you have the Developer's kit installed\r
-(compilers and makefile)</span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>Follow the Unix Procedure</span></p>\r
-\r
-<p class=Mylist><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<h3><a name="_Toc235958471"><span lang=EN-US>CLUSTER Installation</span></a></h3>\r
-\r
-<p class=MyNormal><span lang=AF>In order to run, T-Coffee must have a value for\r
-the http_proxy and for the E-mail. In order to do so you can either:</span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>export the following values:</span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>export\r
-http_proxy_4_TCOFFEE=&quot;proxy&quot; or &quot;&quot; if no proxy</span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>export EMAIL_4_TCOFFEE=&quot;your\r
-email&quot;</span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>OR </span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>modify the file ~/.t_coffee/t_coffee_env</span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>OR</span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>add to your command line: t_coffee \85.\r
--proxy=&lt;proxy&gt; -email=&lt;email</span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>if you have no proxy: t_coffee \85 -proxy\r
--email=&lt;email&gt;</span></p>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<h3><a name="_Toc235958472"><span lang=EN-US>If you have PDB installed:</span></a></h3>\r
-\r
-<p class=MyNormal><span lang=AF>Assuming you have a standard PDB installation\r
-in your file system</span></p>\r
-\r
-<p class=example2CxSpFirst><span lang=EN-US>setenv (or export)<span\r
-style='mso-spacerun:yes'>  </span>PDB_DIR &lt;abs path&gt;/data/structures/all/pdb/</span></p>\r
-\r
-<p class=example2CxSpMiddle><span lang=EN-US>OR</span></p>\r
-\r
-<p class=example2CxSpLast><span lang=EN-US>setenv (or export)<span\r
-style='mso-spacerun:yes'>  </span>PDB_DIR &lt;abs\r
-path&gt;/structures/divided/pdb/</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>If you do not have PDB installed, don't worry,\r
-t_coffee will go and fetch any structure it needs directly from the PDB\r
-repository. It will simply be a bit slower than if you had PDB locally. </span></p>\r
-\r
-<h2><a name="_Toc102494675"></a><a name="_Toc102494295"></a><a\r
-name="_Toc101065206"></a><a name="_Toc235958473"><span style='mso-bookmark:\r
-_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:\r
-_Toc102494675'><span lang=EN-US>Installing BLAST for T-Coffee</span></span></span></span></a><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'></span></span></span></h2>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>BLAST is a program that search sequence databases for homologues of a\r
-query sequence. It works for proteins and Nucleic Acids. In theory BLAST is\r
-just a package like any, but in practice things are a bit more complex. To run\r
-well, BLST requires up to date databases (that can be fairly large, like NR or\r
-UNIPROT) and a powerful computer.</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>Fortunately, an increasing number of institutes or companies are now providing\r
-BLAST clients that run over the net. It means that all you need is a small\r
-program that send your query to the big server and gets the results back. This\r
-prevents you from the hassle of installing and maintaining BLAST, but of course\r
-it is less private and you rely on the network and the current load of these\r
-busy servers.</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>Thanks to its interaction with BLAST, T-Coffee can gather structures\r
-and protein profiles and deliver an alignment significantly more accurate than\r
-the default you would get with T-Coffee or any similar method.</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>Let us go through the various modes available for T-Coffee</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><a name="_Toc235958474"><span lang=EN-US>Why\r
-Do I need BLAST with T-Coffee?</span></a></span></span></span></h3>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>The most accurate modes of T-Coffe scan the databases for templates\r
-that they use to align the sequences. There are currently two types of templates\r
-for proteins:</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>structures (PDB) that can be found by a blastp against the PDB database\r
-and profiles that can be constructed with eiether a blastp or a psiblast\r
-against nr or uniprot.</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>These templates are automatically built if you use:</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:\r
-1'>   </span>t_coffee &lt;yourseq&gt; -mode expresso</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><span style='mso-tab-count:1'>         </span>that fetches aand uses\r
-pdb templates, or</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:\r
-1'>   </span><span style='mso-tab-count:1'>       </span>t_coffee &lt;your\r
-seq&gt; -mode psicoffee</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><span style='mso-tab-count:1'>         </span>that fetches and uses\r
-profile templates, or</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:\r
-1'>   </span><span style='mso-tab-count:1'>       </span>t_coffee &lt;your\r
-seq&gt; -mode accurate</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><span style='mso-tab-count:1'>         </span>that does everything and\r
-tries to use the best template. Now that you see why it is useful let's see how\r
-to get BLAST up and running, from the easy solution to tailor made ones.</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><a name="_Toc235958475"><span lang=EN-US>Using\r
-the EBI BLAST Client</span></a></span></span></span></h3>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>This is by far the easiest (and the default mode). The perl clients are\r
-already incorporated in T-Coffeem and all you need is the SOAP::Lite perl\r
-library. In theory, T-Coffee should have already installed this library during\r
-the standard installation. Yet, this requires having toot access. If you did\r
-not have it at the time of the installation, or if you need your system administrator\r
-to install SOAP::Lite, simply follow the instruction provided on the website:</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:\r
-1'>   </span>http://search.cpan.org/~byrne/SOAP-Lite-0.60a</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>It really is worth the effort, since the EBI is providing one of the\r
-best webservice available around, and most notably, the only public psiblast\r
-via a web service.</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><span style='mso-spacerun:yes'> </span></span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>Another important point is that the EBI requires your E-mail address to\r
-process your queries. Normally, T-Coffee should have asked you to provide this\r
-address. If you have not, or if you have provided a phony address, you should\r
-correct this by directly editing the file</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:\r
-1'>   </span>~/.t_coffee/email.txt</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><b><span\r
-lang=AF>Be Careful! </span></b><span lang=AF>If you provide a fake E-mail, the\r
-EBI may suspend the service for all machines associated with your IP address\r
-(that could mean your entire lab, or entire institute, or even the entire\r
-country or, but I doubt it, the whole universe).</span></span></span></span></p>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><a name="_Toc235958476"><span lang=EN-US>Using\r
-the NCBI BLAST Client</span></a></span></span></span></h3>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>The NCBI is the next best alternative. In my hand it was always a bit\r
-slower and most of all, it does not incorporate PSI-BLAST (as a web sevice). A\r
-big miss. The NCBI web blast client is a small executable that you should\r
-install on your system following the instructions given on this link</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US>ftp://ftp.ncbi.nih.gov/blast/executables/LATEST</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>Simply go for <b>netbl,</b> download the executable that corresponds to\r
-your architecture (cygwin users should go for the win executable). Despite all\r
-the files that come along the executable blastcl3 is a stand alone executable\r
-that you can safely move to your $BIN.</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>All you will then need to do is to make sure that T-Coffee uses the\r
-right client, when you run it.</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US>-blast_server=NCBI</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>No need for any E-mail here, but you don't get psiblast, and whenever\r
-T-Coffee wants to use it, blastp will be used instead.</span></span></span></span></p>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><a name="_Toc235958477"><span lang=EN-US>Using\r
-another Client</span></a></span></span></span></h3>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>You may have your own client (lucky you). If that is so, all you need\r
-is to make sure that this client is complient with the blast command line. If\r
-your client is named foo.pl, all you need to to is run T-Coffee with</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US>-blast_server=CLIENT_foo.pl</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>Foo will be called as if it were blastpgp, and it is your responsability\r
-to make sure it can handle the following command line:</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US>foo.pl -p &lt;method&gt; -d\r
-&lt;db&gt; -i &lt;infile&gt; -o &lt;outfile&gt; -m 7</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>method can either be blastp or psiblast.</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>infile is a FASTA file</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>-m7 triggers the XML output. T-Coffee is able to parse both the EBI XML\r
-output and the NCBI XML output.</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>If foo.pl behaves differently, the easiest will probably be to write a\r
-wrapper around it so that wrapped_foo.pl behaves like blastpgp</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><a name="_Toc235958478"><span lang=EN-US>Using\r
-a BLAST local version on UNIX</span></a></span></span></span></h3>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>If you have blastpgp installed, you can run it instead of the remote\r
-clients by using:</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US>-blast_server=LOCAL</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><span style='mso-spacerun:yes'> </span>The documnentation for blastpgp\r
-can be found on:</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US>www.ncbi.nlm.nih.gov/staff/tao/URLAPI/blastpgp.html</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>and the package is part of the standard BLAST distribution</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US>ftp://ftp.ncbi.nih.gov/blast/executables/LATEST</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>Depending on your system, your own skills, your requirements and on\r
-more parameters than I have fingers to count, installing a BLAST server suited\r
-for your needs can range from a 10 minutes job to an achivement spread over\r
-several generations. So at this point, you should roam the NCBI website for\r
-suitable information.</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>If you want to have your own BLAST server to run your own databases,\r
-you should know that it is possible to control both the database and the\r
-program used by BLAST:</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>-prot_db: will specify the database used by all the psi-blast modes</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpLast><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>-pdb_db: will specify the database used by the pdb modes</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><a name="_Toc235958479"><span lang=EN-US>Using\r
-a BLAST local version on Windows/cygwin</span></a></span></span></span></h3>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>For those of you using cygwin, be careful. While cygwin behaves like a\r
-UNIX system, the BLAST executable required for cygwin (win32) is expecting\r
-WINDOWS path and not UNIX path. This has three important consequences:</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>1- the ncbi file declaring the Data directory must be:</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><span style='mso-tab-count:1'>         </span>C:WINDOWS//ncbi.init<span\r
-style='mso-spacerun:yes'>  </span>[at the root of your WINDOWS]</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>2- the address mentionned with this file must be WINDOWS formated, for\r
-instance, on my system:</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>Data=C:\cygwin\home\notredame\blast\data</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>3- When you pass database addresses to BLAST, these must be in Windows\r
-format:</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><span style='mso-tab-count:1'>         </span>-protein_db=&quot;c:/somewhere/somewhereelse/database&quot;</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>(using the slash (/) or the andtislash (\) does not matter on new\r
-systems but I would reommand against incorporating white spaces.</span></span></span></span></p>\r
-\r
-<h2><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><a name="_Toc235958480"><span lang=EN-US>Installing\r
-Other Companion Packages</span></a></span></span></span></h2>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>T-Coffee is meant to interact with as many packages as possible, either\r
-for aligning or using predictions. If you type </span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:\r
-1'>   </span>t_coffee</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>You will receive a list of supported packages that looks like the next\r
-table. In theory, most of these packages can be installed by T-Coffee</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>****** Pairwise Sequence Alignment Methods:</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>--------------------------------------------</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>fast_pair <span style='mso-spacerun:yes'>         </span>built_in</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>exon3_pair<span style='mso-spacerun:yes'>         </span>built_in</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>exon2_pair<span style='mso-spacerun:yes'>         </span>built_in</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>exon_pair<span style='mso-spacerun:yes'>          </span>built_in</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>slow_pair<span style='mso-spacerun:yes'>          </span>built_in</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>proba_pair<span style='mso-spacerun:yes'>         </span>built_in</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>lalign_id_pair<span style='mso-spacerun:yes'>     </span>built_in</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>seq_pair<span style='mso-spacerun:yes'>           </span>built_in</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>externprofile_pair built_in</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>hh_pair<span style='mso-spacerun:yes'>       </span><span\r
-style='mso-spacerun:yes'>     </span>built_in</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>profile_pair<span style='mso-spacerun:yes'>       </span>built_in</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>cdna_fast_pair<span style='mso-spacerun:yes'>     </span>built_in</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>cdna_cfast_pair<span style='mso-spacerun:yes'>    </span>built_in</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>clustalw_pair<span style='mso-spacerun:yes'>     \r
-</span>ftp://www.ebi.ac.uk/pub/clustalw</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>mafft_pair<span style='mso-spacerun:yes'>        \r
-</span>http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>mafftjtt_pair<span style='mso-spacerun:yes'>      </span>http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>mafftgins_pair<span style='mso-spacerun:yes'>    \r
-</span>http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>dialigntx_pair<span style='mso-spacerun:yes'>    \r
-</span>http://dialign-tx.gobics.de/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>dialignt_pair<span style='mso-spacerun:yes'>     \r
-</span>http://dialign-t.gobics.de/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>poa_pair<span style='mso-spacerun:yes'>           </span>http://www.bioinformatics.ucla.edu/poa/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>probcons_pair<span style='mso-spacerun:yes'>     \r
-</span>http://probcons.stanford.edu/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>muscle_pair<span style='mso-spacerun:yes'>       \r
-</span>http://www.drive5.com/muscle/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>t_coffee_pair<span style='mso-spacerun:yes'>     \r
-</span>http://www.tcoffee.org</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>pcma_pair<span style='mso-spacerun:yes'>         \r
-</span>ftp://iole.swmed.edu/pub/PCMA/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>kalign_pair<span style='mso-spacerun:yes'>       \r
-</span>http://msa.cgb.ki.se</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>amap_pair<span style='mso-spacerun:yes'>         \r
-</span>http://bio.math.berkeley.edu/amap/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>proda_pair<span style='mso-spacerun:yes'>        \r
-</span>http://bio.math.berkeley.edu/proda/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>prank_pair<span style='mso-spacerun:yes'>        \r
-</span>http://www.ebi.ac.uk/goldman-srv/prank/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>consan_pair<span style='mso-spacerun:yes'>       \r
-</span>http://selab.janelia.org/software/consan/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>****** Pairwise Structural Alignment Methods:</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>--------------------------------------------</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>align_pdbpair<span style='mso-spacerun:yes'>      </span>built_in</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>lalign_pdbpair<span style='mso-spacerun:yes'>     </span>built_in</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>extern_pdbpair<span style='mso-spacerun:yes'>     </span>built_in</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>thread_pair<span style='mso-spacerun:yes'>        </span>built_in</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>fugue_pair<span style='mso-spacerun:yes'>        \r
-</span>http://www-cryst.bioc.cam.ac.uk/fugue/download.html</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>pdb_pair<span style='mso-spacerun:yes'>           </span>built_in</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>sap_pair<span style='mso-spacerun:yes'>          \r
-</span>http://www-cryst.bioc.cam.ac.uk/fugue/download.html</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>mustang_pair<span style='mso-spacerun:yes'>      \r
-</span>http://www.cs.mu.oz.au/~arun/mustang/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>tmalign_pair<span style='mso-spacerun:yes'>      \r
-</span>http://zhang.bioinformatics.ku.edu/TM-align/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>****** Multiple Sequence Alignment Methods:</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>--------------------------------------------</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>clustalw_msa<span style='mso-spacerun:yes'>      \r
-</span>ftp://www.ebi.ac.uk/pub/clustalw</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>mafft_msa<span style='mso-spacerun:yes'>         \r
-</span>http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>mafftjtt_msa<span style='mso-spacerun:yes'>      \r
-</span>http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>mafftgins_msa<span style='mso-spacerun:yes'>     \r
-</span>http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>dialigntx_msa<span style='mso-spacerun:yes'>     \r
-</span>http://dialign-tx.gobics.de/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>dialignt_msa<span style='mso-spacerun:yes'>      \r
-</span>http://dialign-t.gobics.de/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>poa_msa<span style='mso-spacerun:yes'>           \r
-</span>http://www.bioinformatics.ucla.edu/poa/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>probcons_msa<span style='mso-spacerun:yes'>      \r
-</span>http://probcons.stanford.edu/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>muscle_msa<span style='mso-spacerun:yes'>        \r
-</span>http://www.drive5.com/muscle/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>t_coffee_msa<span style='mso-spacerun:yes'>      \r
-</span>http://www.tcoffee.org</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>pcma_msa<span style='mso-spacerun:yes'>          \r
-</span>ftp://iole.swmed.edu/pub/PCMA/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>kalign_msa<span style='mso-spacerun:yes'>        \r
-</span>http://msa.cgb.ki.se</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>amap_msa<span style='mso-spacerun:yes'>          \r
-</span>http://bio.math.berkeley.edu/amap/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>proda_msa<span style='mso-spacerun:yes'>         \r
-</span>http://bio.math.berkeley.edu/proda/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>prank_msa<span style='mso-spacerun:yes'>         \r
-</span>http://www.ebi.ac.uk/goldman-srv/prank/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>#######<span style='mso-spacerun:yes'>   </span>Prediction Methods\r
-available to generate Templates</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>-------------------------------------------------------------</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>RNAplfold<span style='mso-spacerun:yes'>         \r
-</span>http://www.tbi.univie.ac.at/~ivo/RNA/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>HMMtop<span style='mso-spacerun:yes'>            \r
-</span>www.enzim.hu/hmmtop/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>GOR4<span style='mso-spacerun:yes'>              \r
-</span>http://mig.jouy.inra.fr/logiciels/gorIV/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>wublast_client<span style='mso-spacerun:yes'>    \r
-</span>http://www.ebi.ac.uk/Tools/webservices/services/wublast</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>blastpgp_client<span style='mso-spacerun:yes'>    </span>http://www.ebi.ac.uk/Tools/webservices/services/blastpgp<span\r
-style='mso-spacerun:yes'>            </span></span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpLast><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>==========================================================</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<h2><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><a name="_Toc235958481"><span lang=EN-US>Installation\r
-of PSI-Coffee and Expresso</span></a></span></span></span></h2>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>PSI-Coffee is a mode of T-Coffee that runs a a Psi-BLAST on each of\r
-your sequences and makes a multiple profile alignment. If you do not have any\r
-structural information, it is by far the most accurate mode of T-Coffee. To use\r
-it, you must have SOAP installed so that the EBI BLAST client can run on your\r
-system.</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>It is a bit slow, but really worth it if your sequences are hard to\r
-align and if the accuracy of your alignment is important. <span\r
-style='mso-spacerun:yes'> </span></span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>To use this mode, try:</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:\r
-1'>   </span>t_coffee &lt;yoursequence&gt; -mode psicoffee</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>Note that because PSI-BLAST is time consuming, T-Coffee stores the runs\r
-in its cache (./tcoffee/cache) so that it does not need to be re-run. It means\r
-that if you re-align your sequences (or add a few extra sequences), things will\r
-be considerably faster.</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>If your installation procedure has managed to compile TMalign, and if\r
-T-Coffee has access to the EBI BLAST server (or any other server) you can also\r
-do the following:</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:\r
-1'>   </span>t_coffee &lt;yoursequence&gt; -mode expresso</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>That will look for structural templates. And if both these modes are\r
-running fine, then you are ready for the best, the &quot;crème de la\r
-crème&quot;:</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:\r
-1'>   </span>t_coffee &lt;yoursequence&gt; -mode accurate</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<h2><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><a name="_Toc235958482"><span lang=EN-US>Installation\r
-of M-Coffee</span></a></span></span></span></h2>\r
-\r
-<p class=MsoNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>M-Coffee is a special mode of T-Coffee that makes it possible to\r
-combine the output of many multiple sequence alignment packages. </span></span></span></span><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US style='mso-ansi-language:\r
-EN-US'><o:p></o:p></span></span></span></span></p>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><a name="_Toc235958483"><span lang=EN-US>Automated\r
-Installation</span></a></span></span></span></h3>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>In the T-Coffee distribution, type:</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US>./install mcoffee</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MsoNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>In theory, this command should download and install every required\r
-package. If, however, it fails, you should switch to the manual installation\r
-(see next).</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>By default these packages will be in </span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US>$HOME/.t_coffee/plugins</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>If you want to have these companion packages in a different directory,\r
-you can either set the environement variable </span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US>PLUGINS_4_TCOFFEE=&lt;plugins\r
-dir&gt;</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>Or use the command line flag -plugin (over-rides every other setting)</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US>t_coffee ...\r
--plugins=&lt;plugins dir&gt;</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><a name="_Toc235958484"><span lang=EN-US>Manual\r
-Installation</span></a></span></span></span></h3>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>M-Coffee requires a standard T-Coffee installation (c.f. previous\r
-section) and the following packages to be installed on your system:</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><span style='mso-tab-count:1'>         </span></span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>Package<span style='mso-tab-count:2'>           </span>Where From</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>==========================================================</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>ClustalW<span style='mso-tab-count:2'>          </span>can interact\r
-with t_coffee</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>----------------------------------------------------------</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>Poa<span style='mso-tab-count:3'>               </span>http://www.bioinformatics.ucla.edu/poa/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>----------------------------------------------------------</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>Muscle<span style='mso-tab-count:2'>            </span>http://www.drive5.com</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US><span style='mso-spacerun:yes'> </span>----------------------------------------------------------</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>ProbCons<span style='mso-tab-count:2'>          </span>http://probcons.stanford.edu/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>ProbConsRNA<span style='mso-tab-count:2'>       </span>http://probcons.stanford.edu/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>----------------------------------------------------------</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>MAFFT<span style='mso-tab-count:1'> </span></span></span></span></span><a\r
-href="http://www.biophys.kyoto-/"><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>http://www.biophys.kyoto-</span></span></span></span><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'></span></span></span></a><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US>u.ac.jp/~katoh/programs/align/mafft/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>----------------------------------------------------------</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>Dialign-T<span style='mso-tab-count:2'>         </span></span></span></span></span><a\r
-href="http://dialign-t.gobics.de/"><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>http://dialign-t.gobics.de/</span></span></span></span><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'></span></span></span></a><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>Dialign-TX<span style='mso-tab-count:2'>        </span></span></span></span></span><a\r
-href="http://dialign-t.gobics.de/"><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>http://dialign-tx.gobics.de/</span></span></span></span><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'></span></span></span></a><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>----------------------------------------------------------</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>PCMA<span style='mso-tab-count:3'>              </span></span></span></span></span><a\r
-href="ftp://iole.swmed.edu/pub/PCMA/"><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>ftp://iole.swmed.edu/pub/PCMA/</span></span></span></span><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'></span></span></span></a><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>----------------------------------------------------------</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>kalign<span style='mso-spacerun:yes'>           \r
-</span>http://msa.cgb.ki.se</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>----------------------------------------------------------</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>amap<span style='mso-spacerun:yes'>             \r
-</span>http://bio.math.berkeley.edu/amap/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>-----------------------------------------------------------</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>proda_msa<span style='mso-spacerun:yes'>       \r
-</span>http://bio.math.berkeley.edu/proda/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>-----------------------------------------------------------</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>prank_msa<span style='mso-spacerun:yes'>        </span>http://www.ebi.ac.uk/goldman-srv/prank/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpLast><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>In our hands all these packages where very straightforward to compile\r
-and install on a standard cygwin or Linux configuration. Just make sure you\r
-have gcc, the C compiler, properly installed.</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>Once the package is compiled and ready to use, make sure that the\r
-executable is on your path, so that t_coffee can find it automatically. Our\r
-favorite procedure is to create a bin directory in the home. If you do so, make\r
-sure this bin is in your path and fill it with all your executables (this is a\r
-standard Unix practice).</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>If for some reason, you do not want this directory to be on your path,\r
-or you want to specify a precise directory containing the executables, you can\r
-use:</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:\r
-1'>   </span>export PLUGINS_4_TCOFFEE=&lt;dir&gt;</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>By default this directory is set to $HOME/.t_coffee/plugins/$OS, but\r
-you can over-ride it with the environement variable or using the flag:</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:\r
-1'>   </span>t_coffee ...-plugins=&lt;dir&gt;</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>If you cannot, or do not want to use a single bin directory, you can\r
-set the following environment variables to the absolute path values of the\r
-executable you want to use. Whenever they are set, these variables will supersede\r
-any other declaration. This is a convenient way to experiment with multiple\r
-package versions.</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:70.2pt;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US>POA_4_TCOOFFEE<br>\r
-CLUSTALW_4_TCOFFEE<br>\r
-POA_4_TCOFFEE<br>\r
-TCOFFEE_4_TCOFFEE<br>\r
-MAFFT_4_TCOFFEE<br>\r
-MUSCLE_4_TCOFFEE<br>\r
-DIALIGNT_4_TCOFFEE<br>\r
-PRANK_4_TCOFFEE<br>\r
-DIALIGNTX_4_TCOFFEE<br>\r
-<span style='mso-spacerun:yes'> </span></span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>For three of these packages, you will need to copy some of the files in\r
-a special T-Coffee directory.</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:\r
-1'>   </span>cp POA_DIR/* ~/.t_coffee/mcoffee/</span></span></span></span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:\r
-1'>   </span>cp DIALIGN-T/conf/*<span style='mso-spacerun:yes'>  </span>~/.t_coffee/mcoffee</span></span></span></span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:\r
-1'>   </span>cp DIALIGN-TX/conf/*<span style='mso-spacerun:yes'> \r
-</span>~/.t_coffee/mcoffee</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>Note that the following files are enough for default usage:</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US>BLOSUM.diag_prob_t10<span\r
-style='mso-spacerun:yes'>   </span>BLOSUM75.scr<span style='mso-spacerun:yes'> \r
-</span>blosum80_trunc.mat<span style='mso-spacerun:yes'>           </span></span></span></span></span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US>dna_diag_prob_100_exp_330000<span\r
-style='mso-spacerun:yes'>  </span>dna_diag_prob_200_exp_110000</span></span></span></span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US>BLOSUM.scr<span\r
-style='mso-spacerun:yes'>             </span>BLOSUM90.scr<span\r
-style='mso-spacerun:yes'>  </span>dna_diag_prob_100_exp_110000</span></span></span></span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US>dna_diag_prob_100_exp_550000<span\r
-style='mso-spacerun:yes'>  </span>dna_diag_prob_250_exp_110000</span></span></span></span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US>BLOSUM75.diag_prob_t2<span\r
-style='mso-spacerun:yes'>  </span>blosum80.mat<span style='mso-spacerun:yes'> \r
-</span>dna_diag_prob_100_exp_220000<span style='mso-spacerun:yes'>  </span></span></span></span></span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US>dna_diag_prob_150_exp_110000<span\r
-style='mso-spacerun:yes'>  </span>dna_matrix.scr</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>If you would rather have the mcoffee directory in some other location,\r
-set the MCOFFEE_4_TCOFFEE environement variable to the propoer directory:</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:\r
-1'>   </span>setenv MCOFFEE_4_TCOFFEE &lt;directory containing mcoffee\r
-files&gt;</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<h2><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><a name="_Toc235958485"><span lang=EN-US>Installation\r
-of APDB and iRMSD</span></a></span></span></span></h2>\r
-\r
-<p class=MsoBodyText><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>APDB and iRMSD are incorporated in T-Coffee. Once t_coffee is\r
-installed, you can invoque these programs by typing:</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:\r
-1'>   </span>t_coffee \96other_pg apdb<br>\r
-<span style='mso-tab-count:1'>   </span>t_coffee \96other_pg irmsd</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<h2><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><a name="_Toc235958486"><span lang=EN-US>Installation\r
-of tRMSD</span></a></span></span></span></h2>\r
-\r
-<p class=MsoBodyText><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>tRMSD comes along with t_coffee but it also requires the package\r
-phylip in order to be functional. Phylip can be obtained from:</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><span style='mso-tab-count:1'>         </span></span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>Package<span style='mso-tab-count:2'>           </span>Function</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>===================================================</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>---------------------------------------------------</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>Phylip<span style='mso-tab-count:2'>            </span>Phylogenetic\r
-tree computation</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US><span style='mso-tab-count:3'>                  </span>evolution.genetics.washington.edu/phylip.html</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpLast><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>---------------------------------------------------</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;text-indent:14.1pt;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US>t_coffee \96other_pg trmsd</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<h2><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US><o:p>&nbsp;</o:p></span></span></span></span></h2>\r
-\r
-<h2><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><a name="_Toc235958487"><span lang=EN-US>Installation\r
-of seq_reformat</span></a></span></span></span></h2>\r
-\r
-<p class=MsoBodyText><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>Seq_reformat is a reformatting package that is part of t_coffee. To\r
-use it (and see the available options), type:</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:\r
-1'>   </span>t_coffee \96other_pg seq_reformat</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<h2><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><a name="_Toc235958488"><span lang=EN-US>Installation\r
-of extract_from_pdb</span></a></span></span></span></h2>\r
-\r
-<p class=MsoBodyText><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>Extract_from_pdb is a PDB reformatting package that is part of\r
-t_coffee. To use it (and see the available options), type.</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:\r
-1'>   </span>t_coffee \96other_pg apdb \96h</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MsoBodyText><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>Extract_from_pdb requires wget in order to automatically fetch PDB\r
-structures.</span></span></span></span></p>\r
-\r
-<p class=MsoBodyText><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<span style='mso-bookmark:_Toc102494675'></span><span style='mso-bookmark:_Toc102494295'></span><span\r
-style='mso-bookmark:_Toc101065206'></span>\r
-\r
-<h2><a name="_Toc235958489"><span lang=EN-US>Installation of 3D-Coffee/Expresso</span></a></h2>\r
-\r
-<p class=MyNormal><span lang=AF>3D-Coffee/Expresso is a special mode of\r
-T-Coffee that makes it possible to combine sequences and structures. The main\r
-difference between Expresso and 3D-Coffee is that Expresso fetches the\r
-structures itself. </span><span lang=EN-US style='mso-ansi-language:EN-US'><o:p></o:p></span></p>\r
-\r
-<h3><a name="_Toc235958490"><span lang=EN-US>Automated Installation</span></a></h3>\r
-\r
-<p class=MyNormal><span lang=AF>In the T-Coffee distribution, type:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>./install\r
-expresso</span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>OR</span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>./install\r
-3dcoffee</span></p>\r
-\r
-</div>\r
-\r
-<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MyNormal><span lang=AF>In theory, this command should download and\r
-install every required package (<b>except fugue</b>). If, however, it fails,\r
-you should switch to the manual installation (see next).</span></p>\r
-\r
-<h3><a name="_Toc235958491"><span lang=EN-US>Manual Installation</span></a></h3>\r
-\r
-<p class=MyNormal><span lang=AF>In order to make the most out of T-Coffee, you\r
-will need to install the following packages (make sure the executable is named\r
-as indicated below):</span></p>\r
-\r
-<p class=MyNormal><span lang=AF><span style='mso-tab-count:1'>         </span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span lang=EN-US>Package<span style='mso-tab-count:\r
-2'>           </span>Function</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>===================================================</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>---------------------------------------------------</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>wget<span style='mso-tab-count:\r
-2'>        </span><span style='mso-tab-count:1'>      </span>3DCoffee </span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US><span style='mso-tab-count:\r
-3'>                  </span>Automatic Downloading of Structures</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>---------------------------------------------------</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>sap<span style='mso-tab-count:\r
-1'>   </span><span style='mso-tab-count:1'>      </span><span style='mso-tab-count:\r
-1'>      </span>structure/structure comparisons </span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>(obtain it from <st1:place\r
-w:st="on">W. Taylor</st1:place>, NIMR-MRC).</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>---------------------------------------------------</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>TMalign<span style='mso-tab-count:\r
-2'>           </span>zhang.bioinformatics.ku.edu/TM-align/</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>---------------------------------------------------</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>mustang<span style='mso-tab-count:\r
-2'>           </span>www.cs.mu.oz.au/~arun/mustang/</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>---------------------------------------------------</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>wublastclient<span\r
-style='mso-spacerun:yes'>     </span>www.ebi.ac.uk/Tools/webservices/clients/wublast</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>---------------------------------------------------</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>Blast<span style='mso-tab-count:\r
-2'>       </span><span style='mso-tab-count:1'>      </span><a\r
-href="http://www.ncbi.nih.nlm.gov/">www.ncbi.nih.nlm.gov</a></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>---------------------------------------------------</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>Fugue*<span style='mso-tab-count:\r
-2'>            </span>protein to structure alignment program</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US><span style='mso-tab-count:\r
-3'>                  </span>http://www-cryst.bioc.cam.ac.uk/fugue/download.html</span></p>\r
-\r
-<p class=examplefileCxSpLast><span lang=EN-US><span style='mso-tab-count:3'>                  </span>***NOT\r
-COMPULSORY***</span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MyNormal><span lang=AF>Once the package is installed, make sure make\r
-sure that the executable is on your path, so that t_coffee can find it\r
-automatically.</span></p>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MyNormal><span lang=AF>The wublast client makes it possible to run\r
-BLAST at the EBI without having to install any database locally. It is an ideal\r
-solution if you are only using expresso occasionally.</span></p>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<h3><a name="_Toc235958492"><span lang=EN-US>Installing Fugue for T-Coffee</span></a></h3>\r
-\r
-<p class=MyNormal><span lang=AF>Uses a standard fugue installation. You only\r
-need to install the following packages:</span></p>\r
-\r
-<p class=MyNormal><span lang=AF><span style='mso-spacerun:yes'> </span>joy,\r
-melody, fugueali, sstruc, hbond</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>If you have root privileges, you can install\r
-the common data in: </span></p>\r
-\r
-<p class=MyNormal><span lang=AF>cp fugue/classdef.dat<span style='mso-tab-count:\r
-1'>           </span>/data/fugue/SUBST/classdef.dat</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>otherwise</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>Setenv MELODY_CLASSDEF=&lt;location&gt;</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>Setenv MELODY_SUBST=fugue/allmat.dat</span></p>\r
-\r
-<p class=MyNormal><span lang=AF><span style='mso-spacerun:yes'> </span></span></p>\r
-\r
-<p class=MyNormal><span lang=AF>All the other configuration files must be in\r
-the right location. </span></p>\r
-\r
-<h2><a name="_Toc235958493"><span lang=EN-US>Installation of R-Coffee</span></a></h2>\r
-\r
-<p class=MyNormal><span lang=AF>R-Coffee is a special mode able to align RNA\r
-sequences while taking into account their secondary structure.</span><span\r
-lang=EN-US style='mso-ansi-language:EN-US'><o:p></o:p></span></p>\r
-\r
-<h3><a name="_Toc235958494"><span lang=EN-US>Automated Installation</span></a></h3>\r
-\r
-<p class=MyNormal><span lang=AF>In the T-Coffee distribution, type:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>./install\r
-rcoffee</span></p>\r
-\r
-</div>\r
-\r
-<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MyNormal><span lang=AF>In theory, this command should download and\r
-install every required package (except <b>consan</b>). If, however, it fails,\r
-you should switch to the manual installation (see next).</span></p>\r
-\r
-<h3><a name="_Toc235958495"><span lang=EN-US>Manual Installation</span></a></h3>\r
-\r
-<p class=MyNormal><span lang=AF>R-Coffee only requires the package <st1:place\r
-w:st="on"><st1:City w:st="on">Vienna</st1:City></st1:place> to be installed, in\r
-order to compute multiple sequence alignments. To make the best out of it, you\r
-should also have all the packages required by M-Coffee</span></p>\r
-\r
-<p class=MyNormal><span lang=AF><span style='mso-tab-count:1'>         </span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span lang=EN-US>Package<span style='mso-tab-count:\r
-2'>           </span>Function</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>===================================================</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>---------------------------------------------------</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>consan<span style='mso-tab-count:\r
-2'>            </span>R-Coffee </span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US><span style='mso-tab-count:\r
-3'>                  </span>Computes highly accurate pairwise Alignments</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US><span style='mso-tab-count:\r
-3'>                  </span>***NOT COMPULSORY***</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US><span style='mso-tab-count:\r
-3'>                  </span>selab.janelia.org/software/consan/</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>---------------------------------------------------</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>RNAplfold<span\r
-style='mso-tab-count:2'>         </span>Computes RNA secondary Structures </span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US><span style='mso-tab-count:\r
-3'>                  </span>www.tbi.univie.ac.at/~ivo/RNA/</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>---------------------------------------------------</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>probconsRNA<span\r
-style='mso-tab-count:2'>       </span>probcons.stanford.edu/</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US><span\r
-style='mso-spacerun:yes'>        </span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>---------------------------------------------------</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>M-Coffee<span style='mso-tab-count:\r
-2'>          </span>T-Coffee and the most common MSA Packages</span></p>\r
-\r
-<p class=examplefileCxSpLast><span lang=EN-US><span style='mso-tab-count:3'>                  </span>(cf\r
-M-Coffee in this installation guide)</span></p>\r
-\r
-</div>\r
-\r
-<h3><a name="_Toc235958496"><span lang=EN-US>Installing ProbbonsRNA for R-Coffee</span></a></h3>\r
-\r
-<p class=MyNormal><span lang=AF>Follow the installation procedure, but make\r
-sure you rename the probcons executable into probconsRNA.</span></p>\r
-\r
-<h3><a name="_Toc235958497"><span lang=EN-US>Installing Consan for R-Coffee</span></a></h3>\r
-\r
-<p class=MyNormal><span lang=AF>In order to insure a proper interface beween\r
-consan and R-Coffee, you must make sure that the file mix80.mod is in the\r
-directory ~/.t_coffee/mcoffee or in the mcoffee directory otherwise declared.</span></p>\r
-\r
-<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 3.0pt;\r
-padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0mm;margin-right:\r
-4.25pt'>\r
-\r
-<p class=ChapterTitle><a name="_Toc235958498"></a><a name="_Toc102494676"></a><a\r
-name="_Toc101065207"><span style='mso-bookmark:_Toc102494676'><span\r
-style='mso-bookmark:_Toc235958498'><span lang=EN-US>Q</span></span></span></a><span\r
-style='mso-bookmark:_Toc235958498'><span lang=EN-US>uick Start</span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MsoBodyText><span lang=EN-US>We only give you the very basics here.\r
-Please use the Tutorial for more detailed information on how to use our tools.</span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.5pt;\r
-padding:0mm 0mm 0mm 0mm;background:#F7CBB7'>\r
-\r
-<p class=Warning><a name="_Toc102494677"></a><a name="_Toc102494296"></a><a\r
-name="_Toc101065208"><span style='mso-bookmark:_Toc102494296'><span\r
-style='mso-bookmark:_Toc102494677'><span lang=EN-US>IMPORTANT: All the files\r
-mentionned here (sampe_seq...) can be found in the example directory of the\r
-distribution.</span></span></span></a></p>\r
-\r
-</div>\r
-\r
-<h2><span style='mso-bookmark:_Toc101065208'><span style='mso-bookmark:_Toc102494296'><span\r
-style='mso-bookmark:_Toc102494677'><a name="_Toc235958499"><span lang=EN-US>T-COFFEE</span></a></span></span></span></h2>\r
-\r
-<p class=MyNormal><span lang=AF>Write your sequences in the same file\r
-(Swiss-prot, Fasta or Pir) and type. </span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee sample_seq1.fasta<span style='mso-spacerun:yes'>  </span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF>This will output two files:</span></p>\r
-\r
-<p class=example2CxSpFirst><span lang=EN-US>sample_seq1.aln: your Multiple\r
-Sequence Alignment</span></p>\r
-\r
-<p class=example2CxSpLast><span lang=EN-US>sample_seq1.dnd: The Guide tree\r
-(newick Format)</span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.5pt;\r
-padding:0mm 0mm 0mm 0mm;background:#F7CBB7'>\r
-\r
-<p class=Warning><span lang=EN-US>IMPORTANT: </span></p>\r
-\r
-<p class=Warning><span lang=EN-US>In theory nucleic acids should be\r
-automatically detected and the default methods should be adapted appropriately.\r
-However, sometimes this may fail, either because the sequences are too short or\r
-contain too many ambiguity codes. </span></p>\r
-\r
-<p class=Warning><span lang=EN-US>When this happens, you are advised to\r
-explicitly set the type of your sequences</span></p>\r
-\r
-<p class=Warning><span lang=EN-US>NOTE: the \96mode=dna is not needed or\r
-supported anymore</span></p>\r
-\r
-</div>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee sample_dnaseq1.fasta \96type=dna</span></p>\r
-\r
-</div>\r
-\r
-<h2><a name="_Toc102494678"></a><a name="_Toc102494297"></a><a\r
-name="_Toc101065209"></a><a name="_Toc235958500"><span style='mso-bookmark:\r
-_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:\r
-_Toc102494678'><span lang=EN-US>M-Coffee</span></span></span></span></a><span\r
-style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span\r
-style='mso-bookmark:_Toc102494678'></span></span></span></h2>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF>M-Coffee is a <st1:place w:st="on">Meta</st1:place> version of T-Coffee\r
-that makes it possible to combine the output of at least eight packages\r
-(Muscle, probcons, poa, dialignT, mafft, clustalw, PCMA and T-Coffee).</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF>If all these packages are already installed on your machine. You must:</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF>1-set the following environment variables</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span\r
-style='mso-bookmark:_Toc102494678'><span lang=EN-US><span style='mso-tab-count:\r
-1'>   </span>export POA_DIR=[absolute path of the POA installation dir]</span></span></span></span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span\r
-style='mso-bookmark:_Toc102494678'><span lang=EN-US><span style='mso-tab-count:\r
-1'>   </span>export DIALIGNT_DIR=[Absolute path of the DIALIGN-T/conf</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF>Once this is done, write your sequences in a file and run: same file\r
-(Swiss-prot, Fasta or Pir) and type. </span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span\r
-style='mso-bookmark:_Toc102494678'><span lang=EN-US>PROMPT: t_coffee\r
-sample_seq1.fasta \96mode mcoffee </span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF>If the program starts complaining one package or the other is missing,\r
-this means you will have to go the hard way and install all these packages\r
-yourself... Proceed to the M-Coffee section for more detailed instructions.</span></span></span></span></p>\r
-\r
-<h2><span style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span\r
-style='mso-bookmark:_Toc102494678'><a name="_Toc235958501"><span lang=EN-US>Expresso</span></a></span></span></span></h2>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF>If you have installed the EBI wublast.pl client, Expresso will BLAST\r
-your sequences against PDB, identify the best targets and use these to align\r
-your proteins.</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span\r
-style='mso-bookmark:_Toc102494678'><span lang=EN-US>PROMPT: t_coffee\r
-sample_seq1.fasta \96mode expresso</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF>If you did not manage to install all the required structural packages\r
-for Expresso, like Fugue or Sap, you can still run expresso by selecting\r
-yourself the structural packages you want to use. For instance, if you'd rather\r
-use TM-Align than sap, try: </span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF><span style='mso-tab-count:1'>         </span></span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span\r
-style='mso-bookmark:_Toc102494678'><span lang=EN-US>PROMPT: t_coffee\r
-sample_seq1.fasta \96template_file EXPRESSO -method TMalign_pair</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<h2><span style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span\r
-style='mso-bookmark:_Toc102494678'><a name="_Toc235958502"><span lang=EN-US>R-Coffee</span></a></span></span></span></h2>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF>R-Coffee can be used to align RNA sequences, using their RNApfold\r
-predicted secondary structures. The best results are obtained by using the\r
-consan pairwise method. If you have consan installed:</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span\r
-style='mso-bookmark:_Toc102494678'><span lang=EN-US>t_coffee\r
-sample_rnaseq1.fasta \96special_mode rcoffee_consan </span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF>This will only work if your sequences are short enough (less than 200\r
-nucleotides). A good alternative is the rmcoffee mode that will run Muscle,\r
-Probcons4RNA and MAfft and then use the secondary structures predicted by\r
-RNApfold. </span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span\r
-style='mso-bookmark:_Toc102494678'><span lang=EN-US>PROMPT: t_coffee\r
-sample_rnaseq1.fasta \96mode mrcoffee </span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF>If you want to decide yourself which methods should be combined by\r
-R-Coffee, run:</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span\r
-style='mso-bookmark:_Toc102494678'><span lang=EN-US>PROMPT: t_coffee\r
-sample_rnaseq1.fasta \96mode rcoffee -method lalign_id_pair slow_pair </span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<h2><span style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span\r
-style='mso-bookmark:_Toc102494678'><span lang=EN-US><br>\r
-<a name="_Toc235958503">iRMSD and APDB</a></span></span></span></span></h2>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF>All you need is a file containing the alignment of sequences with a\r
-known structure. These sequences must be named according to their PDB ID,\r
-followed by the chain index ( 1aabA for instance). All the sequences do not\r
-need to have a known structure, but at least two need to have it.</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF>Given the alignment:</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:42.55pt;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span\r
-style='mso-bookmark:_Toc102494678'><span lang=EN-US>PROMPT: t_coffee \96other_pg\r
-irmsd -aln 3d_sample4.aln </span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<h2><span style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span\r
-style='mso-bookmark:_Toc102494678'><a name="_Toc235958504"><span lang=EN-US>tRMSD</span></a></span></span></span></h2>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF>tRMSD is a structure based clustering method using the iRMSD to drive\r
-the clustering. The T-RMSD supports all the parameters supported by iRMSD or\r
-APDB.</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:42.55pt;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span\r
-style='mso-bookmark:_Toc102494678'><span lang=EN-US>PROMPT: t_coffee \96other_pg\r
-trmsd -aln 3d_sample5.aln -template_file 3d_sample5.template_list </span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=EN-US style='mso-ansi-language:EN-US'>3d_sample5.aln is a multiple\r
-alignment in which each sequence has a known structure. The file </span><span\r
-lang=AF>3d_sample5.template_list is a fasta like file declaring the structure\r
-associated with each sequence, in the form: </span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6;margin-left:0mm;margin-right:10.0mm'>\r
-\r
-<p class=examplefilesmall><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=EN-US>&gt; &lt;seq_name&gt; _P_ &lt;PDB structure file or name&gt; </span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=EN-US>******* 3d_sample5.template_list ********<span style='mso-tab-count:\r
-1'>      </span></span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=EN-US>&gt;2UWI-3A _P_ 2UWI-3.pdb</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=EN-US>&gt;2UWI-2A _P_ 2UWI-2.pdb</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=EN-US>&gt;2UWI-1A _P_ 2UWI-1.pdb</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=EN-US>&gt;2HEY-4R _P_ 2HEY-4.pdb</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=EN-US>...</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpLast><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=EN-US>**************************************</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF>The program then outputs a series of files</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=EN-US style='font-size:8.0pt'>Template Type: [3d_sample5.template_list]\r
-Mode Or File: [3d_sample5.template_list] [Start]<o:p></o:p></span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=EN-US style='font-size:8.0pt'><span style='mso-spacerun:yes'>        \r
-</span>[Sample Columns][TOT=<span style='mso-spacerun:yes'>   </span>51][100\r
-%][ELAPSED TIME:<span style='mso-spacerun:yes'>    </span>0 sec.]<o:p></o:p></span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=EN-US style='font-size:8.0pt'><span style='mso-spacerun:yes'>   </span><span\r
-style='mso-spacerun:yes'>      </span>[Tree Cmp][TOT=<span\r
-style='mso-spacerun:yes'>   </span>13][ 92 %][ELAPSED TIME:<span\r
-style='mso-spacerun:yes'>    </span>0 sec.]<o:p></o:p></span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=EN-US style='font-size:8.0pt'><span style='mso-spacerun:yes'> </span>####\r
-File Type=<span style='mso-spacerun:yes'>   </span>TreeList Format=<span\r
-style='mso-spacerun:yes'>     </span>newick Name= 3d_sample5.tot_pos_list<o:p></o:p></span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=EN-US style='font-size:8.0pt'><span style='mso-spacerun:yes'> </span>####\r
-File Type=<span style='mso-spacerun:yes'>       </span>Tree Format=<span\r
-style='mso-spacerun:yes'>     </span>newick Name= 3d_sample5.struc_tree10<o:p></o:p></span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=EN-US style='font-size:8.0pt'><span style='mso-spacerun:yes'> </span>####\r
-File Type=<span style='mso-spacerun:yes'>       </span>Tree Format=<span\r
-style='mso-spacerun:yes'>     </span>newick Name= 3d_sample5.struc_tree50<o:p></o:p></span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=EN-US style='font-size:8.0pt'><span style='mso-spacerun:yes'> </span>####\r
-File Type=<span style='mso-spacerun:yes'>       </span>Tree Format=<span\r
-style='mso-spacerun:yes'>     </span>newick Name= 3d_sample5.struc_tree100<o:p></o:p></span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=EN-US style='font-size:8.0pt'><span style='mso-spacerun:yes'> </span>####\r
-File Type= Colored MSA Format= score_html Name= 3d_sample5.struc_tree.html<o:p></o:p></span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpLast><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=EN-US><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF>3d_sample5.tot_pos_list <span style='mso-tab-count:1'>      </span>is a\r
-list of the tRMSD tree associated with every position. </span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF>3d_sample5.struc_tree100<span style='mso-tab-count:1'>   </span>is a\r
-consensus tree (phylip/consense) of the trees contained in the previous file. <b>This\r
-file is the default output<o:p></o:p></b></span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF>3d_sample5.struc_tree10<span style='mso-tab-count:1'>     </span>is a\r
-consensus tree (phylip/consense) of the 10% trees having the higest average\r
-agreement with the rest</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF>3d_sample5.struc_tree10<span style='mso-tab-count:1'>     </span>is a\r
-consensus tree (phylip/consense) of the 50% trees having the higest average\r
-agreement with the rest</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF>3d_sample5.html<span style='mso-tab-count:1'>      </span>is a colored\r
-version of the output showing in red the positions that give the highest\r
-support to 3d_sample5.struc_tree100</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<h2><span style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span\r
-style='mso-bookmark:_Toc102494678'><a name="_Toc235958505"><span lang=EN-US>MOCCA</span></a></span></span></span></h2>\r
-\r
-<p class=MyNormal><span lang=AF>Write your sequences in the same file\r
-(Swiss-prot, Fasta or Pir) and type. </span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee \96other_pg mocca sample_seq1.fasta </span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF>This command output one files (&lt;your\r
-sequences&gt;.mocca_lib) and starts an interactive menu. </span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 3.0pt;\r
-padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0mm;margin-right:\r
-4.25pt'>\r
-\r
-<p class=ChapterTitle><a name="_Toc235958506"></a><a name="_Toc102494679"></a><a\r
-name="_Toc101065210"><span style='mso-bookmark:_Toc102494679'><span\r
-style='mso-bookmark:_Toc235958506'><span lang=EN-US>Recent M</span></span></span></a><span\r
-style='mso-bookmark:_Toc235958506'><span lang=EN-US>odifications</span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF>Warning: This log of recent modifications is\r
-not as thorough and accurate as it should be.</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>-5.80 Novel assembly algorithm\r
-(linked_pair_wise) and the primary library is now made of probcons style\r
-pairwise alignments (proba_pair)</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>-4.30 and upward: the FAQ has moved into a new\r
-tutorial document</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>-4.30 and upward: -in has will be deprecated\r
-and replaced by the flags: -profile,-method,-aln,-seq,-pdb</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>-4.02: -mode=dna is still available but not any\r
-more needed or supported. Use type=protein or dna if you need to force things</span></p>\r
-\r
-<p class=MyNormal><b style='mso-bidi-font-weight:normal'><span lang=AF>-</span></b><span\r
-lang=AF>3.28: corrected a bug that prevents short sequences from being\r
-correctly aligned</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>-Use of @ as a separator when specifying\r
-methods parameters</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>-The most notable modifications have to do with\r
-the structure of the input. From version 2.20, all files must be tagged to\r
-indicate their nature (A: alignment, S: Sequence, L: Library\85). We are becoming\r
-stricter, but that\92s for your own good\85 </span></p>\r
-\r
-<p class=MyNormal><span lang=AF>Another important modification has to do with\r
-the flag -matrix: it now controls the matrix being used for the computation </span></p>\r
-\r
-<span lang=AF style='font-size:11.0pt;font-family:"Times New Roman";mso-fareast-font-family:\r
-"Times New Roman";mso-bidi-font-family:"Courier New";mso-ansi-language:AF;\r
-mso-fareast-language:EN-US;mso-bidi-language:AR-SA'><br clear=all\r
-style='page-break-before:always'>\r
-</span>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 3.0pt;\r
-padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0mm;margin-right:\r
-4.25pt'>\r
-\r
-<p class=ChapterTitle><a name="_Toc235958507"><span lang=EN-US>Reference Manual</span></a></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MyNormal><span lang=AF>This reference manual gives a list of all the\r
-flags that can be used to modify the behavior of T-Coffee. For your\r
-convenience, we have grouped them according to their nature. To display a list\r
-of all the flags used in the version of T-Coffee you are using (along with\r
-their default value), type:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee </span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF>Or</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee \96help </span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF>Or</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee \96help \96in</span><span class=MyNormalChar><span lang=EN-US\r
-style='font-size:11.0pt;mso-ansi-language:EN-US'><o:p></o:p></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF>Or any other parameter</span></p>\r
-\r
-<h2><a name="_Toc102494743"></a><a name="_Toc102494358"></a><a\r
-name="_Toc101065212"><span style='mso-bookmark:_Toc102494358'><span\r
-style='mso-bookmark:_Toc102494743'><span lang=EN-US><o:p>&nbsp;</o:p></span></span></span></a></h2>\r
-\r
-<h2><span style='mso-bookmark:_Toc101065212'><span style='mso-bookmark:_Toc102494358'><span\r
-style='mso-bookmark:_Toc102494743'><a name="_Toc235958508"><span lang=EN-US>Environment\r
-Variables</span></a></span></span></span></h2>\r
-\r
-<p class=MsoBodyText><span style='mso-bookmark:_Toc101065212'><span\r
-style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span\r
-lang=EN-US>It is possible to modify T-Coffee\92s behavior by setting any of the\r
-following environement variables. On the bash shell, use export VAR=\94value\94. On\r
-the cshell, use set $VAR=\94xxx\94</span></span></span></span></p>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065212'><span style='mso-bookmark:_Toc102494358'><span\r
-style='mso-bookmark:_Toc102494743'><a name="_Toc235958509"><span lang=EN-US>http_proxy_4_TCOFFEE</span></a></span></span></span></h3>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065212'><span\r
-style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span\r
-lang=AF>Sets the http_proxy and HTTP_proxy values used by T-Coffee. </span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065212'><span\r
-style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span\r
-lang=AF>These values get supersede http_proxy and HTTP_proxy.\r
-http_proxy_4_TCOFFEE gets superseded by the command line values (-proxy and\r
--email)</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065212'><span\r
-style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span\r
-lang=AF>If you have no proxy, just set this value to an empty string.</span></span></span></span></p>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065212'><span style='mso-bookmark:_Toc102494358'><span\r
-style='mso-bookmark:_Toc102494743'><a name="_Toc235958510"><span lang=EN-US>email_4_TCOFFEE</span></a></span></span></span></h3>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065212'><span\r
-style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span\r
-lang=AF>Set the E-mail values provided to web services called upon by T-Coffee.\r
-Can be over-riden by the flag <i>-email.<o:p></o:p></i></span></span></span></span></p>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065212'><span style='mso-bookmark:_Toc102494358'><span\r
-style='mso-bookmark:_Toc102494743'><a name="_Toc235958511"><span lang=EN-US>DIR_4_TCOFFEE</span></a></span></span></span></h3>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065212'><span\r
-style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span\r
-lang=AF>By default this variable is set to $HOME/.t_coffee. This is where\r
-T-Coffee expects to find its cache, tmp dir and possibly any temporary data\r
-stored by the program.</span></span></span></span></p>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065212'><span style='mso-bookmark:_Toc102494358'><span\r
-style='mso-bookmark:_Toc102494743'><a name="_Toc235958512"><span lang=EN-US>TMP_4_TCOFFEE</span></a></span></span></span></h3>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065212'><span\r
-style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span\r
-lang=AF>By default this variable is set to $HOME/.t_coffee/tmp. This is where\r
-T-Coffee stores temporary files.</span></span></span></span></p>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065212'><span style='mso-bookmark:_Toc102494358'><span\r
-style='mso-bookmark:_Toc102494743'><a name="_Toc235958513"><span lang=EN-US>CACHE_4_TCOFFEE</span></a></span></span></span></h3>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065212'><span\r
-style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span\r
-lang=AF>By default this variable is set to $HOME/.t_coffee/cache. This is where\r
-T-Coffee stores any data expensive to obtain: pdb files, sap alignments....</span></span></span></span></p>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065212'><span style='mso-bookmark:_Toc102494358'><span\r
-style='mso-bookmark:_Toc102494743'><span lang=EN-US>PLUGINS_4_TCOFFEE</span></span></span></span></h3>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065212'><span\r
-style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span\r
-lang=AF>By default all the companion packages are searched in the directory\r
-DIR_4_TCOFFEE/plugins/&lt;OS&gt;. This variable overrides the default. This\r
-variable can also be overriden by the <i>-plugins</i> T-Coffee flag</span></span></span></span></p>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065212'><span style='mso-bookmark:_Toc102494358'><span\r
-style='mso-bookmark:_Toc102494743'><a name="_Toc235958514"><span lang=EN-US>NO_ERROR_REPORT_4_TCOFFEE</span></a></span></span></span></h3>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065212'><span\r
-style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span\r
-lang=AF>By default this variable is no set. Set it if you do not want the\r
-program to generate a verbose error output file (useful for running a server).</span></span></span></span></p>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065212'><span style='mso-bookmark:_Toc102494358'><span\r
-style='mso-bookmark:_Toc102494743'><a name="_Toc235958515"><span lang=EN-US>PDB_DIR</span></a></span></span></span></h3>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065212'><span\r
-style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span\r
-lang=AF>Indicate the location of your local PDB installation.</span></span></span></span></p>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065212'><span style='mso-bookmark:_Toc102494358'><span\r
-style='mso-bookmark:_Toc102494743'><a name="_Toc235958516"><span lang=EN-US>NO_WARNING_4_TCOFFEE</span></a></span></span></span></h3>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065212'><span\r
-style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span\r
-lang=AF>Suppresses all the warnings.</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065212'><span\r
-style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<h2><span style='mso-bookmark:_Toc101065212'><span style='mso-bookmark:_Toc102494358'><span\r
-style='mso-bookmark:_Toc102494743'><a name="_Toc235958517"><span lang=EN-US>Setting\r
-up the T-Coffee environment variables</span></a></span></span></span></h2>\r
-\r
-<p class=MsoBodyText><span style='mso-bookmark:_Toc101065212'><span\r
-style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span\r
-lang=EN-US>T-Coffee can have its own environment file. This environment is kept\r
-in a file named $HOME/.t_coffee/t_coffee_env and can be edited. The value of\r
-any legal variable can be modified through that file. For instance, here is an\r
-example of a configuration file when not requiring a proxy.</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc101065212'><span\r
-style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span\r
-lang=EN-US>http_proxy_4_TCOFFEE=</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpLast><span style='mso-bookmark:_Toc101065212'><span\r
-style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span\r
-lang=EN-US>EMAIL_4_TCOFFEE=cedric.notredame@europe.com</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.5pt;\r
-padding:0mm 0mm 0mm 0mm;background:#F7CBB7'>\r
-\r
-<p class=Warning><span style='mso-bookmark:_Toc101065212'><span\r
-style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span\r
-lang=EN-US>IMPORTANT: </span></span></span></span></p>\r
-\r
-<p class=Warning style='text-align:justify;text-indent:35.4pt;background:#F7CBB7'><span\r
-style='mso-bookmark:_Toc101065212'><span style='mso-bookmark:_Toc102494358'><span\r
-style='mso-bookmark:_Toc102494743'><span lang=EN-US>-proxy, -email &gt;&gt;\r
-t_coffee_env &gt;&gt; env</span></span></span></span></p>\r
-\r
-<p class=Warning style='text-align:justify;background:#F7CBB7'><span\r
-style='mso-bookmark:_Toc101065212'><span style='mso-bookmark:_Toc102494358'><span\r
-style='mso-bookmark:_Toc102494743'><span lang=EN-US><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MsoBodyText><span style='mso-bookmark:_Toc101065212'><span\r
-style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span\r
-lang=EN-US><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<p class=MsoBodyText><span style='mso-bookmark:_Toc101065212'><span\r
-style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span\r
-lang=EN-US><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<h2><span style='mso-bookmark:_Toc101065212'><span style='mso-bookmark:_Toc102494358'><span\r
-style='mso-bookmark:_Toc102494743'><a name="_Toc235958518"><span lang=EN-US>Well\r
-Behaved Parameters</span></a></span></span></span></h2>\r
-\r
-<h3><a name="_Toc235958519"></a><a name="_Toc102494744"></a><a\r
-name="_Toc102494359"></a><a name="_Toc101065213"><span style='mso-bookmark:\r
-_Toc102494359'><span style='mso-bookmark:_Toc102494744'><span style='mso-bookmark:\r
-_Toc235958519'><span lang=EN-US>Separation</span></span></span></span></a></h3>\r
-\r
-<p class=MyNormal><span lang=AF>You can use any kind of separator you want\r
-(i.e. ,; &lt;space&gt;=). The syntax used in this document is meant to be\r
-consistent with that of ClustalW. However, in order to take advantage of the\r
-automatic filename compleation provided by many shells, you can replace \93=\94 and\r
-\93,\94 with a space.</span></p>\r
-\r
-<h3><a name="_Toc235958520"></a><a name="_Toc102494745"></a><a\r
-name="_Toc102494360"></a><a name="_Toc101065214"><span style='mso-bookmark:\r
-_Toc102494360'><span style='mso-bookmark:_Toc102494745'><span style='mso-bookmark:\r
-_Toc235958520'><span lang=EN-US>Posix</span></span></span></span></a></h3>\r
-\r
-<p class=MyNormal><span lang=AF>T-Coffee is not POSIX compliant.</span></p>\r
-\r
-<h3><a name="_Toc235958521"></a><a name="_Toc102494746"></a><a\r
-name="_Toc102494361"></a><a name="_Toc101065215"><span style='mso-bookmark:\r
-_Toc102494361'><span style='mso-bookmark:_Toc102494746'><span style='mso-bookmark:\r
-_Toc235958521'><span lang=EN-US>Entering the right parameters</span></span></span></span></a></h3>\r
-\r
-<p class=MyNormal><span lang=AF>There are many ways to enter parameters in\r
-T-Coffee, see the -parameter flag in </span></p>\r
-\r
-<p class=Noteboxtitle><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.5pt;\r
-padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#FFFF89'>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut align=center\r
-style='text-align:center;background:#FFFF89'><span lang=EN-US style='font-size:\r
-20.0pt;mso-bidi-font-size:10.0pt'>Parameters Priority<o:p></o:p></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US>In\r
-general you will not need to use these complicated parameters. Yet, if you find\r
-yourself typing long command lines on a regular basis, it may be worth reading\r
-this section.</span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US>One\r
-may easily feel confused with the various manners in which the parameters can\r
-be passed to t_coffee. The reason for these many mechanisms is that they allow\r
-several levels of intervention. For instance, you may install t_coffee for all\r
-the users and decide that the defaults we provide are not the proper ones\85 In\r
-this case, you will need to make your own t_coffee_default file.</span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US>Later\r
-on, a user may find that he/she needs to keep re-using a specific set of\r
-parameters, different from those in t_coffee_default, hence the possibility to\r
-write an extra parameter file: parameters. In summary:</span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US>-parameters\r
-&gt; prompt parameters &gt; -t_coffee_defaults &gt; -mode</span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US>This\r
-means that -<i>parameters</i> supersede all the others, while parameters\r
-provided via -<i>special mode</i> are the weakest.</span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<h2><a name="_Toc235958522"></a><a name="_Toc102494747"></a><a\r
-name="_Toc102494362"></a><a name="_Toc101065216"><span style='mso-bookmark:\r
-_Toc102494362'><span style='mso-bookmark:_Toc102494747'><span style='mso-bookmark:\r
-_Toc235958522'><span lang=EN-US>Parameters Syntax</span></span></span></span></a></h2>\r
-\r
-<p class=flag><a name="_Toc235958523"></a><a name="_Toc102494748"></a><a\r
-name="_Toc101065218"><span style='mso-bookmark:_Toc102494748'><span\r
-style='mso-bookmark:_Toc235958523'><span lang=AF>No Flag</span></span></span></a></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>If no flag is used<b\r
-style='mso-bidi-font-weight:normal'> </b><i style='mso-bidi-font-style:normal'>&lt;your\r
-sequence&gt; </i>must be the first argument. See format for further\r
-information.</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee sample_seq1.fasta </span></p>\r
-\r
-</div>\r
-\r
-<p class=flagdescription><span lang=EN-US>Which is equivalent to</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee Ssample_seq1.fasta </span></p>\r
-\r
-</div>\r
-\r
-<p class=flagdescription><span lang=EN-US>When you do so, <b style='mso-bidi-font-weight:\r
-normal'>sample_seq1</b> is used as a name prefix for every file the program\r
-outputs.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958524"></a><a name="_Toc102494749"></a><a\r
-name="_Toc101065219"><span style='mso-bookmark:_Toc102494749'><span\r
-style='mso-bookmark:_Toc235958524'><span lang=AF>-parameters</span></span></span></a><span\r
-lang=AF style='background:gray;mso-highlight:gray'><o:p></o:p></span></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--parameters=parameters_file<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: no parameters file</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Indicates a file containing extra parameters.\r
-Parameters read this way behave as if they had been added on the right end of\r
-the command line that they either supersede(one value parameter) or complete\r
-(list of values). For instance, the following file (parameter.file) could be\r
-used </span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span lang=EN-US>*******sample_param_file.param********<span\r
-style='mso-tab-count:1'>   </span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US><span style='mso-tab-count:\r
-1'>      </span>-in=Ssample_seq1.fasta,Mfast_pair</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US><span style='mso-tab-count:\r
-1'>      </span>-output=msf_aln</span></p>\r
-\r
-<p class=examplefileCxSpLast><span lang=EN-US>**************************************</span></p>\r
-\r
-</div>\r
-\r
-<p class=Note><span lang=EN-US style='mso-ansi-language:EN-US'>Note: This is\r
-one of the exceptions (with \96infile) where the identifier tag (S,A,L,M\85) can be\r
-omitted. Any dataset provided this way will be assumed to be a sequence (S).\r
-These exceptions have been designed to keep the program compatible with\r
-ClustalW.<o:p></o:p></span></p>\r
-\r
-<p class=Note><span lang=EN-US style='mso-ansi-language:EN-US'>Note: This\r
-parameter file can ONLY contain valid parameters. Comments are not allowed.\r
-Parameters passed this way will be checked like normal parameters.<o:p></o:p></span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Used with:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee -parameters=sample_param_file.param</span></p>\r
-\r
-</div>\r
-\r
-<p class=flagdescription><span lang=EN-US>Will cause t_coffee to apply the\r
-fast_pair method onto to the sequences contained in sample_seq.fasta. If you\r
-wish, you can also pipe these arguments into t_coffee, by naming the parameter\r
-file &quot;stdin&quot; (as a rule, any file named stdin is expected to receive\r
-its content via the stdin)</span></p>\r
-\r
-<p class=example2><span lang=EN-US>cat sample_param_file.param<span\r
-style='mso-spacerun:yes'>  </span>| t_coffee -parameters=stdin <a\r
-name="_Toc101065220"></a></span></p>\r
-\r
-<p class=flag><span style='mso-bookmark:_Toc101065220'><a name="_Toc235958525"></a><a\r
-name="_Toc102494750"><span style='mso-bookmark:_Toc235958525'><span lang=AF>-t_coffee_defaults</span></span></a></span></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--t_coffee_defaults=&lt;file_name&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: not used.</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>This flag tells the program to use\r
-some default parameter file for t_coffee. The format of that file is the same\r
-as the one used with -parameters. The file used is either:</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'>            </span>1.\r
-&lt;file name&gt; if a name has been specified</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'>            </span>2.<span\r
-style='mso-spacerun:yes'>  </span><b>~/.t_coffee_defaults </b>if no file was\r
-specified</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'>            </span>3.\r
-The file indicated by the environment variable <b>TCOFFEE_DEFAULTS</b></span></p>\r
-\r
-<p class=flag><a name="_Toc235958526"><span lang=AF>-mode</span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage: -mode=\r
-hard coded mode<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: not used.</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>It indicates that t_coffee will use\r
-some hard coded parameters. These include:</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'>            </span><b\r
-style='mso-bidi-font-weight:normal'>quickaln</b>: very fast approximate\r
-alignment</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'>            </span><b\r
-style='mso-bidi-font-weight:normal'>dali</b>: a mode used to combine dali\r
-pairwise alignments</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'>            </span><b\r
-style='mso-bidi-font-weight:normal'>evaluate</b>: defaults for evaluating an\r
-alignment</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'>            </span><b\r
-style='mso-bidi-font-weight:normal'>3dcoffee</b>: runs t_coffee with the\r
-3dcoffee parameterization</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Other modes exist that are not yet\r
-fully supported<span style='mso-tab-count:1'> </span></span></p>\r
-\r
-<p class=flag><a name="_Toc235958527"></a><a name="_Toc102494752"></a><a\r
-name="_Toc101065222"><span style='mso-bookmark:_Toc102494752'><span\r
-style='mso-bookmark:_Toc235958527'><span lang=AF>-score</span></span></span></a><span\r
-style='mso-bookmark:_Toc102494752'><span style='mso-bookmark:_Toc235958527'><span\r
-lang=AF> [Deprecated]</span></span></span></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--score<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: not used</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Toggles on the evaluate mode and\r
-causes t_coffee to evaluates a precomputed alignment provided via <b>-infile=&lt;alignment&gt;</b>.\r
-The flag <b>-output</b> must be set to an appropriate format (i.e.\r
--output=score_ascii, score_html or score_pdf). A better default parameterization\r
-is obtained when using the flag <b>-mode=evaluate.</b></span></p>\r
-\r
-<p class=flag><a name="_Toc235958528"></a><a name="_Toc102494753"><span\r
-style='mso-bookmark:_Toc235958528'><span lang=AF>-evaluate</span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--evaluate<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: not used</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Replaces \96score. This flag toggles on\r
-the evaluate mode and causes t_coffee to evaluates a pre-computed alignment\r
-provided via <b>-infile=&lt;alignment&gt;</b>. The flag <b>-output</b> must be\r
-set to an appropriate format (i.e. -output=score_ascii, score_html or\r
-score_pdf). </span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>The main purpose of \96evaluate is to\r
-let you control every aspect of the evaluation. Yet it is advisable to use\r
-pre-defined parameterization: <b>mode=evaluate.</b></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee \96infile=sample_aln1.aln -mode=evaluate </span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee \96infile=sample_seq1.aln \96in<span style='mso-spacerun:yes'> \r
-</span>Lsample_lib1.tc_lib \96mode=evaluate </span></p>\r
-\r
-</div>\r
-\r
-<p class=flag><a name="_Toc235958529"></a><a name="_Toc102494754"></a><a\r
-name="_Toc101065223"><span style='mso-bookmark:_Toc102494754'><span\r
-style='mso-bookmark:_Toc235958529'><span lang=AF>-convert [cw]</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--convert<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: turned off</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Toggles on the conversion mode and\r
-causes T-Coffee to convert the sequences, alignments, libraries or structures\r
-provided via the <b>-infile</b> and <b>-in</b> flags. The output format must be\r
-set via the <b>-output</b> flag. This flag can also be used if you simply want\r
-to compute a library (i.e. you have an alignment and you want to turn it into a\r
-library).</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>This flag is ClustalW compliant.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958530"></a><a name="_Toc102494755"></a><a\r
-name="_Toc101065224"><span style='mso-bookmark:_Toc102494755'><span\r
-style='mso-bookmark:_Toc235958530'><span lang=AF>-do_align [cw]</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-do_align<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: turned on</span></p>\r
-\r
-<h2><a name="_Toc235958531"></a><a name="_Toc102494756"></a><a\r
-name="_Toc102494363"></a><a name="_Toc101065225"><span style='mso-bookmark:\r
-_Toc102494363'><span style='mso-bookmark:_Toc102494756'><span style='mso-bookmark:\r
-_Toc235958531'><span lang=EN-US>Special Parameters</span></span></span></span></a></h2>\r
-\r
-<p class=flag><a name="_Toc235958532"></a><a name="_Toc102494757"></a><a\r
-name="_Toc101065226"><span style='mso-bookmark:_Toc102494757'><span\r
-style='mso-bookmark:_Toc235958532'><span lang=AF>-version</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--version<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: not used</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Returns the current version number</span></p>\r
-\r
-<p class=flag><a name="_Toc102494758"></a><a name="_Toc101065227"></a><a\r
-name="_Toc235958533"><span style='mso-bookmark:_Toc101065227'><span\r
-style='mso-bookmark:_Toc102494758'><span lang=AF>-proxy</span></span></span></a><span\r
-style='mso-bookmark:_Toc101065227'><span style='mso-bookmark:_Toc102494758'></span></span></p>\r
-\r
-<p class=flagusage><span style='mso-bookmark:_Toc101065227'><span\r
-style='mso-bookmark:_Toc102494758'><span lang=EN-US style='mso-ansi-language:\r
-EN-US'>Usage: -proxy=&lt;proxy&gt;<o:p></o:p></span></span></span></p>\r
-\r
-<p class=instruction><span style='mso-bookmark:_Toc101065227'><span\r
-style='mso-bookmark:_Toc102494758'><span lang=EN-US>Default: not used</span></span></span></p>\r
-\r
-<p class=flagdescription><span style='mso-bookmark:_Toc101065227'><span\r
-style='mso-bookmark:_Toc102494758'><span lang=EN-US>Sets the proxy used by\r
-HTTP_proxy AND http_proxy. Setting with the propmpt supersedes ANY other\r
-setting.</span></span></span></p>\r
-\r
-<p class=flagdescription><span style='mso-bookmark:_Toc101065227'><span\r
-style='mso-bookmark:_Toc102494758'><span lang=EN-US>Note that if you use no\r
-proxy, you should set</span></span></span></p>\r
-\r
-<p class=flagdescription><span style='mso-bookmark:_Toc101065227'><span\r
-style='mso-bookmark:_Toc102494758'><span lang=EN-US><span style='mso-tab-count:\r
-1'>            </span>-proxy</span></span></span></p>\r
-\r
-<p class=flag><span style='mso-bookmark:_Toc101065227'><span style='mso-bookmark:\r
-_Toc102494758'><a name="_Toc235958534"><span lang=AF>-email</span></a></span></span></p>\r
-\r
-<p class=flagusage><span style='mso-bookmark:_Toc101065227'><span\r
-style='mso-bookmark:_Toc102494758'><span lang=EN-US style='mso-ansi-language:\r
-EN-US'>Usage: -email=&lt;email&gt;<o:p></o:p></span></span></span></p>\r
-\r
-<p class=instruction><span style='mso-bookmark:_Toc101065227'><span\r
-style='mso-bookmark:_Toc102494758'><span lang=EN-US>Default: not used</span></span></span></p>\r
-\r
-<p class=flagdescription><span style='mso-bookmark:_Toc101065227'><span\r
-style='mso-bookmark:_Toc102494758'><span lang=EN-US>Sets your email value as\r
-provided to web services</span></span></span></p>\r
-\r
-<p class=flag><span style='mso-bookmark:_Toc101065227'><span style='mso-bookmark:\r
-_Toc102494758'><a name="_Toc235958535"><span lang=AF>-check_configuration</span></a></span></span></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--check_configuration<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: not used</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Checks your system to determine\r
-whether all the programs T-Coffee can interact with are installed.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958536"></a><a name="_Toc102494759"></a><a\r
-name="_Toc101065228"><span style='mso-bookmark:_Toc102494759'><span\r
-style='mso-bookmark:_Toc235958536'><span lang=AF>-cache</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--cache=&lt;use, update, ignore, &lt;filename&gt;&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -cache=use</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>By default, t_coffee stores in a\r
-cache directory, the results of computationally expensive (structural\r
-alignment) or network intensive (BLAST search) operations.<a\r
-name="_Toc101065229"></a></span></p>\r
-\r
-<p class=flag><span style='mso-bookmark:_Toc101065229'><a name="_Toc235958537"></a><a\r
-name="_Toc102494760"><span style='mso-bookmark:_Toc235958537'><span lang=AF>-update</span></span></a></span></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--update<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: turned off</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Causes a <span\r
-class=StyleflagdescriptionBoldItalicChar>wget</span> access that checks whether\r
-the t_coffee version you are using needs updating.<a name="_Toc101065230"></a></span></p>\r
-\r
-<p class=flag><span style='mso-bookmark:_Toc101065230'><a name="_Toc235958538"></a><a\r
-name="_Toc102494761"><span style='mso-bookmark:_Toc235958538'><span lang=AF>-full_log</span></span></a></span></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--full_log=&lt;filename&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: turned off</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Causes t_coffee to output a full log\r
-file that contains all the input/output files.<a name="_Toc101065231"></a></span></p>\r
-\r
-<p class=flag><span style='mso-bookmark:_Toc101065231'><a name="_Toc235958539"></a><a\r
-name="_Toc102494762"><span style='mso-bookmark:_Toc235958539'><span lang=AF>-plugins</span></span></a></span></p>\r
-\r
-<p class=flagusage><span style='mso-bookmark:_Toc101065231'><span\r
-style='mso-bookmark:_Toc102494762'><span style='mso-bookmark:_Toc235958539'><span\r
-lang=EN-US style='mso-ansi-language:EN-US'>Usage: -plugins=&lt;dir&gt;<o:p></o:p></span></span></span></span></p>\r
-\r
-<p class=instruction><span style='mso-bookmark:_Toc101065231'><span\r
-style='mso-bookmark:_Toc102494762'><span style='mso-bookmark:_Toc235958539'><span\r
-lang=EN-US>Default: default</span></span></span></span></p>\r
-\r
-<p class=flagdescription><span style='mso-bookmark:_Toc101065231'><span\r
-style='mso-bookmark:_Toc102494762'><span style='mso-bookmark:_Toc235958539'><span\r
-lang=EN-US>Specifies the directory in which the companion packages (other\r
-multiple aligners used by M-Coffee, structural aligners, etc\85) are kept as an\r
-alternative, you can also set the environment variable PLUGINS_4_TCOFFEE</span></span></span></span></p>\r
-\r
-<p class=flagdescription><span style='mso-bookmark:_Toc101065231'><span\r
-style='mso-bookmark:_Toc102494762'><span style='mso-bookmark:_Toc235958539'><span\r
-lang=EN-US>The default is ~/.t_coffee/plugins/</span></span></span></span></p>\r
-\r
-<p class=flag><span style='mso-bookmark:_Toc101065231'><span style='mso-bookmark:\r
-_Toc102494762'><span style='mso-bookmark:_Toc235958539'><span lang=AF>-other_pg</span></span></span></span></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--other_pg=&lt;filename&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: turned off</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Some rumours claim that Tetris is\r
-embedded within T-Coffee and could be ran using some special set of commands.\r
-We wish to deny these rumours, although we may admit that several interesting\r
-reformatting programs are now embedded in t_coffee and can be ran through the\r
-\96other_pg flag.</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee \96other_pg=seq_reformat </span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee \96other_pg=unpack_all </span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee \96other_pg=unpack_extract_from_pdb </span></p>\r
-\r
-</div>\r
-\r
-<h2><a name="_Toc235958540"></a><a name="_Toc102494763"></a><a\r
-name="_Toc102494364"></a><a name="_Toc101065232"><span style='mso-bookmark:\r
-_Toc102494364'><span style='mso-bookmark:_Toc102494763'><span style='mso-bookmark:\r
-_Toc235958540'><span lang=EN-US>Input</span></span></span></span></a><span\r
-lang=EN-US> </span></h2>\r
-\r
-<h3><a name="_Toc235958541"></a><a name="_Toc102494764"></a><a\r
-name="_Toc102494365"></a><a name="_Toc101065233"><span style='mso-bookmark:\r
-_Toc102494365'><span style='mso-bookmark:_Toc102494764'><span style='mso-bookmark:\r
-_Toc235958541'><span lang=EN-US>Sequence Input</span></span></span></span></a></h3>\r
-\r
-<p class=flag><a name="_Toc235958542"></a><a name="_Toc102494765"></a><a\r
-name="_Toc101065234"><span style='mso-bookmark:_Toc102494765'><span\r
-style='mso-bookmark:_Toc235958542'><span lang=AF>-infile [cw]</span></span></span></a></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>To remain compatible with ClustalW,\r
-it is possible to indicate the sequences with this flag</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee -infile=sample_seq1.fasta </span></p>\r
-\r
-</div>\r
-\r
-<p class=Note><span lang=EN-US style='mso-ansi-language:EN-US'>Note: Common\r
-multiple sequence alignments format constitute a valid input format.<o:p></o:p></span></p>\r
-\r
-<p class=Note><span lang=EN-US style='mso-ansi-language:EN-US'>Note: T-Coffee\r
-automatically removes the gaps </span><i><span lang=EN-US style='mso-ansi-language:\r
-EN-US;mso-bidi-font-weight:bold'>before</span></i><span lang=EN-US\r
-style='mso-ansi-language:EN-US'> doing the alignment. This behaviour is different\r
-from that of ClustalW where the gaps are kept.<o:p></o:p></span></p>\r
-\r
-<p class=flag><a name="_Toc235958543"></a><a name="_Toc102494766"></a><a\r
-name="_Toc101065235"><span style='mso-bookmark:_Toc102494766'><span\r
-style='mso-bookmark:_Toc235958543'><span lang=AF>-in</span></span></span></a><span\r
-style='mso-bookmark:_Toc102494766'><span style='mso-bookmark:_Toc235958543'><span\r
-lang=AF> (Cf \96in from the Method and Library Input section)</span></span></span></p>\r
-\r
-<p class=flag><a name="_Toc235958544"></a><a name="_Toc102494767"></a><a\r
-name="_Toc101065236"><span style='mso-bookmark:_Toc102494767'><span\r
-style='mso-bookmark:_Toc235958544'><span lang=AF>-get_type</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--get_type<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: turned off</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Forces t_coffee to identify the\r
-sequences type (PROTEIN, DNA).</span></p>\r
-\r
-<p class=flag><a name="_Toc235958545"></a><a name="_Toc102494768"></a><a\r
-name="_Toc101065237"><span style='mso-bookmark:_Toc102494768'><span\r
-style='mso-bookmark:_Toc235958545'><span lang=AF>-type [cw]</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--type=DNA ¦ PROTEIN¦ DNA_PROTEIN<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -type=&lt;automatically set&gt;</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>This flag sets the type of the\r
-sequences. If omitted, the type is guessed automatically. This flag is\r
-compatible with ClustalW.</span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.5pt;\r
-padding:0mm 0mm 0mm 0mm;background:#F7CBB7'>\r
-\r
-<p class=Warning><span lang=EN-US>Warning:<span style='mso-spacerun:yes'> \r
-</span>In case of low complexity or short sequences, it is recommended to set\r
-the type manually.<a name="_Toc101065238"></a></span></p>\r
-\r
-</div>\r
-\r
-<p class=flag><span style='mso-bookmark:_Toc101065238'><a name="_Toc235958546"></a><a\r
-name="_Toc102494769"><span style='mso-bookmark:_Toc235958546'><span lang=AF>-seq</span></span></a></span></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--seq=[&lt;P,S&gt;&lt;name&gt;,]<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: none</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>-seq is now the recommended flag to provide\r
-your sequences. It behaves mostly like the -in flag.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958547"></a><a name="_Toc102494770"></a><a\r
-name="_Toc101065239"><span style='mso-bookmark:_Toc102494770'><span\r
-style='mso-bookmark:_Toc235958547'><span lang=AF>-seq_source</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--seq_source=&lt;ANY or<span style='mso-spacerun:yes'>  </span>_LS or LS &gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: ANY.</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>You may not want to combine all the\r
-provided sequences into a single sequence list. You can do by specifying that\r
-you do not want to treat all the \96in files as potential sequence sources.</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>-seq_source=_LA indicates that\r
-neither sequences provided via the A (Alignment) flag or via the L (Library\r
-flag) should be added to the sequence list.</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>-seq_source=S means that only\r
-sequences provided via the S tag will be considered. All the other sequences\r
-will be ignored.</span></p>\r
-\r
-<p class=Note><span lang=EN-US style='mso-ansi-language:EN-US'>Note:<span\r
-style='mso-spacerun:yes'>  </span>This flag is mostly designed for interactions\r
-between T-Coffee and T-CoffeeDPA (the large scale version of T-Coffee).</span><span\r
-lang=EN-US style='mso-ansi-language:EN-US;mso-bidi-font-weight:bold'><o:p></o:p></span></p>\r
-\r
-<h3><a name="_Toc235958548"></a><a name="_Toc102494771"></a><a\r
-name="_Toc102494366"></a><a name="_Toc101065241"><span style='mso-bookmark:\r
-_Toc102494366'><span style='mso-bookmark:_Toc102494771'><span style='mso-bookmark:\r
-_Toc235958548'><span lang=EN-US>Structure Input</span></span></span></span></a></h3>\r
-\r
-<p class=flag><a name="_Toc235958549"></a><a name="_Toc102494772"></a><a\r
-name="_Toc101065242"><span style='mso-bookmark:_Toc102494772'><span\r
-style='mso-bookmark:_Toc235958549'><span lang=AF>-pdb</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-pdb=&lt;pdbid1&gt;,&lt;pdbid2&gt;\85[Max 200]<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: None</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Reads or fetch a pdb file. It is\r
-possible to specify a chain or even a sub-chain:</span></p>\r
-\r
-<p class=example2><span lang=EN-US>PDBID(PDB_CHAIN)[opt] (FIRST,LAST)[opt]<a\r
-name="_Toc101065243"></a></span></p>\r
-\r
-<p class=flagdescription><span style='mso-bookmark:_Toc101065243'><span\r
-lang=EN-US>It is also possible to input structures via the \96in flag. In that\r
-case, you will need to use the TAG identifier:</span></span></p>\r
-\r
-<p class=example2><span style='mso-bookmark:_Toc101065243'><span lang=EN-US>-in\r
-Ppdb1 Ppdb2\85 </span></span></p>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065243'><a name="_Toc235958550"></a><a\r
-name="_Toc102494773"></a><a name="_Toc102494367"><span style='mso-bookmark:\r
-_Toc102494773'><span style='mso-bookmark:_Toc235958550'><span lang=EN-US>Tree\r
-Input</span></span></span></a></span></h3>\r
-\r
-<p class=flag><a name="_Toc235958551"></a><a name="_Toc102494774"></a><a\r
-name="_Toc101065244"><span style='mso-bookmark:_Toc102494774'><span\r
-style='mso-bookmark:_Toc235958551'><span lang=AF>-usetree</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--usetree=&lt;tree file&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: No file specified</span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Format: newick tree format (ClustalW\r
-Style)</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>This flag indicates that rather than\r
-computing a new dendrogram, t_coffee must use a pre-computed one. The tree\r
-files are in phylips format and compatible with ClustalW. In most cases, using\r
-a pre-computed tree will halve the computation time required by t_coffee. It is\r
-also possible to use trees output by ClustalW, Phylips and any other program.</span></p>\r
-\r
-<h3><a name="_Toc235958552"></a><a name="_Toc102494775"></a><a\r
-name="_Toc102494368"></a><a name="_Toc101065245"><span style='mso-bookmark:\r
-_Toc102494368'><span style='mso-bookmark:_Toc102494775'><span style='mso-bookmark:\r
-_Toc235958552'><span lang=EN-US>Structures, Sequences Methods and Library Input</span></span></span></span></a><span\r
-style='mso-bookmark:_Toc235958552'><span lang=EN-US> via the </span></span><span\r
-style='mso-bookmark:_Toc235958552'><span lang=EN-US style='font-family:Symbol;\r
-mso-ascii-font-family:"Arial Black"'>&#150;</span><span lang=EN-US>in Flag</span></span></h3>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.5pt;\r
-padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#FFFF89'>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut align=center\r
-style='text-align:center;background:#FFFF89'><a name="_Toc101065246"><span\r
-lang=EN-US style='font-size:20.0pt;mso-bidi-font-size:10.0pt'>The -in Flag and\r
-its Identifier TAGS<o:p></o:p></span></a></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span\r
-style='mso-bookmark:_Toc101065246'><span lang=EN-US><o:p>&nbsp;</o:p></span></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span\r
-style='mso-bookmark:_Toc101065246'><span lang=EN-US>&lt;-in&gt; is the real\r
-grinder of T-Coffee. Sequences, methods and alignments all pass through so that\r
-T-Coffee can turn it all into a single list of constraints (the library).\r
-Everything is done automatically with T-Coffee going through each file to\r
-extract the sequences it contains. The methods are then applied to the\r
-sequences. Pre-compiled constraint list can also be provided. Each file\r
-provided via this flag must be preceded with a symbol (Identifier TAG) that\r
-indicates its nature to T-Coffee. The TAGs currently supported are the\r
-following:</span></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span\r
-style='mso-bookmark:_Toc101065246'><span lang=EN-US><o:p>&nbsp;</o:p></span></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span\r
-style='mso-bookmark:_Toc101065246'><span lang=EN-US>P<span style='mso-tab-count:\r
-1'>         </span>PDB structure</span></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span\r
-style='mso-bookmark:_Toc101065246'><span lang=EN-US>S <span style='mso-tab-count:\r
-1'>         </span>for sequences (use it as well to treat an MSA as unaligned\r
-sequences)</span></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span\r
-style='mso-bookmark:_Toc101065246'><span lang=EN-US><o:p>&nbsp;</o:p></span></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span\r
-style='mso-bookmark:_Toc101065246'><span lang=EN-US>M <span style='mso-tab-count:\r
-1'>       </span>Methods used to build the library</span></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span\r
-style='mso-bookmark:_Toc101065246'><span lang=EN-US>L <span style='mso-tab-count:\r
-1'>        </span>Pre-computed T-Coffee library</span></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span\r
-style='mso-bookmark:_Toc101065246'><span lang=EN-US>A <span style='mso-tab-count:\r
-1'>        </span>Multiple Alignments that must be turned into a Library</span></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span\r
-style='mso-bookmark:_Toc101065246'><span lang=EN-US><o:p>&nbsp;</o:p></span></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span\r
-style='mso-bookmark:_Toc101065246'><span lang=EN-US>X <span style='mso-tab-count:\r
-1'>        </span>Substitution matrices.</span></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:\r
-35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:\r
-_Toc101065246'><span lang=EN-US>R <span style='mso-tab-count:1'>        </span><span\r
-style='mso-tab-count:1'>            </span>Profiles. This is a legal multiple\r
-alignments that will be treated as single sequences (the sequences it contains\r
-will not be realigned). </span></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:\r
-35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:\r
-_Toc101065246'><span lang=EN-US><o:p>&nbsp;</o:p></span></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:\r
-35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:\r
-_Toc101065246'><span lang=EN-US>If you do not want to use the TAGS, you will\r
-need to use the following flags in replacement of -in. Do not use the TAGS when\r
-using these flags:</span></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:\r
-35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:\r
-_Toc101065246'><span lang=EN-US><o:p>&nbsp;</o:p></span></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:\r
-35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:\r
-_Toc101065246'><span lang=EN-US>-aln <span style='mso-tab-count:3'>                            </span>Alignments\r
-<span style='mso-tab-count:1'>   </span>(A)</span></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:\r
-35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:\r
-_Toc101065246'><span lang=EN-US>-profile<span style='mso-tab-count:1'>           </span>Profiles\r
-<span style='mso-tab-count:1'>          </span>(R)</span></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:\r
-35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:\r
-_Toc101065246'><span lang=EN-US>-method<span style='mso-tab-count:1'>          </span>Method\r
-<span style='mso-tab-count:1'>         </span>(M)</span></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:\r
-35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:\r
-_Toc101065246'><span lang=EN-US>-seq<span style='mso-tab-count:3'>                             </span>Sequences\r
-<span style='mso-tab-count:1'>     </span>(S)</span></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:\r
-35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:\r
-_Toc101065246'><span lang=EN-US>-lib<span style='mso-tab-count:3'>                              </span>Libraries<span\r
-style='mso-tab-count:1'>        </span>(L)<a name="_Toc102494776"></a></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=flag><span style='mso-bookmark:_Toc101065246'><span style='mso-bookmark:\r
-_Toc102494776'><a name="_Toc235958553"><span lang=AF>-in</span></a></span></span></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--in=[&lt;P,S,A,L,M,X&gt;&lt;name&gt;,]<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default:\r
--in=Mlalign_id_pair,Mclustalw_pair</span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.5pt;\r
-padding:0mm 0mm 0mm 0mm;background:#F7CBB7'>\r
-\r
-<p class=Warning><span lang=EN-US>Note: -in can be replaced with the combined\r
-usage of -aln, iprofile, .pdb, .lib, -method.</span></p>\r
-\r
-</div>\r
-\r
-<p class=flagdescription><span lang=EN-US>See the box for an explanation of the\r
--in flag. The following argument passed via -in</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee\r
--in=Ssample_seq1.fasta,Asample_aln1.aln,Asample_aln2.msf,Mlalign_id_pair,Lsample_lib1.tc_lib\r
-\96outfile=outaln</span></p>\r
-\r
-</div>\r
-\r
-<p class=flagdescription><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>This command will trigger the following\r
-chain of events:</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>1-Gather all the sequences</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Sequences within all the provided\r
-files are pooled together. Format recognition is automatic. Duplicates are\r
-removed (if they have the same name). Duplicates in a single file are only\r
-tolerated in FASTA format file, although they will cause sequences to be\r
-renamed.</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>In the above case, the total set of\r
-sequences will be made of sequences contained in sequences1.seq,\r
-alignment1.aln, alignment2.msf and library.lib, plus the sequences initially\r
-gathered<span style='mso-spacerun:yes'>  </span>by -infile.</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>2-Turn alignments into libraries</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>alignment1.aln and alignment2.msf\r
-will be read and turned into libraries. Another library will be produced by\r
-applying the method lalign_id_pair to the set of sequences previously obtained\r
-(1). The final library used for the alignment will be the combination of all\r
-this information. </span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Note as well the following rules: </span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=flagdescription><b style='mso-bidi-font-weight:normal'><span\r
-lang=EN-US>1-Order</span></b><span lang=EN-US style='mso-bidi-font-weight:bold'>:</span><span\r
-lang=EN-US> The order in which sequences, methods, alignments and libraries are\r
-fed in is irrelevant.</span></p>\r
-\r
-<p class=flagdescription><b style='mso-bidi-font-weight:normal'><span\r
-lang=EN-US>2-Heterogeneity</span></b><span lang=EN-US style='mso-bidi-font-weight:\r
-bold'>:</span><span lang=EN-US> There is no need for each element (A, S, L) to\r
-contain the same sequences.</span></p>\r
-\r
-<p class=flagdescription><b style='mso-bidi-font-weight:normal'><span\r
-lang=EN-US>3-No Duplicate</span></b><span lang=EN-US style='mso-bidi-font-weight:\r
-bold'>:</span><span lang=EN-US> Each file should contain only one copy of each\r
-sequence. Duplicates are only allowed in FASTA files but will cause the\r
-sequences to be renamed.</span></p>\r
-\r
-<p class=flagdescription><b style='mso-bidi-font-weight:normal'><span\r
-lang=EN-US>4-Reconciliation</span></b><span lang=EN-US style='mso-bidi-font-weight:\r
-bold'>:</span><span lang=EN-US> If two files (for instance two alignments)\r
-contain different versions of the same sequence due to an indel, a new sequence\r
-will be reconstructed and used instead:</span></p>\r
-\r
-<p class=example2CxSpFirst><span lang=EN-US>aln 1:hgab1 <span style='mso-tab-count:\r
-1'>  </span>AAAAABAAAAA</span></p>\r
-\r
-<p class=example2CxSpLast><span lang=EN-US>aln 2:hgab1<span style='mso-tab-count:\r
-1'>   </span>AAAAAAAAAACCC</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>will cause the program to reconstruct\r
-and use the following sequence </span></p>\r
-\r
-<p class=example2><span lang=EN-US>hgab1<span style='mso-tab-count:1'>   </span>AAAAABAAAAACCC\r
-</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>This can be useful if you are trying\r
-to combine several runs of blast, or structural information where residues may\r
-have been deleted. However substitutions are forbidden. If two sequences with\r
-the same name cannot be merged, they will cause the program to exit with an\r
-information message.</span></p>\r
-\r
-<p class=flagdescription><b style='mso-bidi-font-weight:normal'><span\r
-lang=EN-US>5-Methods</span></b><span lang=EN-US style='mso-bidi-font-weight:\r
-bold'>:</span><span lang=EN-US> The method describer can either be built in\r
-(See ### for a list of all the available methods) or be a file describing the\r
-method to be used. The exact syntax is provided in part 4 of this manual.</span></p>\r
-\r
-<p class=flagdescription><b style='mso-bidi-font-weight:normal'><span\r
-lang=EN-US>6-Substitution Matrices</span></b><span lang=EN-US style='mso-bidi-font-weight:\r
-bold'>: </span><span lang=EN-US>If the method is a substitution matrix (X) then\r
-no other type of information should be provided. For instance:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee sample_seq1.fasta -in=Xpam250mt<span style='mso-spacerun:yes'> \r
-</span>-gapopen=-10<span style='mso-spacerun:yes'>  </span>-gapext=-1 </span></p>\r
-\r
-</div>\r
-\r
-<p class=flagdescription><span lang=EN-US>This command results in a progressive\r
-alignment carried out on the sequences in seqfile. The procedure does not use\r
-any more the T-Coffee concistency based algorithm, but switches to a standard\r
-progressive alignment algorithm (like ClustalW or Pileup) much less accurate.\r
-In this context, appropriate gap penalties should be provided. The matrices are\r
-in the file source/matrices.h. Add-Hoc matrices can also be provided by the\r
-user (see the matrices format section at the end of this manual).</span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.5pt;\r
-padding:0mm 0mm 0mm 0mm;background:#F7CBB7'>\r
-\r
-<p class=Warning><span lang=EN-US>Warning: Xmatrix does not have the same\r
-effect as using the -matrix flag.<span style='mso-spacerun:yes'>  </span>The\r
--matrix defines the matrix that will be used while compiling the library while\r
-the Xmatrix defines the matrix used when assembling the final alignment.</span></p>\r
-\r
-</div>\r
-\r
-<h3><a name="_Toc235958554"></a><a name="_Toc102494777"></a><a\r
-name="_Toc102494369"></a><a name="_Toc101065247"><span style='mso-bookmark:\r
-_Toc102494369'><span style='mso-bookmark:_Toc102494777'><span style='mso-bookmark:\r
-_Toc235958554'><span lang=EN-US>Profile Input</span></span></span></span></a></h3>\r
-\r
-<p class=flag><a name="_Toc235958555"></a><a name="_Toc102494778"></a><a\r
-name="_Toc101065248"><span style='mso-bookmark:_Toc102494778'><span\r
-style='mso-bookmark:_Toc235958555'><span lang=AF>-profile</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--profile=[&lt;name&gt;,] maximum of 200 profiles.<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: no default</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>This flag causes T-Coffee to treat\r
-multiple alignments as a single sequences, thus making it possible to make\r
-multiple profile alignments. The profile-profile alignment is controlled by <span\r
-style='mso-bidi-font-weight:bold'>-profile_mode</span> and <span\r
-style='mso-bidi-font-weight:bold'>-profile_comparison</span>. When provided\r
-with the <b style='mso-bidi-font-weight:normal'>-in</b> flag, profiles must be\r
-preceded with the letter R.</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee \96profile sample_aln1.aln,sample_aln2.aln \96outfile=profile_aln</span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee \96in Rsample_aln1.aln,Rsample_aln2.aln,Mslow_pair,Mlalign_id_pair\r
-\96outfile=profile_aln</span></p>\r
-\r
-</div>\r
-\r
-<p class=flagdescription><span lang=EN-US>Note that when using \96template_file,\r
-the program will also look for the templates associated with the profiles, even\r
-if the profiles have been provided as templates themselves (however it will not\r
-look for the template of the profile templates of the profile templates\85)</span></p>\r
-\r
-<p class=flag><a name="_Toc235958556"></a><a name="_Toc102494779"></a><a\r
-name="_Toc101065249"><span style='mso-bookmark:_Toc102494779'><span\r
-style='mso-bookmark:_Toc235958556'><span lang=AF>-profile1 [cw]</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--profile1=[&lt;name&gt;], one name only<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: no default</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Similar to the previous one and was\r
-provided for compatibility with ClustalW.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958557"></a><a name="_Toc102494780"></a><a\r
-name="_Toc101065250"><span style='mso-bookmark:_Toc102494780'><span\r
-style='mso-bookmark:_Toc235958557'><span lang=AF>-profile2 [cw]</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--profile1=[&lt;name&gt;], one name only<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: no default</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Similar to the previous one and was\r
-provided for compatibility with ClustalW.</span></p>\r
-\r
-<h2><a name="_Toc235958558"></a><a name="_Toc102494781"></a><a\r
-name="_Toc102494370"></a><a name="_Toc101065251"><span style='mso-bookmark:\r
-_Toc102494370'><span style='mso-bookmark:_Toc102494781'><span style='mso-bookmark:\r
-_Toc235958558'><span lang=EN-US>Alignment Computation</span></span></span></span></a></h2>\r
-\r
-<h3><a name="_Toc235958559"></a><a name="_Toc102494782"></a><a\r
-name="_Toc102494371"></a><a name="_Toc101065252"><span style='mso-bookmark:\r
-_Toc102494371'><span style='mso-bookmark:_Toc102494782'><span style='mso-bookmark:\r
-_Toc235958559'><span lang=EN-US>Library Computation: Methods</span></span></span></span></a></h3>\r
-\r
-<p class=flag><a name="_Toc235958560"></a><a name="_Toc102494783"><span\r
-style='mso-bookmark:_Toc235958560'><span lang=AF>-lalign_n_top</span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--lalign_n_top=&lt;Integer&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -lalign_n_top=10</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Number of alignment reported by the\r
-local method (lalign).</span></p>\r
-\r
-<p class=flag><a name="_Toc235958561"></a><a name="_Toc102494784"><span\r
-style='mso-bookmark:_Toc235958561'><span lang=AF>-align_pdb_param_file</span></span></a></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Unsuported</span></p>\r
-\r
-<p class=flag><a name="_Toc235958562"></a><a name="_Toc102494785"><span\r
-style='mso-bookmark:_Toc235958562'><span lang=AF>-align_pdb_hasch_mode</span></span></a></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Unsuported<a name="_Toc101065253"></a></span></p>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065253'><a name="_Toc235958563"></a><a\r
-name="_Toc102494786"></a><a name="_Toc102494372"><span style='mso-bookmark:\r
-_Toc102494786'><span style='mso-bookmark:_Toc235958563'><span lang=EN-US>Library\r
-Computation: Extension</span></span></span></a></span></h3>\r
-\r
-<p class=flag><a name="_Toc101065255"></a><a name="_Toc235958564"></a><a\r
-name="_Toc102494787"></a><a name="_Toc101065254"><span style='mso-bookmark:\r
-_Toc102494787'><span style='mso-bookmark:_Toc235958564'><span style='mso-bookmark:\r
-_Toc101065255'><span lang=AF>-</span></span></span></span></a><span\r
-style='mso-bookmark:_Toc102494787'><span style='mso-bookmark:_Toc235958564'><span\r
-style='mso-bookmark:_Toc101065255'><span lang=AF>lib_list [Unsupported]</span></span></span></span><span\r
-style='mso-bookmark:_Toc101065255'></span></p>\r
-\r
-<p class=flagusage><span style='mso-bookmark:_Toc101065255'><span lang=EN-US\r
-style='mso-ansi-language:EN-US'>Usage:<span style='mso-spacerun:yes'> \r
-</span>-lib_list=&lt;filename&gt; <o:p></o:p></span></span></p>\r
-\r
-<p class=instruction><span style='mso-bookmark:_Toc101065255'><span lang=EN-US>Default:unset</span></span></p>\r
-\r
-<p class=flagdescription><span style='mso-bookmark:_Toc101065255'><span\r
-lang=EN-US>Use this flag if you do not want the library computation to take\r
-into account all the possible pairs in your dataset. For instance</span></span></p>\r
-\r
-<p class=flagdescription><span style='mso-bookmark:_Toc101065255'><span\r
-lang=EN-US>Format:</span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc101065255'><span\r
-lang=EN-US><span style='mso-tab-count:1'>      </span>2 Name1 name2 </span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065255'><span\r
-lang=EN-US><span style='mso-tab-count:1'>      </span>2 Name1 name4</span></span></p>\r
-\r
-<p class=examplefileCxSpLast><span style='mso-bookmark:_Toc101065255'><span\r
-lang=EN-US><span style='mso-tab-count:1'>      </span>3 Name1 Name2 Name3\85</span></span></p>\r
-\r
-</div>\r
-\r
-<p class=flagdescription><span style='mso-bookmark:_Toc101065255'><span\r
-lang=EN-US><span style='mso-tab-count:1'>            </span>(the line 3 would\r
-be used by a multiple alignment method).</span></span></p>\r
-\r
-<p class=flag><span style='mso-bookmark:_Toc101065255'><a name="_Toc235958565"></a><a\r
-name="_Toc102494788"><span style='mso-bookmark:_Toc235958565'><span lang=AF>-do_normalise</span></span></a></span></p>\r
-\r
-<p class=flagusage><span style='mso-bookmark:_Toc101065255'><span lang=EN-US\r
-style='mso-ansi-language:EN-US'>Usage:<span style='mso-spacerun:yes'> \r
-</span>-do_normalise=&lt;0 or a positive value&gt; <o:p></o:p></span></span></p>\r
-\r
-<p class=instruction><span style='mso-bookmark:_Toc101065255'><span lang=EN-US>Default:-do_normalise=1000</span></span></p>\r
-\r
-<p class=instruction><span style='mso-bookmark:_Toc101065255'><span lang=EN-US>Development\r
-Only</span></span></p>\r
-\r
-<p class=flagdescription><span style='mso-bookmark:_Toc101065255'><span\r
-lang=EN-US>When using a value different from 0, this flag sets the score of the\r
-highest scoring pair to 1000. </span></span></p>\r
-\r
-<p class=flag><span style='mso-bookmark:_Toc101065255'><a name="_Toc235958566"></a><a\r
-name="_Toc102494789"><span style='mso-bookmark:_Toc235958566'><span lang=AF>-extend</span></span></a></span></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-extend=&lt;0,1 or a positive value&gt; <o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default:-extend=1</span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Development Only</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>When turned on, this flag indicates\r
-that the library extension should be carried out when performing the multiple\r
-alignment. If <b>-extend =0</b>, the extension is not made, if it is set to 1,\r
-the extension is made on all the pairs in the library. If the extension is set\r
-to another positive value, the extension is only carried out on pairs having a weight\r
-value superior to the specified limit.<a name="_Toc101065256"></a></span></p>\r
-\r
-<p class=flag><span style='mso-bookmark:_Toc101065256'><a name="_Toc235958567"></a><a\r
-name="_Toc102494790"><span style='mso-bookmark:_Toc235958567'><span lang=AF>-extend_mode</span></span></a></span></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-extend=&lt;string&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default:-extend=very_fast_triplet</span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Warning: Development Only</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Controls the algorithm for matrix\r
-extension. Available modes include:</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>relative_triplet<span\r
-style='mso-tab-count:2'>                  </span>Unsupported</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>g_coffee<span style='mso-tab-count:\r
-3'>                                           </span>Unsupported</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>g_coffee_quadruplets<span\r
-style='mso-tab-count:1'>    </span>Unsupported</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>fast_triplet<span style='mso-tab-count:\r
-2'>                        </span>Fast triplet extension</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>very_fast_triplet<span\r
-style='mso-tab-count:2'>                             </span>slow triplet\r
-extension, limited to the <b>-max_n_pair</b> best sequence pairs when aligning\r
-two profiles</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>slow_triplet<span style='mso-tab-count:\r
-2'>                       </span>Exhaustive use of all the triplets</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>mixt<span style='mso-tab-count:3'>                                   </span>Unsupported</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>quadruplet<span style='mso-tab-count:\r
-2'>                        </span>Unsupported</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>test<span style='mso-tab-count:3'>                                     </span>Unsupported</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>matrix<span style='mso-tab-count:\r
-3'>                                               </span>Use of the matrix <b>-matrix<o:p></o:p></b></span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>fast_matrix<span style='mso-tab-count:\r
-2'>                      </span>Use of the matrix <b>-matrix</b>. Profiles are\r
-turned into consensus</span></p>\r
-\r
-<p class=flag><a name="_Toc235958568"></a><a name="_Toc102494791"></a><a\r
-name="_Toc101065257"><span style='mso-bookmark:_Toc102494791'><span\r
-style='mso-bookmark:_Toc235958568'><span lang=AF>-max_n_pair</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-max_n_pair=&lt;integer&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default:-extend=10</span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Development Only</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Controls the number of pairs\r
-considered by the <b>-extend_mode</b>=very_fast_triplet. Setting it to 0 forces\r
-all the pairs to be considered (equivalent to <b>-extend_mode</b>=slow_triplet).</span></p>\r
-\r
-<p class=flag><a name="_Toc235958569"></a><a name="_Toc102494792"></a><a\r
-name="_Toc101065258"><span style='mso-bookmark:_Toc102494792'><span\r
-style='mso-bookmark:_Toc235958569'><span lang=AF>-seq_name_for_quadruplet</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>Unsupported<o:p></o:p></span></p>\r
-\r
-<p class=flag><a name="_Toc235958570"></a><a name="_Toc102494793"></a><a\r
-name="_Toc101065259"><span style='mso-bookmark:_Toc102494793'><span\r
-style='mso-bookmark:_Toc235958570'><span lang=AF>-compact</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>Unsupported<o:p></o:p></span></p>\r
-\r
-<p class=flag><a name="_Toc235958571"></a><a name="_Toc102494794"></a><a\r
-name="_Toc101065260"><span style='mso-bookmark:_Toc102494794'><span\r
-style='mso-bookmark:_Toc235958571'><span lang=AF>-clean</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>Unsupported<o:p></o:p></span></p>\r
-\r
-<p class=flag><a name="_Toc235958572"></a><a name="_Toc102494795"></a><a\r
-name="_Toc101065261"><span style='mso-bookmark:_Toc102494795'><span\r
-style='mso-bookmark:_Toc235958572'><span lang=AF>-maximise</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>Unsupported<o:p></o:p></span></p>\r
-\r
-<p class=flag><a name="_Toc235958573"></a><a name="_Toc102494796"></a><a\r
-name="_Toc101065262"><span style='mso-bookmark:_Toc102494796'><span\r
-style='mso-bookmark:_Toc235958573'><span lang=AF>-do_self</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>Flag -do_self<o:p></o:p></span></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Default: No<o:p></o:p></span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>This flag causes the extension to\r
-carried out within the sequences (as opposed to between sequences). This is\r
-necessary when looking for internal repeats with Mocca.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958574"></a><a name="_Toc102494797"></a><a\r
-name="_Toc101065263"><span style='mso-bookmark:_Toc102494797'><span\r
-style='mso-bookmark:_Toc235958574'><span lang=AF>-seq_name_for_quadruplet</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>Unsupported<o:p></o:p></span></p>\r
-\r
-<p class=flag><a name="_Toc235958575"></a><a name="_Toc102494798"></a><a\r
-name="_Toc101065264"><span style='mso-bookmark:_Toc102494798'><span\r
-style='mso-bookmark:_Toc235958575'><span lang=AF>-weight</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-weight=&lt;winsimN, sim or\r
-sim_&lt;matrix_name or matrix_file&gt; or &lt;integer value&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -weight=sim</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Weight defines the way alignments are\r
-weighted when turned into a library. <span\r
-style='mso-spacerun:yes'> </span>Overweighting can be obtained with the\r
-OW&lt;X&gt; weight mode.</span></p>\r
-\r
-<p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar><span\r
-lang=EN-US><o:p>&nbsp;</o:p></span></span></p>\r
-\r
-<p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar><span\r
-lang=EN-US>winsimN </span></span><span lang=EN-US>indicates that the weight\r
-assigned to a given pair will be equal to the percent identity within a window\r
-of 2N+1 length centered on that pair. For instance winsim10 defines a window of\r
-10 residues around the pair being considered. This gives its own weight to each\r
-residue in the output library. In our hands, this type of weighting scheme has\r
-not provided any significant improvement over the standard sim value.</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee sample_seq1.fasta -weight=winsim10 \96out_lib=test.tc_lib </span></p>\r
-\r
-</div>\r
-\r
-<p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar><span\r
-lang=EN-US>sim</span></span><span lang=EN-US> indicates that the weight equals\r
-the average identity within the sequences containing the matched residues.</span></p>\r
-\r
-<p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar><span\r
-lang=EN-US>OW&lt;X&gt;</span></span><span\r
-class=StyleflagdescriptionBoldItalicChar><span lang=EN-US style='font-style:\r
-normal;mso-bidi-font-style:italic'> </span></span><span\r
-class=StyleflagdescriptionBoldItalicChar><span lang=EN-US style='font-weight:\r
-normal;mso-bidi-font-weight:bold;font-style:normal;mso-bidi-font-style:italic'>Will\r
-cause the sim weight to be multiplied by X<o:p></o:p></span></span></p>\r
-\r
-<p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar><span\r
-lang=EN-US>sim_matrix_name</span></span><span lang=EN-US> indicates the average\r
-identity with two residues regarded as identical when their substitution value\r
-is positive. The valid matrices names are in <i style='mso-bidi-font-style:\r
-normal'>matrices.h (pam250mt) .</i>Matrices not found in this header are\r
-considered to be filenames. See the format section for matrices. For instance, <i\r
-style='mso-bidi-font-style:normal'>-weight=sim_pam250mt</i> indicates that the\r
-grouping used for similarity will be the set of classes with positive\r
-substitutions. </span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee sample_seq1.fasta -weight=winsim10 \96out_lib=test.tc_lib </span></p>\r
-\r
-</div>\r
-\r
-<p class=flagdescription><span lang=EN-US>Other groups include </span></p>\r
-\r
-<p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar><span\r
-lang=EN-US>sim_clustalw_col</span></span><i style='mso-bidi-font-style:normal'><span\r
-lang=EN-US> </span></i><span lang=EN-US>( categories of clustalw marked with :)</span></p>\r
-\r
-<p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar><span\r
-lang=EN-US>sim_clustalw_dot</span></span><span lang=EN-US> ( categories of\r
-clustalw marked with .)</span></p>\r
-\r
-<p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar><span\r
-lang=EN-US>Value</span></span><i style='mso-bidi-font-style:normal'><span\r
-lang=EN-US> </span></i><span lang=EN-US>indicates that all the pairs found in\r
-the alignments must be given the same weight equal to value. This is useful\r
-when the alignment one wishes to turn into a library must be given a\r
-pre-specified score (for instance if they come from a structure\r
-super-imposition program). Value is an integer:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee sample_seq1.fasta -weight=1000 \96out_lib=test.tc_lib </span></p>\r
-\r
-</div>\r
-\r
-<h3><a name="_Toc235958576"></a><a name="_Toc102494799"></a><a\r
-name="_Toc102494373"></a><a name="_Toc101065265"><span style='mso-bookmark:\r
-_Toc102494373'><span style='mso-bookmark:_Toc102494799'><span style='mso-bookmark:\r
-_Toc235958576'><span lang=EN-US>Tree Computation</span></span></span></span></a></h3>\r
-\r
-<p class=flag><a name="_Toc235958577"></a><a name="_Toc102494800"></a><a\r
-name="_Toc101065266"><span style='mso-bookmark:_Toc102494800'><span\r
-style='mso-bookmark:_Toc235958577'><span lang=AF>-</span></span></span></a><span\r
-style='mso-bookmark:_Toc235958577'><span lang=AF>distance_matrix_mode</span></span></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--distance_matrix_mode=&lt;slow, fast, very_fast&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: very_fast</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>This flag indicates the method used\r
-for computing the distance matrix (distance between every pair of sequences)\r
-required for the computation of the dendrogram. </span></p>\r
-\r
-<p class=flagdescription><b style='mso-bidi-font-weight:normal'><span\r
-lang=EN-US>Slow</span></b><span lang=EN-US> <span style='mso-tab-count:1'>  </span>The\r
-chosen dp_mode using the extended library, </span></p>\r
-\r
-<p class=flagdescription><b style='mso-bidi-font-weight:normal'><span\r
-lang=EN-US>fast</span></b><span lang=EN-US>:<span style='mso-spacerun:yes'>  \r
-</span><span style='mso-tab-count:1'> </span>The fasta dp_mode using the\r
-extended library.</span></p>\r
-\r
-<p class=flagdescription><b style='mso-bidi-font-weight:normal'><span\r
-lang=EN-US>very_fast</span></b><span lang=EN-US><span style='mso-tab-count:\r
-1'>          </span>The fasta dp_mode using blosum62mt.</span></p>\r
-\r
-<p class=flagdescription><b style='mso-bidi-font-weight:normal'><span\r
-lang=EN-US>ktup<span style='mso-tab-count:1'>    </span></span></b><span\r
-lang=EN-US>Ktup matching (Muscle kind) </span></p>\r
-\r
-<p class=flagdescription><b style='mso-bidi-font-weight:normal'><span\r
-lang=EN-US>aln<span style='mso-tab-count:2'>                      </span></span></b><span\r
-lang=EN-US>Read the distances on a precomputed MSA</span></p>\r
-\r
-<p class=flag><a name="_Toc235958578"></a><a name="_Toc102494801"></a><a\r
-name="_Toc101065267"><span style='mso-bookmark:_Toc102494801'><span\r
-style='mso-bookmark:_Toc235958578'><span lang=AF>-quicktree [CW]</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--quicktree<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Description: Causes T-Coffee to compute a\r
-fast approximate guide tree</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>This flag is kept for compatibility with\r
-ClustalW. It indicates that:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee sample_seq1.fasta \96distance_matrix_mode=very_fast </span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee sample_seq1.fasta \96quicktree </span></p>\r
-\r
-</div>\r
-\r
-<h3><a name="_Toc235958579"></a><a name="_Toc102494802"></a><a\r
-name="_Toc102494374"></a><a name="_Toc101065268"><span style='mso-bookmark:\r
-_Toc102494374'><span style='mso-bookmark:_Toc102494802'><span style='mso-bookmark:\r
-_Toc235958579'><span lang=EN-US>Pair-wise Alignment Computation</span></span></span></span></a></h3>\r
-\r
-<p class=Noteboxtitle><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.5pt;\r
-padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#FFFF89'>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut align=center\r
-style='text-align:center;background:#FFFF89'><span lang=EN-US style='font-size:\r
-20.0pt'>Controlling Alignment Computation<o:p></o:p></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US>Most\r
-parameters in this section refer to the alignment mode fasta_pair_wise and\r
-cfatsa_pair_wise. When using these alignment modes, things proceed as follow:</span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US>1-Sequences\r
-are recoded using a degenerated alphabet provided with &lt;-sim_matrix&gt; </span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US>2-Recoded\r
-sequences are then hashed into ktuples of size <u>&lt;-ktup&gt;</u></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US>3-Dynamic\r
-programming runs on the <u>&lt;-ndiag&gt;</u> best diagonals whose score is\r
-higher than <u>&lt;-diag_threshold&gt;</u>, the way diagonals are scored is\r
-controlled via <u>&lt;-diag_mode&gt;</u> .</span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US>4-The\r
-Dynamic computation is made to optimize either the library scoring scheme (as\r
-defined by the <u>-in</u> flag) or a substitution matrix as provided via the <u>-matrix</u>\r
-flag. The penalty scheme is defined by <u>-gapopen</u> and <u>-gapext</u>. If <u>-gapopen</u>\r
-is undefined, the value defined in <u>-cosmetic_penalty</u> is used instead.</span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US>5-Terminal\r
-gaps are scored according to <u>-tg_mode</u></span></p>\r
-\r
-</div>\r
-\r
-<p class=noteboxbody><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=flag><a name="_Toc235958580"></a><a name="_Toc102494803"></a><a\r
-name="_Toc101065269"><span style='mso-bookmark:_Toc102494803'><span\r
-style='mso-bookmark:_Toc235958580'><span lang=AF>-dp_mode</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-dp_mode=&lt;string&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -dp_mode=cfasta_fair_wise</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>This flag indicates the type of\r
-dynamic programming used by the program:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee sample_seq1.fasta \96dp_mode myers_miller_pair_wise </span></p>\r
-\r
-</div>\r
-\r
-<p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar><span\r
-lang=EN-US>gotoh_pair_wise</span></span><span lang=EN-US>: implementation of\r
-the gotoh algorithm (quadratic in memory and time)</span></p>\r
-\r
-<p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar><span\r
-lang=EN-US>myers_miller_pair_wise</span></span><span lang=EN-US>:\r
-implementation of the Myers and Miller dynamic programming algorithm (\r
-quadratic in time and linear in space). This algorithm is recommended for very\r
-long sequences. It is about 2 times slower than gotoh and only accepts <i\r
-style='mso-bidi-font-style:normal'>tg_mode=1or 2 (i.e. gaps penalized for\r
-opening).<o:p></o:p></i></span></p>\r
-\r
-<p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar><span\r
-lang=EN-US>fasta_pair_wise</span></span><i style='mso-bidi-font-style:normal'><span\r
-lang=EN-US>: </span></i><span lang=EN-US>implementation of the fasta algorithm.\r
-The sequence is hashed, looking for <i style='mso-bidi-font-style:normal'>ktuples</i>\r
-words. Dynamic programming is only carried out on the <i style='mso-bidi-font-style:\r
-normal'>ndiag</i> best scoring diagonals. This is much faster but less accurate\r
-than the two previous. This mode is controlled by the parameters <b>-ktuple,\r
--diag_mode and -ndiag<o:p></o:p></b></span></p>\r
-\r
-<p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar><span\r
-lang=EN-US>cfasta_pair_wise</span></span><span lang=EN-US>: c stands for\r
-checked. It is the same algorithm. The dynamic programming is made on the <i\r
-style='mso-bidi-font-style:normal'>ndiag</i> best diagonals, and then on the\r
-2*ndiags, and so on until the scores converge. Complexity will depend on the\r
-level of divergence of the sequences, but will usually be L*log(L), with an\r
-accuracy comparable to the two first mode ( this was checked on BaliBase). This\r
-mode is controlled by the parameters <b>-ktuple, -diag_mode and \96ndiag<o:p></o:p></b></span></p>\r
-\r
-<p class=Note><span lang=EN-US style='mso-ansi-language:EN-US'>Note: Users may\r
-find by looking into the code that other modes with fancy names exists\r
-(viterby_pair_wise\85) Unless mentioned in this documentation, these modes are\r
-not supported.<o:p></o:p></span></p>\r
-\r
-<p class=flag><a name="_Toc235958581"></a><a name="_Toc102494804"></a><a\r
-name="_Toc101065270"><span style='mso-bookmark:_Toc102494804'><span\r
-style='mso-bookmark:_Toc235958581'><span lang=AF>-ktuple</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-ktuple=&lt;value&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -ktuple=1 or 2</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Indicates the ktuple size for\r
-cfasta_pair_wise dp_mode and fasta_pair_wise. It is set to 1 for proteins, and\r
-2 for DNA. The alphabet used for protein can be a degenerated version, set with\r
-<b><u>-sim_matrix.</u></b>. </span></p>\r
-\r
-<p class=flag><a name="_Toc235958582"></a><a name="_Toc102494805"></a><a\r
-name="_Toc101065271"><span style='mso-bookmark:_Toc102494805'><span\r
-style='mso-bookmark:_Toc235958582'><span lang=AF>-ndiag</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-ndiag=&lt;value&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -ndiag=0</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Indicates the number of diagonals\r
-used by the <i>fasta_pair_wise</i> algorithm (cf <b>-dp_mode</b>). When<span\r
-style='mso-spacerun:yes'>  </span><b>-ndiag=0</b>, n_diag=Log (length of the\r
-smallest sequence)+1. </span></p>\r
-\r
-<p class=Note><span lang=EN-US style='mso-ansi-language:EN-US'>When \96ndiag and\r
-\96diag_threshold are set, diagonals are selected if and only if they fulfill\r
-both conditions.<o:p></o:p></span></p>\r
-\r
-<p class=flag><a name="_Toc235958583"></a><a name="_Toc102494806"></a><a\r
-name="_Toc101065272"><span style='mso-bookmark:_Toc102494806'><span\r
-style='mso-bookmark:_Toc235958583'><span lang=AF>-diag_mode</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-diag_mode=&lt;value&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -diag_mode=0</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Indicates the manner in which\r
-diagonals are scored during the fasta hashing. </span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>0: indicates that the score of a\r
-diagonal is equal to the sum of the scores of the exact matches it contains. </span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>1 indicates that this score is set\r
-equal to the score of the best uninterrupted segment (useful when dealing with\r
-fragments of sequences).</span></p>\r
-\r
-<p class=flag><a name="_Toc235958584"></a><a name="_Toc102494807"></a><a\r
-name="_Toc101065273"><span style='mso-bookmark:_Toc102494807'><span\r
-style='mso-bookmark:_Toc235958584'><span lang=AF>-diag_threshold</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-diag_threshold=&lt;value&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -diag_threshold=0</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Sets the value of the threshold when\r
-selecting diagonals. </span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>0: indicates that \96ndiag should be\r
-used to select the diagonals (cf \96ndiag section).</span></p>\r
-\r
-<p class=flag><a name="_Toc235958585"></a><a name="_Toc102494808"></a><a\r
-name="_Toc101065274"><span style='mso-bookmark:_Toc102494808'><span\r
-style='mso-bookmark:_Toc235958585'><span lang=AF>-sim_matrix</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-sim_matrix=&lt;string&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -sim_matrix=vasiliky</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Indicates the manner in which the\r
-amino acid alphabet is degenerated when hashing in the fasta_pairwise dynamic\r
-programming. Standard ClustalW matrices are all valid. They are used to define\r
-groups of amino acids having positive substitution values. In T-Coffee, the\r
-default is a 13 letter grouping named Vasiliky, with residues grouped as\r
-follows:</span></p>\r
-\r
-<p class=example2><span lang=EN-US>rk, de, qh, vilm, fy (other residues kept\r
-alone).</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>This alphabet is set with the flag <b>-sim_matrix=vasiliky</b>.\r
-In order to keep the alphabet non degenerated, <b>-sim_matrix=idmat </b>can be\r
-used to retain the standard alphabet.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958586"></a><a name="_Toc102494809"></a><a\r
-name="_Toc101065275"><span style='mso-bookmark:_Toc102494809'><span\r
-style='mso-bookmark:_Toc235958586'><span lang=AF>-matrix [CW]</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-matrix=&lt;blosum62mt&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -matrix=blosum62mt</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>The usage of this flag has been\r
-modified from previous versions, due to frequent mistakes in its usage. This\r
-flag sets the matrix that will be used by alignment methods within t_coffee\r
-(slow_pair, lalign_id_pair). It does not affect external methods (like\r
-clustal_pair, clustal_aln\85). </span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Users can also provide their own\r
-matrices, using the matrix format described in the appendix.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958587"></a><a name="_Toc102494810"></a><a\r
-name="_Toc101065276"><span style='mso-bookmark:_Toc102494810'><span\r
-style='mso-bookmark:_Toc235958587'><span lang=AF>-nomatch</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-nomatch=&lt;positive value&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -nomatch=0</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Indicates the penalty to associate\r
-with a match. When using a library, all matches are positive or equal to 0.\r
-Matches equal to 0 are unsupported by the library but non-penalized. Setting\r
-nomatch to a non-negative value makes it possible to penalize these null\r
-matches and prevent unrelated sequences from being aligned (this can be useful\r
-when the alignments are meant to be used for structural modeling).</span></p>\r
-\r
-<p class=flag><a name="_Toc235958588"></a><a name="_Toc102494811"></a><a\r
-name="_Toc101065277"><span style='mso-bookmark:_Toc102494811'><span\r
-style='mso-bookmark:_Toc235958588'><span lang=AF>-gapopen</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-gapopen=&lt;negative value&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -gapopen=0</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Indicates the penalty applied for\r
-opening a gap. The penalty must be negative. If no value is provided when using\r
-a substitution matrix, a value will be automatically computed.</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Here are some guidelines regarding\r
-the tuning of gapopen and gapext. In T-Coffee matches get a score between 0\r
-(match) and 1000 (match perfectly consistent with the library). The default\r
-cosmetic penalty is set to -50 (5% of a perfect match). If you want to tune\r
--gapoen and see a strong effect, you should therefore consider values between 0\r
-and -1000. </span></p>\r
-\r
-<p class=flag><a name="_Toc235958589"></a><a name="_Toc102494812"></a><a\r
-name="_Toc101065278"><span style='mso-bookmark:_Toc102494812'><span\r
-style='mso-bookmark:_Toc235958589'><span lang=AF>-gapext</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-gapext=&lt;negative value&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -gapext=0</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Indicates the penalty applied for\r
-extending a gap (cf <b><u>-gapopen</u></b>)</span></p>\r
-\r
-<p class=flag><a name="_Toc235958590"></a><a name="_Toc102494813"></a><a\r
-name="_Toc101065279"><span style='mso-bookmark:_Toc102494813'><span\r
-style='mso-bookmark:_Toc235958590'><span lang=AF>-fgapopen</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Unsupported<o:p></o:p></span></p>\r
-\r
-<p class=flag><a name="_Toc235958591"></a><a name="_Toc102494814"></a><a\r
-name="_Toc101065280"><span style='mso-bookmark:_Toc102494814'><span\r
-style='mso-bookmark:_Toc235958591'><span lang=AF>-fgapext</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Unsupported<o:p></o:p></span></p>\r
-\r
-<p class=flag><a name="_Toc235958592"></a><a name="_Toc102494815"></a><a\r
-name="_Toc101065281"><span style='mso-bookmark:_Toc102494815'><span\r
-style='mso-bookmark:_Toc235958592'><span lang=AF>-cosmetic_penalty</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-cosmetic_penalty=&lt;negative value&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -cosmetic_penalty=-50</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Indicates the penalty applied for\r
-opening a gap. This penalty is set to a very low value. It will only have an\r
-influence on the portions of the alignment that are unalignable. It will not\r
-make them more correct, but only more pleasing to the eye ( i.e. Avoid\r
-stretches of lonely residues).</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>The cosmetic penalty is automatically\r
-turned off if a substitution matrix is used rather than a library.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958593"></a><a name="_Toc102494816"></a><a\r
-name="_Toc101065282"><span style='mso-bookmark:_Toc102494816'><span\r
-style='mso-bookmark:_Toc235958593'><span lang=AF>-tg_mode</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-tg_mode=&lt;0, 1, or 2&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -tg_mode=1</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>0: terminal gaps penalized with <span\r
-class=StyleflagdescriptionBoldItalicChar>-gapopen + -gapext*len<o:p></o:p></span></span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>1: terminal gaps penalized with a <span\r
-class=StyleflagdescriptionBoldItalicChar>-gapext*len<o:p></o:p></span></span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>2: terminal gaps unpenalized.</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<h3><a name="_Toc235958594"></a><a name="_Toc102494817"></a><a\r
-name="_Toc102494375"></a><a name="_Toc101065283"><span style='mso-bookmark:\r
-_Toc102494375'><span style='mso-bookmark:_Toc102494817'><span style='mso-bookmark:\r
-_Toc235958594'><span lang=EN-US>Weighting Schemes</span></span></span></span></a></h3>\r
-\r
-<p class=flag><a name="_Toc235958595"></a><a name="_Toc102494818"></a><a\r
-name="_Toc101065284"><span style='mso-bookmark:_Toc102494818'><span\r
-style='mso-bookmark:_Toc235958595'><span lang=AF>-seq_weight</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--seq_weight=&lt;t_coffee or &lt;file_name&gt;&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -seq_weight=t_coffee</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>These are the individual weights\r
-assigned to each sequence. The t_coffee weights try to compensate the bias in\r
-consistency caused by redundancy in the sequences.</span></p>\r
-\r
-<p class=Formula><span lang=EN-US><span style='mso-tab-count:1'>            </span>sim(A,B)=%similarity\r
-between A and B, between 0 and 1. </span></p>\r
-\r
-<p class=Formula><span lang=EN-US><span style='mso-tab-count:1'>            </span>weight(A)=1/sum(sim(A,X)^3)</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Weights are normalized so that their\r
-sum equals the number of sequences. They are applied onto the primary library\r
-in the following manner:</span></p>\r
-\r
-<p class=Formula><span lang=EN-US><span style='mso-tab-count:1'>            </span>res_score(Ax,By)=Min(weight(A),\r
-weight(B))*res_score(Ax, By)</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>These are very simple weights. Their\r
-main goal is to prevent a single sequence present in many copies to dominate\r
-the alignment.</span></p>\r
-\r
-<p class=Note><span lang=EN-US style='mso-ansi-language:EN-US'>Note: The\r
-library output by -out_lib is the un-weighted<span style='mso-spacerun:yes'> \r
-</span>library. <o:p></o:p></span></p>\r
-\r
-<p class=Note><span lang=EN-US style='mso-ansi-language:EN-US'>Note: Weights\r
-can be output using the -outseqweight flag.<o:p></o:p></span></p>\r
-\r
-<p class=Note><span lang=EN-US style='mso-ansi-language:EN-US'>Note: You can\r
-use your own weights (see the format section). <o:p></o:p></span></p>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<h3><a name="_Toc235958596"></a><a name="_Toc102494819"></a><a\r
-name="_Toc102494376"></a><a name="_Toc101065285"><span style='mso-bookmark:\r
-_Toc102494376'><span style='mso-bookmark:_Toc102494819'><span style='mso-bookmark:\r
-_Toc235958596'><span lang=EN-US>Multiple Alignment Computation</span></span></span></span></a></h3>\r
-\r
-<p class=flag><a name="_Toc235958597"></a><a name="_Toc102494820"></a><a\r
-name="_Toc101065286"><span style='mso-bookmark:_Toc102494820'><span\r
-style='mso-bookmark:_Toc235958597'><span lang=AF>-msa_mode</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--msa_mode=&lt;tree,graph,precomputed&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -evaluate_mode=tree</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Unsupported</span></p>\r
-\r
-<p class=flag><a name="_Toc102494821"></a><a name="_Toc101065287"></a><a\r
-name="_Toc235958598"><span style='mso-bookmark:_Toc101065287'><span\r
-style='mso-bookmark:_Toc102494821'><span lang=AF>-one2all</span></span></span></a><span\r
-style='mso-bookmark:_Toc101065287'><span style='mso-bookmark:_Toc102494821'></span></span></p>\r
-\r
-<p class=flagusage><span style='mso-bookmark:_Toc101065287'><span\r
-style='mso-bookmark:_Toc102494821'><span lang=EN-US style='mso-ansi-language:\r
-EN-US'>Usage: -one2all=&lt;name&gt;<o:p></o:p></span></span></span></p>\r
-\r
-<p class=instruction><span style='mso-bookmark:_Toc101065287'><span\r
-style='mso-bookmark:_Toc102494821'><span lang=EN-US>Default: not used</span></span></span></p>\r
-\r
-<p class=flagdescription><span style='mso-bookmark:_Toc101065287'><span\r
-style='mso-bookmark:_Toc102494821'><span lang=EN-US>Will generate a one to all\r
-library with respect to the specified sequence and will then align all the\r
-sequences in turn to that sequence, in a sequence determined by the order in\r
-which the sequences were provided.<span style='mso-spacerun:yes'>  </span></span></span></span></p>\r
-\r
-<p class=flagdescription><span style='mso-bookmark:_Toc101065287'><span\r
-style='mso-bookmark:_Toc102494821'><b style='mso-bidi-font-weight:normal'><span\r
-lang=EN-US>\96profile_comparison =profile</span></b><span lang=EN-US>, the MSAs\r
-provided via \96profile are vectorized and the function specified by\r
-\96profile_comparison is used to make profile profile alignments. In that case,\r
-the complexity is NL^2</span></span></span></p>\r
-\r
-<p class=flag><span style='mso-bookmark:_Toc101065287'><span style='mso-bookmark:\r
-_Toc102494821'><a name="_Toc235958599"><span lang=AF>-profile</span></a></span></span><span\r
-style='mso-bookmark:_Toc235958599'><span lang=AF>_comparison</span></span></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--profile_mode=&lt;fullN,profile&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -profile_mode=full50</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>The profile mode flag controls the\r
-multiple profile alignments in T-Coffee. There are two instances where t_coffee\r
-can make multiple profile alignments:</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>1-When N, the number of sequences is\r
-higher than <b style='mso-bidi-font-weight:normal'>\96maxnseq, </b>the program\r
-switches to its multiple profile alignment mode (t_coffee_dpa).</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>2-When MSAs are provided via the <b\r
-style='mso-bidi-font-weight:normal'>\96profile</b> flag or via <b\r
-style='mso-bidi-font-weight:normal'>\96profile1</b> and <b style='mso-bidi-font-weight:\r
-normal'>\96profile2</b>. </span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>In these situations, the\r
-\96profile_mode value influences the alignment computation, these values are:</span></p>\r
-\r
-<p class=flagdescription><b style='mso-bidi-font-weight:normal'><span\r
-lang=EN-US>\96profile_comparison =profile</span></b><span lang=EN-US>, the MSAs\r
-provided via \96profile are vectorized and the function specified by\r
-\96profile_comparison is used to make profile profile alignments. In that case,\r
-the complexity is NL^2</span></p>\r
-\r
-<p class=flagdescription><span class=ListChar><b style='mso-bidi-font-weight:\r
-normal'><span lang=EN-US style='font-size:12.0pt;mso-bidi-font-size:10.0pt'>-profile_comparison=fullN</span></b></span><span\r
-lang=EN-US>, N is an integer value that can omitted. <i style='mso-bidi-font-style:\r
-normal'>Full</i> indicates that given two profiles, the alignment will be based\r
-on a library that includes every possible pair of sequences between the two\r
-profiles. If N is set, then the library will be restricted to the N most\r
-similar pairs of sequences between the two profiles, as judged from a measure\r
-made on a pairwise alignment of these two profiles.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958600"></a><a name="_Toc102494822"></a><a\r
-name="_Toc101065288"><span style='mso-bookmark:_Toc102494822'><span\r
-style='mso-bookmark:_Toc235958600'><span lang=AF>-profile_</span></span></span></a><span\r
-style='mso-bookmark:_Toc235958600'><span lang=AF>mode</span></span></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--profile_mode=&lt;cw_profile_profile, muscle_profile_profile, multi_channel&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -profile_mode=cw_profile_profile</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>When <b style='mso-bidi-font-weight:\r
-normal'>\96profile_comparison=profile</b>, this flag selects a profile scoring\r
-function.</span></p>\r
-\r
-<h3><a name="_Toc235958601"></a><a name="_Toc102494823"></a><a\r
-name="_Toc102494377"></a><a name="_Toc101065289"><span style='mso-bookmark:\r
-_Toc102494377'><span style='mso-bookmark:_Toc102494823'><span style='mso-bookmark:\r
-_Toc235958601'><span lang=EN-US>Alignment Post-Processing</span></span></span></span></a></h3>\r
-\r
-<p class=flag><a name="_Toc235958602"></a><a name="_Toc102494824"></a><a\r
-name="_Toc101065290"><span style='mso-bookmark:_Toc102494824'><span\r
-style='mso-bookmark:_Toc235958602'><span lang=AF>-clean_aln</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-clean_aln<span style='mso-spacerun:yes'> \r
-</span><o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default:-clean_aln</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>This flag causes T-Coffee to\r
-post-process the multiple alignment. Residues that have a reliability score\r
-smaller or equal to -clean_threshold (as given by an evaluation that uses\r
--clean_evaluate_mode)<span style='mso-spacerun:yes'>  </span>are realigned to\r
-the rest of the alignment. Residues with a score higher than the threshold\r
-constitute a rigid framework that cannot be altered.</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>The cleaning algorithm is greedy. It\r
-starts from the top left segment of low constituency residues and works its way\r
-left to right, top to bottom along the alignment. You can require this\r
-operation to be carried out for several cycles using the -clean_iterations\r
-flag.</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>The rationale behind this operation\r
-is mostly cosmetic. In order to ensure a decent looking alignment, the gop is\r
-set to -20 and the gep to -1. There is no penalty for terminal gaps, and the\r
-matrix is blosum62mt.</span></p>\r
-\r
-<p class=Note><span lang=EN-US style='mso-ansi-language:EN-US'>Note: Gaps are\r
-always considered to have a reliability score of 0.<o:p></o:p></span></p>\r
-\r
-<p class=Note><span class=WarningChar><span lang=EN-US>Note: The use of the\r
-cleaning option can result in memory overflow when aligning large</span></span><span\r
-lang=EN-US style='mso-ansi-language:EN-US'> </span><span class=WarningChar><span\r
-lang=EN-US>sequences,<o:p></o:p></span></span></p>\r
-\r
-<p class=flag><a name="_Toc235958603"></a><a name="_Toc102494825"></a><a\r
-name="_Toc101065291"><span style='mso-bookmark:_Toc102494825'><span\r
-style='mso-bookmark:_Toc235958603'><span lang=AF>-clean_threshold</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-clean_threshold=&lt;0-9&gt;<span\r
-style='mso-spacerun:yes'>  </span><o:p></o:p></span></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Default:-clean_aln=1<o:p></o:p></span></p>\r
-\r
-<p class=MyNormal><span lang=AF>See -clean_aln for details.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958604"></a><a name="_Toc102494826"></a><a\r
-name="_Toc101065292"><span style='mso-bookmark:_Toc102494826'><span\r
-style='mso-bookmark:_Toc235958604'><span lang=AF>-clean_iteration</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-clean_iteration=&lt;value between 1 and\r
-&gt;<span style='mso-spacerun:yes'>  </span><o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default:-clean_iteration=1</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>See -clean_aln for details.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958605"></a><a name="_Toc102494827"></a><a\r
-name="_Toc101065293"><span style='mso-bookmark:_Toc102494827'><span\r
-style='mso-bookmark:_Toc235958605'><span lang=AF>-clean_evaluation_mode</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-clean_iteration=&lt;evaluation_mode\r
-&gt;<span style='mso-spacerun:yes'>  </span><o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default:-clean_iteration=t_coffee_non_extended</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Indicates the mode used for the\r
-evaluation that will indicate the segments that should be realigned. See\r
--evaluation_mode for the list of accepted modes.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958606"></a><a name="_Toc102494828"></a><a\r
-name="_Toc101065294"><span style='mso-bookmark:_Toc102494828'><span\r
-style='mso-bookmark:_Toc235958606'><span lang=AF>-iterate</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--iterate=&lt;integer&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -iterate=0</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Sequences are extracted in turn and\r
-realigned to the MSA. If iterate is set to -1, each sequence is realigned,\r
-otherwise the number of iterations is set by \96iterate.</span></p>\r
-\r
-<h2><a name="_Toc235958607"></a><a name="_Toc102494829"></a><a\r
-name="_Toc102494378"></a><a name="_Toc101065295"><span style='mso-bookmark:\r
-_Toc102494378'><span style='mso-bookmark:_Toc102494829'><span style='mso-bookmark:\r
-_Toc235958607'><span lang=EN-US>CPU Control</span></span></span></span></a></h2>\r
-\r
-<h3><a name="_Toc235958608"></a><a name="_Toc102494830"></a><a\r
-name="_Toc102494379"></a><a name="_Toc101065296"><span style='mso-bookmark:\r
-_Toc102494379'><span style='mso-bookmark:_Toc102494830'><span style='mso-bookmark:\r
-_Toc235958608'><span lang=EN-US>Multithreading</span></span></span></span></a></h3>\r
-\r
-<p class=flag><a name="_Toc235958609"></a><a name="_Toc102494831"></a><a\r
-name="_Toc101065297"><span style='mso-bookmark:_Toc102494831'><span\r
-style='mso-bookmark:_Toc235958609'><span lang=AF>-multi_core </span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-multi_core=</span> templates_jobs_relax_msa<span\r
-lang=EN-US style='mso-ansi-language:EN-US'><o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: 0</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Specifies that the steps of T-Coffee\r
-that should be multi threaded. by default all relevant steps are.</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee sample_seq2.fasta -multi_core jobs</span></p>\r
-\r
-</div>\r
-\r
-<p class=flag><a name="_Toc235958610"></a><a name="_Toc102494832"></a><a\r
-name="_Toc102494380"></a><a name="_Toc101065298"><span style='mso-bookmark:\r
-_Toc102494380'><span style='mso-bookmark:_Toc102494832'><span style='mso-bookmark:\r
-_Toc235958610'><span lang=AF>-n_core </span></span></span></span></a></p>\r
-\r
-<p class=flagusage><span style='mso-bookmark:_Toc101065298'><span\r
-style='mso-bookmark:_Toc102494380'><span style='mso-bookmark:_Toc102494832'><span\r
-style='mso-bookmark:_Toc235958610'><span lang=EN-US style='mso-ansi-language:\r
-EN-US'>Usage:<span style='mso-spacerun:yes'>  </span>-n_core=</span><span\r
-lang=EN-US> </span>&lt;number of cores&gt;</span></span></span></span><span\r
-style='mso-bookmark:_Toc101065298'><span style='mso-bookmark:_Toc102494380'><span\r
-style='mso-bookmark:_Toc102494832'><span style='mso-bookmark:_Toc235958610'><span\r
-lang=EN-US style='mso-ansi-language:EN-US'><o:p></o:p></span></span></span></span></span></p>\r
-\r
-<p class=instruction><span style='mso-bookmark:_Toc101065298'><span\r
-style='mso-bookmark:_Toc102494380'><span style='mso-bookmark:_Toc102494832'><span\r
-style='mso-bookmark:_Toc235958610'><span lang=EN-US>Default: 0</span></span></span></span></span></p>\r
-\r
-<p class=flagdescription><span style='mso-bookmark:_Toc101065298'><span\r
-style='mso-bookmark:_Toc102494380'><span style='mso-bookmark:_Toc102494832'><span\r
-style='mso-bookmark:_Toc235958610'><span lang=EN-US>Default indicates that all\r
-cores will be used, as indicated by the environment via:</span></span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065298'><span style='mso-bookmark:_Toc102494380'><span\r
-style='mso-bookmark:_Toc102494832'><span style='mso-bookmark:_Toc235958610'><span\r
-lang=EN-US>PROMPT: t_coffee sample_seq2.fasta -multi_core jobs</span></span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065298'><span style='mso-bookmark:_Toc102494380'><span\r
-style='mso-bookmark:_Toc102494832'><span style='mso-bookmark:_Toc235958610'><span\r
-lang=EN-US><o:p>&nbsp;</o:p></span></span></span></span></span></h3>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065298'><span style='mso-bookmark:_Toc102494380'><span\r
-style='mso-bookmark:_Toc102494832'><span style='mso-bookmark:_Toc235958610'><span\r
-lang=EN-US>Limits</span></span></span></span></span></h3>\r
-\r
-<p class=flag><a name="_Toc235958611"></a><a name="_Toc102494833"></a><a\r
-name="_Toc101065299"><span style='mso-bookmark:_Toc102494833'><span\r
-style='mso-bookmark:_Toc235958611'><span lang=AF>-mem_mode</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>deprecated</span><span lang=EN-US\r
-style='mso-ansi-language:EN-US;mso-bidi-font-weight:bold'><o:p></o:p></span></p>\r
-\r
-<p class=flag><a name="_Toc235958612"></a><a name="_Toc102494834"></a><a\r
-name="_Toc101065300"><span style='mso-bookmark:_Toc102494834'><span\r
-style='mso-bookmark:_Toc235958612'><span lang=AF>-ulimit</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-ulimit=&lt;value&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -ulimit=0</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Specifies the upper limit of memory\r
-usage (in Megabytes). Processes exceeding this limit will automatically exit. A\r
-value 0 indicates that no limit applies.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958613"></a><a name="_Toc102494835"></a><a\r
-name="_Toc101065301"><span style='mso-bookmark:_Toc102494835'><span\r
-style='mso-bookmark:_Toc235958613'><span lang=AF>-maxlen</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-maxlen=&lt;value, 0=nolimit&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -maxlen=1000</span><span\r
-lang=EN-US style='mso-bidi-font-weight:bold'><o:p></o:p></span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Indicates the maximum length of the\r
-sequences. <a name="_Toc101065302"></a></span></p>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065302'><a name="_Toc235958614"></a><a\r
-name="_Toc102494836"></a><a name="_Toc102494381"><span style='mso-bookmark:\r
-_Toc102494836'><span style='mso-bookmark:_Toc235958614'><span lang=EN-US>Aligning\r
-more than 100 sequences with DPA</span></span></span></a></span></h3>\r
-\r
-<p class=flag><a name="_Toc235958615"></a><a name="_Toc102494837"></a><a\r
-name="_Toc101065303"><span style='mso-bookmark:_Toc102494837'><span\r
-style='mso-bookmark:_Toc235958615'><span lang=AF>-maxnseq</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-maxnseq=&lt;value, 0=nolimit&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -maxnseq=50</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Indicates the maximum number of\r
-sequences before triggering the use of t_coffee_dpa.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958616"></a><a name="_Toc102494838"></a><a\r
-name="_Toc101065304"><span style='mso-bookmark:_Toc102494838'><span\r
-style='mso-bookmark:_Toc235958616'><span lang=AF>-dpa_master_aln</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--dpa_master_aln=&lt;File, method&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -dpa_master_aln=NO</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>When using dpa, t_coffee needs a seed\r
-alignment that can be computed using any appropriate method. By default,\r
-t_coffee computes a fast approximate alignment.</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>A pre-alignment can be provided\r
-through this flag, as well as any program using the following syntax:</span></p>\r
-\r
-<p class=example2><span lang=EN-US>your_script \96in &lt;fasta_file&gt; -out\r
-&lt;file_name&gt;</span></p>\r
-\r
-<p class=flag><a name="_Toc235958617"></a><a name="_Toc102494839"></a><a\r
-name="_Toc101065305"><span style='mso-bookmark:_Toc102494839'><span\r
-style='mso-bookmark:_Toc235958617'><span lang=AF>-dpa_maxnseq</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--dpa_maxnseq=&lt;integer value&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -dpa_maxnseq=30</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Maximum number of sequences aligned\r
-simultaneously when DPA is ran. Given the tree computed from the master\r
-alignment, a node is sent to computation if it controls more than <b\r
-style='mso-bidi-font-weight:normal'>\96dpa_maxnseq</b> OR if it controls a pair\r
-of sequences having less than <b style='mso-bidi-font-weight:normal'>\96dpa_min_score2</b>\r
-percent ID.<a name="_Toc101065306"></a></span></p>\r
-\r
-<p class=flag><span style='mso-bookmark:_Toc101065306'><a name="_Toc235958618"></a><a\r
-name="_Toc102494840"><span style='mso-bookmark:_Toc235958618'><span lang=AF>-dpa_min_score1</span></span></a></span></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--dpa_min_score1=&lt;integer value&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -dpa_min_score1=95</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Threshold for not realigning the\r
-sequences within the master alignment. Given this alignment and the associated\r
-tree, sequences below a node are not realigned if none of them has less than<b\r
-style='mso-bidi-font-weight:normal'> \96dpa_min_score1</b> % identity.<a\r
-name="_Toc101065307"></a></span></p>\r
-\r
-<p class=flag><span style='mso-bookmark:_Toc101065307'><a name="_Toc235958619"></a><a\r
-name="_Toc102494841"><span style='mso-bookmark:_Toc235958619'><span lang=AF>-dpa_min_score2</span></span></a></span></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--dpa_min_score2<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -dpa_min_score2</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Maximum number of sequences aligned\r
-simultaneously when DPA is ran. Given the tree computed from the master\r
-alignment, a node is sent to computation if it controls more than <b\r
-style='mso-bidi-font-weight:normal'>\96dpa_maxnseq</b> OR if it controls a pair\r
-of sequences having less than <b style='mso-bidi-font-weight:normal'>\96dpa_min_score2</b>\r
-percent ID.<a name="_Toc101065308"></a></span></p>\r
-\r
-<p class=flag><span style='mso-bookmark:_Toc101065308'><a name="_Toc235958620"></a><a\r
-name="_Toc102494842"><span style='mso-bookmark:_Toc235958620'><span lang=AF>-dap_tree\r
-[NOT IMPLEMENTED]</span></span></a></span></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-dpa_tree=&lt;filename&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -unset</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Guide tree used in DPA. This is a\r
-newick tree where the distance associated with each node is set to the minimum\r
-pairwise distance among all considered sequences.</span></p>\r
-\r
-<h2><a name="_Toc235958621"></a><a name="_Toc102494843"></a><a\r
-name="_Toc102494382"></a><a name="_Toc101065309"><span style='mso-bookmark:\r
-_Toc102494382'><span style='mso-bookmark:_Toc102494843'><span style='mso-bookmark:\r
-_Toc235958621'><span lang=EN-US>Using Structures</span></span></span></span></a><a\r
-name="_Toc101065310"></a></h2>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065310'><a name="_Toc235958622"></a><a\r
-name="_Toc102494844"></a><a name="_Toc102494383"><span style='mso-bookmark:\r
-_Toc102494844'><span style='mso-bookmark:_Toc235958622'><span lang=EN-US>Generic</span></span></span></a></span></h3>\r
-\r
-<p class=flag><a name="_Toc235958623"><span lang=AF>-mode</span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage: -mode=3dcoffee<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: turned off</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Runs t_coffee with the 3dcoffee mode\r
-(cf next section).</span></p>\r
-\r
-<p class=flag><a name="_Toc235958624"></a><a name="_Toc102494846"></a><a\r
-name="_Toc101065312"><span style='mso-bookmark:_Toc102494846'><span\r
-style='mso-bookmark:_Toc235958624'><span lang=AF>-check_pdb_status</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--check_pdb_status<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: turned off</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Forces t_coffee to run\r
-extract_from_pdb to check the pdb status of each sequence. This can\r
-considerably slow down the program.</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<h3><a name="_Toc235958625"></a><a name="_Toc102494847"></a><a\r
-name="_Toc102494384"></a><a name="_Toc101065313"><span style='mso-bookmark:\r
-_Toc102494384'><span style='mso-bookmark:_Toc102494847'><span style='mso-bookmark:\r
-_Toc235958625'><span lang=EN-US>3D Coffee: Using SAP</span></span></span></span></a></h3>\r
-\r
-<p class=flagdescription><span lang=EN-US>It is possible to use t_coffee to\r
-compute multiple structural alignments. To do so, ensure that you have the sap\r
-program installed.</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee \96pdb=struc1.pdb,struc2.pdb,struc3.pdb -method sap_pair</span></p>\r
-\r
-</div>\r
-\r
-<p class=flagdescription><span lang=EN-US>Will combine the pairwise alignments\r
-produced by SAP.<span style='mso-spacerun:yes'>  </span>There are currently\r
-four methods that can be interfaced with t_coffee:</span></p>\r
-\r
-<p class=flagdescription style='text-indent:28.25pt'><span lang=EN-US>sap_pair:\r
-that uses the sap algorithm</span></p>\r
-\r
-<p class=flagdescription style='text-indent:28.25pt'><span lang=EN-US>align_pdb:\r
-uses a t_coffee implementation of sap, not as accurate.</span></p>\r
-\r
-<p class=flagdescription style='text-indent:28.25pt'><span lang=EN-US>tmaliagn_pair\r
-(http://zhang.bioinformatics.ku.edu/TM-align/)</span></p>\r
-\r
-<p class=flagdescription style='text-indent:28.25pt'><span lang=EN-US>mustang_pair\r
-(http://www.cs.mu.oz.au/~arun/mustang)</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>When providing a PDB file, the\r
-computation is only carried out on the first chain of this file. If your\r
-original file contains several chain, you should extract the chain you want to\r
-work on. You can use <b style='mso-bidi-font-weight:normal'>t_coffee \96other_pg\r
-extract_from_pdb </b>or any pdb handling program.</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>If you are working with public PDB\r
-files, you can use the PDB identifier and specify the chain by adding its index\r
-to the identifier (i.e. 1pdbC). If your structure is an NMR structure, you are\r
-advised to provide the program with one structure only.</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>If you wish to align only a portion\r
-of the structure, you should extract it yourself from the pdb file, using <b\r
-style='mso-bidi-font-weight:normal'>t_coffee \96other_pg extract_from_pdb </b>or\r
-any pdb handling program.</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>You can provide t_coffee with a\r
-mixture of sequences and structure. In this case, you should use the special\r
-mode:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee \96mode 3dcoffee \96seq 3d_sample3.fasta -template_file\r
-template_file.template</span></p>\r
-\r
-</div>\r
-\r
-<h3><a name="_Toc235958626"></a><a name="_Toc102494848"></a><a\r
-name="_Toc102494385"></a><a name="_Toc101065314"><span style='mso-bookmark:\r
-_Toc102494385'><span style='mso-bookmark:_Toc102494848'><span style='mso-bookmark:\r
-_Toc235958626'><span lang=EN-US>Using/finding PDB templates for the Sequences</span></span></span></span></a></h3>\r
-\r
-<p class=flag><a name="_Toc235958627"></a><a name="_Toc102494849"></a><a\r
-name="_Toc101065315"><span style='mso-bookmark:_Toc102494849'><span\r
-style='mso-bookmark:_Toc235958627'><span lang=AF>-template_file</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US;mso-bidi-font-weight:\r
-bold'>Usage</span><span lang=EN-US style='mso-ansi-language:EN-US'>:\r
--template_file =<o:p></o:p></span></p>\r
-\r
-<p class=flagusage style='text-indent:28.25pt'><span lang=EN-US\r
-style='mso-ansi-language:EN-US'>&lt;filename, <o:p></o:p></span></p>\r
-\r
-<p class=flagusage style='margin-left:77.95pt'><span lang=EN-US\r
-style='mso-ansi-language:EN-US'>SCRIPT_scriptame, <o:p></o:p></span></p>\r
-\r
-<p class=flagusage style='margin-left:77.95pt'><span lang=EN-US\r
-style='mso-ansi-language:EN-US'>SELF_TAG <o:p></o:p></span></p>\r
-\r
-<p class=flagusage style='margin-left:77.95pt'><span lang=EN-US\r
-style='mso-ansi-language:EN-US'>SEQFILE_TAG_filename,<o:p></o:p></span></p>\r
-\r
-<p class=flagusage style='margin-left:77.95pt'><span lang=EN-US\r
-style='mso-ansi-language:EN-US'>no&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: no</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>This flag instructs t_coffee on the\r
-templates that will be used when combining several types of information. For\r
-instance, when using structural information, this file will indicate the\r
-structural template that corresponds to your sequences. The identifier T\r
-indicates that the file should be a FASTA like file, formatted as follows.\r
-There are several ways to pass the templates:</span></p>\r
-\r
-<p class=flagheading2><span lang=EN-US>Predefined Modes</span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>EXPRESSO: will use the EBI server to find\r
-_P_ templates</span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>PSIBLAST: will use the EBI sever to find\r
-profiles </span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=flagheading2><span lang=EN-US>File name</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>This file contains the\r
-sequence/template association it uses a FASTA-like format, as follows:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span lang=EN-US>&gt;&lt;sequence name&gt; _P_\r
-&lt;pdb template&gt;</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>&gt;&lt;sequence name&gt; _G_\r
-&lt;gene template&gt;</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>&gt;&lt;sequence name&gt; _R_\r
-&lt;MSA template&gt;</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>&gt;&lt;sequence name&gt; _F_\r
-&lt;RNA Secondary Structure&gt;</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>&gt;&lt;sequence name&gt; _T_\r
-&lt;Transmembrane Secondary Structure&gt;</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>&gt;&lt;sequence name&gt; _E_\r
-&lt;Protein Secondary Structure&gt;</span></p>\r
-\r
-<p class=examplefileCxSpLast><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-</div>\r
-\r
-<p class=flagdescription><span lang=EN-US>Each template will be used in place\r
-of the sequence with the appropriate method. For instance, structural templates\r
-will be aligned with sap_pair and the information thus generated will be\r
-transferred onto the alignment.</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Note the following rule:</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'>            </span>-Each\r
-sequence can have one template of each type (structural, genomics\85)</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'>            </span>-Each\r
-sequence can only have one template of a given type</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'>            </span>-Several\r
-sequences can share the same template</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'>            </span>-All\r
-the sequences do not need to have a template</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>The type of template on which a\r
-method works is declared with the SEQ_TYPE parameter in the method\r
-configuration file:</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'>            </span>SEQ_TYPE<span\r
-style='mso-tab-count:1'>          </span>S: a method that uses sequences </span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'>            </span>SEQ_TYPE<span\r
-style='mso-tab-count:1'>          </span>PS: a pairwise method that aligns\r
-sequences and structures</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'>            </span>SEQ_TYPE<span\r
-style='mso-tab-count:1'>          </span>P: a method that aligns structures\r
-(sap for instance)</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>There are 4 tags identifying the\r
-template type:</span></p>\r
-\r
-<p class=flagdescription style='text-indent:28.25pt'><span lang=EN-US>_P_<span\r
-style='mso-tab-count:1'>         </span>Structural templates: a pdb identifier\r
-OR a pdb file</span></p>\r
-\r
-<p class=flagdescription style='margin-left:106.2pt;text-indent:-35.4pt'><span\r
-lang=EN-US>_G_<span style='mso-tab-count:1'>        </span>Genomic templates: a\r
-protein sequence where boundary amino-acid have been recoded with ( o:0, i:1,\r
-j:2)</span></p>\r
-\r
-<p class=flagdescription style='text-indent:28.25pt'><span lang=EN-US>_R_<span\r
-style='mso-tab-count:1'>        </span>Profile Templates: a file containing a\r
-multiple sequence alignment</span></p>\r
-\r
-<p class=flagdescription style='text-indent:28.25pt'><span lang=EN-US>_F_<span\r
-style='mso-tab-count:1'>         </span>RNA secondary Structures</span></p>\r
-\r
-<p class=flagdescription style='text-indent:28.25pt'><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>More than one template file can be\r
-provided. There is no need to have one template for every sequence in the\r
-dataset. </span></p>\r
-\r
-<p class=flagdescription style='text-indent:28.25pt'><span lang=EN-US>_P_, _G_,\r
-and _R_ are known as <b style='mso-bidi-font-weight:normal'>template TAGS<o:p></o:p></b></span></p>\r
-\r
-<p class=flagheading2><span lang=EN-US>2-SCRIPT_&lt;scriptname&gt;</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Indicates that filename is a script\r
-that will be used to generate a valid template file. The script will run on a\r
-file containing all your sequences using the following syntax:</span></p>\r
-\r
-<p class=example2><span lang=EN-US>scriptname \96infile=&lt;your sequences&gt;\r
--outfile=&lt;template_file&gt;</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>It is also possible to pass some\r
-parameters, use @ as a separator and # in place of the = sign. For instance, if\r
-you want to call the a script named blast.pl with the foloowing parameters;</span></p>\r
-\r
-<p class=example2><span lang=EN-US>blast.pl -db=pdb -dir=/local/test</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Use</span></p>\r
-\r
-<p class=example2><span lang=EN-US>SCRIPT_blast.pl@db#pdb@dir#/local/test</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Bear in mind that the input output\r
-flags will then be concatenated to this command line so that t_coffee ends up\r
-calling the program using the following system call:</span></p>\r
-\r
-<p class=example2><span lang=EN-US>blast.pl -db=pdb -dir=/local/test\r
--infile=&lt;some tmp file&gt; -outfile=&lt;another tmp file&gt;</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=flagheading2><span lang=EN-US>3-SELF_TAG</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>TAG can take the value of any of the known\r
-TAGS (_S_, _G_, _P_). SELF indicates that the original name of the sequence\r
-will be used to fetch the template: </span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee 3d_sample2.fasta \96template_file SELF_P_</span></p>\r
-\r
-</div>\r
-\r
-<p class=flagdescription><span lang=EN-US>The previous command will work\r
-because the sequences in 3d_sample3 are named </span></p>\r
-\r
-<p class=flagheading2><span lang=EN-US>4-SEQFILE_TAG_filename</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Use this flag if your templates are\r
-in filename, and are named according to the sequences. For instance, if your\r
-protein sequences have been recoded with Exon/Intron information, you should\r
-have the recoded sequences names according to the original:</span></p>\r
-\r
-<p class=example2><span lang=EN-US>SEQFILE_G_recodedprotein.fasta<span\r
-style='mso-tab-count:1'>  </span></span></p>\r
-\r
-<p class=flag><a name="_Toc235958628"></a><a name="_Toc102494850"></a><a\r
-name="_Toc101065316"><span style='mso-bookmark:_Toc102494850'><span\r
-style='mso-bookmark:_Toc235958628'><span lang=AF>-struc_to_use</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--struc_to_use=&lt;struc1, struc2\85&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -struc_to_use=NULL</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Restricts the 3Dcoffee to a set of\r
-pre-defined structures.</span></p>\r
-\r
-<h2><a name="_Toc235958629"></a><a name="_Toc102494851"></a><a\r
-name="_Toc102494386"></a><a name="_Toc101065317"><span style='mso-bookmark:\r
-_Toc102494386'><span style='mso-bookmark:_Toc102494851'><span style='mso-bookmark:\r
-_Toc235958629'><span lang=EN-US>Multiple Local Alignments</span></span></span></span></a></h2>\r
-\r
-<p class=MyNormal><span lang=AF>It is possible to compute multiple local alignments,\r
-using the moca routine. MOCA is a routine that allows extracting all the local\r
-alignments that show some similarity with another predefined fragment.</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>'mocca' is a perl script that calls t-coffee\r
-and provides it with the appropriate parameters.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958630"></a><a name="_Toc102494852"></a><a\r
-name="_Toc101065318"><span style='mso-bookmark:_Toc102494852'><span\r
-style='mso-bookmark:_Toc235958630'><span lang=AF>-domain</span></span></span></a><span\r
-style='mso-bookmark:_Toc102494852'><span style='mso-bookmark:_Toc235958630'><span\r
-lang=AF>/-mocca</span></span></span></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--domain<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: not set</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>This flag indicates that t_coffee\r
-will run using the domain mode. All the sequences will be concatenated, and the\r
-resulting sequence will be compared to itself using lalign_rs_s_pair mode\r
-(lalign of the sequence against itself using keeping the lalign raw score).\r
-This step is the most computer intensive, and it is advisable to save the\r
-resulting file.</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee -in Ssample_seq1.fasta,Mlalign_rs_s_pair\r
--out_lib=sample_lib1.mocca_lib -domain -start=100 -len=50 </span></p>\r
-\r
-</div>\r
-\r
-<p class=flagdescription><span lang=EN-US>This instruction will use the\r
-fragment 100-150 on the concatenated sequences, as a template for the extracted\r
-repeats. The extraction will only be made once. The library will be placed in\r
-the file &lt;lib name&gt;.</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>If you want, you can test other\r
-coordinates for the repeat, such as </span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee -in sample_lib1.mocca_lib -domain -start=100 -len=60 </span></p>\r
-\r
-</div>\r
-\r
-<p class=flagdescription><span lang=EN-US>This run will use the fragment\r
-100-160, and will be much faster because it does not need to re-compute the\r
-lalign library. </span></p>\r
-\r
-<p class=flag><a name="_Toc235958631"></a><a name="_Toc102494853"></a><a\r
-name="_Toc101065319"><span style='mso-bookmark:_Toc102494853'><span\r
-style='mso-bookmark:_Toc235958631'><span lang=AF>-start</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--start=&lt;int value&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: not set</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>This flag indicates the starting\r
-position of the portion of sequence that will be used as a template for the\r
-repeat extraction. The value assumes that all the sequences have been\r
-concatenated, and is given on the resulting sequence.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958632"></a><a name="_Toc102494854"></a><a\r
-name="_Toc101065320"><span style='mso-bookmark:_Toc102494854'><span\r
-style='mso-bookmark:_Toc235958632'><span lang=AF>-len</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--len=&lt;int value&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: not set</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>This flag indicates the length of the\r
-portion of sequence that will be used as a template.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958633"></a><a name="_Toc102494855"></a><a\r
-name="_Toc101065321"><span style='mso-bookmark:_Toc102494855'><span\r
-style='mso-bookmark:_Toc235958633'><span lang=AF>-scale</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--scale=&lt;int value&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -scale=-100</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>This flag indicates the value of the\r
-threshold for extracting the repeats. The actual threshold is equal to:</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'>            </span>motif_len*scale</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Increase the scale </span><span\r
-lang=EN-US style='font-family:Wingdings;mso-ascii-font-family:"Times New Roman";\r
-mso-hansi-font-family:"Times New Roman";mso-char-type:symbol;mso-symbol-font-family:\r
-Wingdings'><span style='mso-char-type:symbol;mso-symbol-font-family:Wingdings'>ó</span></span><span\r
-lang=EN-US>Increase sensitivity </span><span lang=EN-US style='font-family:\r
-Wingdings;mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman";\r
-mso-char-type:symbol;mso-symbol-font-family:Wingdings'><span style='mso-char-type:\r
-symbol;mso-symbol-font-family:Wingdings'>ó</span></span><span lang=EN-US> More\r
-alignments( i.e. -50).</span></p>\r
-\r
-<p class=flag><a name="_Toc235958634"></a><a name="_Toc102494856"></a><a\r
-name="_Toc101065322"><span style='mso-bookmark:_Toc102494856'><span\r
-style='mso-bookmark:_Toc235958634'><span lang=AF>-domain_interactive [Examples]</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--domain_interactive<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: unset</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Launches an interactive mocca\r
-session.</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee -in Lsample_lib3.tc_lib,Mlalign_rs_s_pair -domain -start=100 -len=60</span></p>\r
-\r
-</div>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6;margin-left:0mm;margin-right:10.0mm'>\r
-\r
-<p class=examplefilesmallCxSpFirst><span lang=EN-US>TOLB_ECOLI_212_26<span\r
-style='mso-tab-count:3'>                 </span><span\r
-style='mso-spacerun:yes'>    </span>211 SKLAYVTFESGR--SALVIQTLANGAVRQV-ASFPRHNGAPAFSPDGSKLAFA</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US>TOLB_ECOLI_165_218<span\r
-style='mso-spacerun:yes'>    </span>164 TRIAYVVQTNGGQFPYELRVSDYDGYNQFVVHRSPQPLMSPAWSPDGSKLAYV</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US>TOLB_ECOLI_256_306<span\r
-style='mso-spacerun:yes'>    </span>255 SKLAFALSKTGS--LNLYVMDLASGQIRQV-TDGRSNNTEPTWFPDSQNLAFT</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US>TOLB_ECOLI_307_350<span\r
-style='mso-spacerun:yes'>    </span>306 -------DQAGR--PQVYKVNINGGAPQRI-TWEGSQNQDADVSSDGKFMVMV</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US>TOLB_ECOLI_351_393<span\r
-style='mso-spacerun:yes'>    </span>350 -------SNGGQ--QHIAKQDLATGGV-QV-LSSTFLDETPSLAPNGTMVIYS<span\r
-style='mso-spacerun:yes'>  </span></span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><span\r
-style='mso-spacerun:yes'>                        </span>1<span\r
-style='mso-spacerun:yes'>           </span>*<span\r
-style='mso-spacerun:yes'>        </span><span\r
-style='mso-spacerun:yes'>     </span>*<span style='mso-spacerun:yes'>   \r
-</span>:<span style='mso-spacerun:yes'>     </span><span\r
-style='mso-spacerun:yes'>     </span>.<span style='mso-spacerun:yes'>  \r
-</span>.:.<span style='mso-spacerun:yes'>  </span>:<span\r
-style='mso-spacerun:yes'>    </span></span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><span\r
-style='mso-spacerun:yes'>        </span>MENU: Type Letter Flag[number] and\r
-Return: ex |10</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><span\r
-style='mso-spacerun:yes'>        </span>|x<span style='mso-spacerun:yes'>     \r
-</span>--&gt;Set<span style='mso-spacerun:yes'>     </span>the START to x</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><span\r
-style='mso-spacerun:yes'>        </span>&gt;x<span\r
-style='mso-spacerun:yes'>      </span>--&gt;Set<span\r
-style='mso-spacerun:yes'>     </span>the LEN<span style='mso-spacerun:yes'>  \r
-</span>to x</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><span\r
-style='mso-spacerun:yes'>        </span>Cx<span style='mso-spacerun:yes'>     \r
-</span>--&gt;Set<span style='mso-spacerun:yes'>     </span>the sCale to x</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><span\r
-style='mso-spacerun:yes'>        </span>Sname<span style='mso-spacerun:yes'>  \r
-</span>--&gt;Save<span style='mso-spacerun:yes'>    </span>the<span\r
-style='mso-spacerun:yes'>  </span>Alignment </span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><span\r
-style='mso-spacerun:yes'>        </span>Bx<span style='mso-spacerun:yes'>     \r
-</span>--&gt;Save<span style='mso-spacerun:yes'>    </span>Goes back x it </span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><span\r
-style='mso-spacerun:yes'>        </span>return<span style='mso-spacerun:yes'> \r
-</span>--&gt;Compute the<span style='mso-spacerun:yes'>  </span>Alignment</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><span\r
-style='mso-spacerun:yes'>        </span>X<span style='mso-spacerun:yes'>      \r
-</span>--&gt;eXit</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US>[ITERATION<span\r
-style='mso-spacerun:yes'>   </span>1] [START=211] [LEN= 50] [SCALE=-100]<span\r
-style='mso-spacerun:yes'>      </span>YOUR CHOICE:</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US>For instance, to set the\r
-length of the domain to 40, type: </span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US>[ITERATION<span\r
-style='mso-spacerun:yes'>   </span>1] [START=211] [LEN= 50] [SCALE=-100]<span\r
-style='mso-spacerun:yes'>      </span>YOUR CHOICE:&gt;40[return]</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US>[return]</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US>Which will generate:</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US>TOLB_ECOLI_212_252<span\r
-style='mso-spacerun:yes'>    </span>211\r
-SKLAYVTFESGRSALVIQTLANGAVRQVASFPRHNGAPAF<span style='mso-spacerun:yes'> \r
-</span>251</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US>TOLB_ECOLI_256_296<span\r
-style='mso-spacerun:yes'>    </span>255\r
-SKLAFALSKTGSLNLYVMDLASGQIRQVTDGRSNNTEPTW<span style='mso-spacerun:yes'> \r
-</span>295</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US>TOLB_ECOLI_300_340<span\r
-style='mso-spacerun:yes'>    </span>299\r
-QNLAFTSDQAGRPQVYKVNINGGAPQRITWEGSQNQDADV<span style='mso-spacerun:yes'> \r
-</span>339</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US>TOLB_ECOLI_344_383<span\r
-style='mso-spacerun:yes'>    </span>343\r
-KFMVMVSSNGGQQHIAKQDLATGGV-QVLSSTFLDETPSL<span style='mso-spacerun:yes'> \r
-</span>382</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US>TOLB_ECOLI_387_427<span\r
-style='mso-spacerun:yes'>    </span>386\r
-TMVIYSSSQGMGSVLNLVSTDGRFKARLPATDGQVKFPAW<span style='mso-spacerun:yes'> \r
-</span>426</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><span\r
-style='mso-spacerun:yes'>                        </span>1<span\r
-style='mso-spacerun:yes'>   </span>:<span style='mso-spacerun:yes'>    \r
-</span>:<span style='mso-spacerun:yes'>     </span>:<span\r
-style='mso-spacerun:yes'>       </span><span\r
-style='mso-spacerun:yes'>    </span>::<span style='mso-spacerun:yes'>        \r
-</span>.<span style='mso-spacerun:yes'>     </span>40</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><span\r
-style='mso-spacerun:yes'>        </span>MENU: Type Letter Flag[number] and\r
-Return: ex |10</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><span\r
-style='mso-spacerun:yes'>        </span>|x<span style='mso-spacerun:yes'>     \r
-</span>--&gt;Set<span style='mso-spacerun:yes'>     </span>the START to x</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><span\r
-style='mso-spacerun:yes'>        </span>&gt;x<span\r
-style='mso-spacerun:yes'>      </span>--&gt;Set<span\r
-style='mso-spacerun:yes'>     </span>the LEN<span style='mso-spacerun:yes'>  \r
-</span>to x</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><span\r
-style='mso-spacerun:yes'>        </span>Cx<span style='mso-spacerun:yes'>     \r
-</span>--&gt;Set<span style='mso-spacerun:yes'>     </span>the sCale to x</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><span\r
-style='mso-spacerun:yes'>        </span>Sname<span style='mso-spacerun:yes'>  \r
-</span>--&gt;Save<span style='mso-spacerun:yes'>    </span>the<span\r
-style='mso-spacerun:yes'>  </span>Alignment </span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><span\r
-style='mso-spacerun:yes'> </span><span style='mso-spacerun:yes'>      \r
-</span>Bx<span style='mso-spacerun:yes'>      </span>--&gt;Save<span\r
-style='mso-spacerun:yes'>    </span>Goes back x it </span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><span\r
-style='mso-spacerun:yes'>        </span>return<span style='mso-spacerun:yes'> \r
-</span>--&gt;Compute the<span style='mso-spacerun:yes'>  </span>Alignment</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><span\r
-style='mso-spacerun:yes'>        </span>X<span style='mso-spacerun:yes'>      \r
-</span>--&gt;eXit</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=examplefilesmallCxSpLast><span lang=EN-US>[ITERATION<span\r
-style='mso-spacerun:yes'>   </span>3] [START=211] [LEN= 40] [SCALE=-100]<span\r
-style='mso-spacerun:yes'>      </span>YOUR CHOICE: </span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>If you want to indicate the\r
-coordinates, relative to a specific sequence, type:</span></p>\r
-\r
-<p class=example2><span lang=EN-US><span style='mso-tab-count:1'>  </span>|&lt;seq_name&gt;:start</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Type S&lt;your name&gt; to save the\r
-current alignment, and extract a new motif. </span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Type X when you are done.</span></p>\r
-\r
-<h2><a name="_Toc235958635"></a><a name="_Toc102494857"></a><a\r
-name="_Toc102494387"></a><a name="_Toc101065323"><span style='mso-bookmark:\r
-_Toc102494387'><span style='mso-bookmark:_Toc102494857'><span style='mso-bookmark:\r
-_Toc235958635'><span lang=EN-US>Output Control</span></span></span></span></a></h2>\r
-\r
-<h3><a name="_Toc235958636"></a><a name="_Toc102494858"></a><a\r
-name="_Toc102494388"></a><a name="_Toc101065324"><span style='mso-bookmark:\r
-_Toc102494388'><span style='mso-bookmark:_Toc102494858'><span style='mso-bookmark:\r
-_Toc235958636'><span lang=EN-US>Generic</span></span></span></span></a></h3>\r
-\r
-<p class=flag><a name="_Toc235958637"></a><a name="_Toc102494859"><span\r
-style='mso-bookmark:_Toc235958637'><span lang=AF>Conventions Regarding\r
-Filenames</span></span></a></p>\r
-\r
-<p class=MyNormal><span lang=AF>stdout, stderr, stdin, no, /dev/null are valid\r
-filenames. They cause the corresponding file to be output in stderr or stdout,\r
-for an input file, stdin causes the program to requests the corresponding file\r
-through pipe. No causes a suppression of the output, as does /dev/null.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958638"></a><a name="_Toc102494860"><span\r
-style='mso-bookmark:_Toc235958638'><span lang=AF>Identifying the Output files\r
-automatically</span></span></a></p>\r
-\r
-<p class=MyNormal><span lang=AF>In the t_coffee output, each output appears in\r
-a line:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefile><span lang=EN-US>##### FILENAME &lt;name&gt; TYPE\r
-&lt;Type&gt; FORMAT &lt;Format&gt;</span></p>\r
-\r
-</div>\r
-\r
-<p class=flag><a name="_Toc102494861"></a><a name="_Toc102494389"></a><a\r
-name="_Toc101065325"></a><a name="_Toc235958639"><span style='mso-bookmark:\r
-_Toc101065325'><span style='mso-bookmark:_Toc102494389'><span style='mso-bookmark:\r
-_Toc102494861'><span lang=AF>-no_warning</span></span></span></span></a><span\r
-style='mso-bookmark:_Toc101065325'><span style='mso-bookmark:_Toc102494389'><span\r
-style='mso-bookmark:_Toc102494861'></span></span></span></p>\r
-\r
-<p class=flagusage><span style='mso-bookmark:_Toc101065325'><span\r
-style='mso-bookmark:_Toc102494389'><span style='mso-bookmark:_Toc102494861'><span\r
-lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-no_warning<o:p></o:p></span></span></span></span></p>\r
-\r
-<p class=instruction><span style='mso-bookmark:_Toc101065325'><span\r
-style='mso-bookmark:_Toc102494389'><span style='mso-bookmark:_Toc102494861'><span\r
-lang=EN-US>Default: Switched off</span></span></span></span></p>\r
-\r
-<p class=flagdescription><span style='mso-bookmark:_Toc101065325'><span\r
-style='mso-bookmark:_Toc102494389'><span style='mso-bookmark:_Toc102494861'><span\r
-lang=EN-US>Suppresseswarning output.<i style='mso-bidi-font-style:normal'><o:p></o:p></i></span></span></span></span></p>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065325'><span style='mso-bookmark:_Toc102494389'><span\r
-style='mso-bookmark:_Toc102494861'><span lang=EN-US><o:p>&nbsp;</o:p></span></span></span></span></h3>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065325'><span style='mso-bookmark:_Toc102494389'><span\r
-style='mso-bookmark:_Toc102494861'><a name="_Toc235958640"><span lang=EN-US>Alignments</span></a></span></span></span></h3>\r
-\r
-<p class=flag><a name="_Toc235958641"></a><a name="_Toc102494862"></a><a\r
-name="_Toc101065326"><span style='mso-bookmark:_Toc102494862'><span\r
-style='mso-bookmark:_Toc235958641'><span lang=AF>-outfile</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-outfile=&lt;out_aln file,default,no&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default:-outfile=default</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Indicates the name of the alignment\r
-output by t_coffee. If the default is used, the alignment is named <i\r
-style='mso-bidi-font-style:normal'>&lt;your sequences&gt;.aln<o:p></o:p></i></span></p>\r
-\r
-<p class=flag><a name="_Toc235958642"></a><a name="_Toc102494863"></a><a\r
-name="_Toc101065327"><span style='mso-bookmark:_Toc102494863'><span\r
-style='mso-bookmark:_Toc235958642'><span lang=AF>-output</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-output=&lt;format1,format2,...&gt; <o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default:-output=clustalw</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Indicates the format used for\r
-outputting the -outfile.</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Supported formats are:</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'>            </span></span></p>\r
-\r
-<p class=flagdescriptionid1><span lang=EN-US>clustalw_aln, clustalw<span\r
-style='mso-tab-count:1'>       </span>: ClustalW format.</span></p>\r
-\r
-<p class=flagdescriptionid1><span lang=EN-US>gcg, msf_aln<span\r
-style='mso-spacerun:yes'>      </span><span style='mso-tab-count:1'>  </span><span\r
-style='mso-tab-count:1'>                </span>: MSF alignment.</span></p>\r
-\r
-<p class=flagdescriptionid1><span lang=EN-US>pir_aln<span style='mso-tab-count:\r
-3'>                                  </span>: pir alignment.</span></p>\r
-\r
-<p class=flagdescriptionid1><span lang=EN-US>fasta_aln<span style='mso-tab-count:\r
-2'>                             </span>: fasta alignment.</span></p>\r
-\r
-<p class=flagdescriptionid1><span lang=EN-US>phylip<span style='mso-tab-count:\r
-3'>                                   </span>: Phylip format.</span></p>\r
-\r
-<p class=flagdescriptionid1><span lang=EN-US>pir_seq<span style='mso-tab-count:\r
-3'>                                  </span>: pir sequences (no gap).</span></p>\r
-\r
-<p class=flagdescriptionid1><span lang=EN-US>fasta_seq<span style='mso-tab-count:\r
-2'>                             </span>: fasta sequences (no gap).</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><span style='mso-tab-count:2'>                            </span></span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>As well as:</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=flagdescriptionid1><span lang=EN-US>score_ascii<span style='mso-tab-count:\r
-1'>           </span>: causes the output of a reliability flag </span></p>\r
-\r
-<p class=flagdescriptionid1><span lang=EN-US>score_html<span style='mso-tab-count:\r
-1'>           </span>: causes the output to be a reliability plot in HTML</span></p>\r
-\r
-<p class=flagdescriptionid1><span lang=EN-US>score_pdf<span style='mso-tab-count:\r
-1'>             </span>: idem in PDF (if ps2pdf is installed on your system).</span></p>\r
-\r
-<p class=flagdescriptionid1><span lang=EN-US>score_ps<span style='mso-tab-count:\r
-1'>               </span><span style='mso-tab-count:1'>                </span>:\r
-idem in postscript.</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>More than one format can be\r
-indicated:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee sample_seq1.fasta -output=clustalw,gcg, score_html </span></p>\r
-\r
-</div>\r
-\r
-<p class=flagdescription><span lang=EN-US>A publication describing the CORE\r
-index is available on:</span></p>\r
-\r
-<p class=MyNormal><span lang=AF><a\r
-href="http://www.tcoffee.org/Publications/Pdf/core.pp.pdf"><span lang=EN-US\r
-style='mso-ansi-language:EN-US'>http://www.tcoffee.org/Publications/Pdf/core.pp.pdf</span></a></span></p>\r
-\r
-<p class=flag><a name="_Toc235958643"></a><a name="_Toc102494864"></a><a\r
-name="_Toc101065328"><span style='mso-bookmark:_Toc102494864'><span\r
-style='mso-bookmark:_Toc235958643'><span lang=AF>-outseqweight</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-outseqweight=&lt;filename&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: not used</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Indicates the name of the file in\r
-which the sequences weights should be saved..</span></p>\r
-\r
-<p class=flag><a name="_Toc235958644"></a><a name="_Toc102494865"></a><a\r
-name="_Toc101065329"><span style='mso-bookmark:_Toc102494865'><span\r
-style='mso-bookmark:_Toc235958644'><span lang=AF>-case</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-case=&lt;keep,upper,lower&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -case=keep</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>Instructs the program on the case to be used in\r
-the output file (Clustalw uses upper case). The default keeps the case and\r
-makes it possible to maintain a mixture of upper and lower case residues.</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>If you need to change the case of your file,\r
-you can use seq_reformat:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee \96other_pg seq_reformat \96in sample_aln1.aln \96action +lower \96output\r
-clustalw </span></p>\r
-\r
-</div>\r
-\r
-<p class=flag><a name="_Toc235958645"></a><a name="_Toc102494866"></a><a\r
-name="_Toc101065330"><span style='mso-bookmark:_Toc102494866'><span\r
-style='mso-bookmark:_Toc235958645'><span lang=AF>-cpu</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>deprecated<o:p></o:p></span></p>\r
-\r
-<p class=flag><a name="_Toc235958646"></a><a name="_Toc102494867"><span\r
-style='mso-bookmark:_Toc235958646'><span lang=AF>-outseqweight</span></span></a></p>\r
-\r
-<p class=MyNormal><span lang=AF>Usage: -outseqweight=&lt;name of the file\r
-containing the weights applied&gt;</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>Default: -outseqweight=no</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>Will cause the program to output the weights\r
-associated with every sequence in the dataset.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958647"></a><a name="_Toc102494868"></a><a\r
-name="_Toc101065331"><span style='mso-bookmark:_Toc102494868'><span\r
-style='mso-bookmark:_Toc235958647'><span lang=AF>-outorder [cw]</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-outorder=&lt;input OR aligned OR\r
-filename&gt; <o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default:-outorder=input</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Sets the order of the sequences in\r
-the output alignment: <b>-outorder=input</b> means the sequences are kept in\r
-the original order. <b>-outorder=aligned</b> means the sequences come in the\r
-order indicated by the tree. This order can be seen as a one-dimensional\r
-projection of the tree distances. <b style='mso-bidi-font-weight:normal'>\96outdorder=&lt;filename&gt;</b>Filename\r
-is a legal fasta file, whose order will be used in the final alignment.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958648"><span lang=AF>-inorder [cw]</span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-inorder=&lt;input OR aligned&gt; <o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default:-inorder=aligned</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Multiple alignments based on dynamic\r
-programming depend slightly on the order in which the incoming sequences are\r
-provided. To prevent this effect sequences are arbitrarily sorted at the\r
-beginning of the program (-inorder=aligned). However, this affects the sequence\r
-order within the library. You can switch this off by ststing \96inorder=input.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958649"></a><a name="_Toc102494869"><span\r
-style='mso-bookmark:_Toc235958649'><span lang=AF>-seqnos</span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-seqnos=&lt;on or off&gt; <o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default:-seqnos=off</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>Causes the output alignment to contain residue\r
-numbers at the end of each line:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span lang=EN-US>T-COFFEE</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>seq1 aaa---aaaa--------aa 9</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>seq2 a-----aa-----------a 4</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>seq1 a-----------------a 11</span></p>\r
-\r
-<p class=examplefileCxSpLast><span lang=EN-US>seq2 aaaaaaaaaaaaaaaaaaa 19</span></p>\r
-\r
-</div>\r
-\r
-<h3><a name="_Toc235958650"></a><a name="_Toc102494870"></a><a\r
-name="_Toc102494390"></a><a name="_Toc101065332"><span style='mso-bookmark:\r
-_Toc102494390'><span style='mso-bookmark:_Toc102494870'><span style='mso-bookmark:\r
-_Toc235958650'><span lang=EN-US>Libraries</span></span></span></span></a></h3>\r
-\r
-<p class=MyNormal><span lang=AF>Although, it does not necessarily do so\r
-explicitly, T-Coffee always end up combining libraries. Libraries are\r
-collections of pairs of residues. Given a set of libraries, T-Coffee makes an\r
-attempt to assemble the alignment with the highest level of consistence. You\r
-can think of the alignment as a timetable. Each library pair would be a request\r
-from students or teachers, and the job of T-Coffee would be to assemble the\r
-time table that makes as many people as possible happy\85</span></p>\r
-\r
-<p class=flag><a name="_Toc235958651"></a><a name="_Toc102494871"><span\r
-style='mso-bookmark:_Toc235958651'><span lang=AF>-out_lib</span></span></a></p>\r
-\r
-<p class=MyNormal><span lang=AF>Usage:<span style='mso-spacerun:yes'> \r
-</span>-out_lib=&lt;name of the library,default,no&gt; </span></p>\r
-\r
-<p class=MyNormal><span lang=AF>Default:-out_lib=default</span></p>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Sets the name of the library output.\r
-Default implies &lt;run_name&gt;.tc_lib</span></p>\r
-\r
-<p class=flag><a name="_Toc235958652"></a><a name="_Toc102494872"></a><a\r
-name="_Toc101065333"><span style='mso-bookmark:_Toc102494872'><span\r
-style='mso-bookmark:_Toc235958652'><span lang=AF>-lib_only</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-lib_only<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: unset</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Causes the program to stop once the\r
-library has been computed. Must be used in conjunction with the flag <b\r
-style='mso-bidi-font-weight:normal'>\96out_lib</b></span></p>\r
-\r
-<h3><a name="_Toc235958653"></a><a name="_Toc102494873"></a><a\r
-name="_Toc102494391"></a><a name="_Toc101065334"><span style='mso-bookmark:\r
-_Toc102494391'><span style='mso-bookmark:_Toc102494873'><span style='mso-bookmark:\r
-_Toc235958653'><span lang=EN-US>Trees</span></span></span></span></a></h3>\r
-\r
-<p class=flag><a name="_Toc235958654"></a><a name="_Toc102494874"></a><a\r
-name="_Toc101065335"><span style='mso-bookmark:_Toc102494874'><span\r
-style='mso-bookmark:_Toc235958654'><span lang=AF>-newtree</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--newtree=&lt;tree file&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: No file specified</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Indicates the name of the file into\r
-which the guide tree will be written. The default will be\r
-&lt;sequence_name&gt;.dnd, or &lt;run_name.dnd&gt;. The tree is written in the\r
-parenthesis format known as newick or <st1:place w:st="on"><st1:State w:st="on">New\r
-  Hampshire</st1:State></st1:place> and used by Phylips (see the format\r
-section).</span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.5pt;\r
-padding:0mm 0mm 0mm 0mm;background:#F7CBB7'>\r
-\r
-<p class=Warning><span lang=EN-US>Do NOT confuse this guide tree with a\r
-phylogenetic tree.</span></p>\r
-\r
-</div>\r
-\r
-<h2><a name="_Toc235958655"></a><a name="_Toc102494875"></a><a\r
-name="_Toc102494392"></a><a name="_Toc101065336"><span style='mso-bookmark:\r
-_Toc102494392'><span style='mso-bookmark:_Toc102494875'><span style='mso-bookmark:\r
-_Toc235958655'><span lang=EN-US>Reliability Estimation</span></span></span></span></a></h2>\r
-\r
-<h3><a name="_Toc235958656"></a><a name="_Toc102494876"></a><a\r
-name="_Toc102494393"></a><a name="_Toc101065337"><span style='mso-bookmark:\r
-_Toc102494393'><span style='mso-bookmark:_Toc102494876'><span style='mso-bookmark:\r
-_Toc235958656'><span lang=EN-US>CORE Computation</span></span></span></span></a></h3>\r
-\r
-<p class=MyNormal><span lang=AF>The CORE is an index that indicates the\r
-consistency between the library of piarwise alignments and the final multiple\r
-alignment. Our experiment indicate that the higher this consistency, the more\r
-reliable the alignment. A publication describing the CORE index can be found\r
-on:</span></p>\r
-\r
-<p class=MyNormal><a name="_Toc102494877"></a><a name="_Toc101065338"><span\r
-style='mso-bookmark:_Toc102494877'></span></a><a\r
-href="http://www.tcoffee.org/Publications/Pdf/core.pp.pdf"><span\r
-style='mso-bookmark:_Toc101065338'><span style='mso-bookmark:_Toc102494877'><span\r
-lang=EN-US style='mso-ansi-language:EN-US'>http://www.tcoffee.org/Publications/Pdf/core.pp.pdf</span></span></span><span\r
-style='mso-bookmark:_Toc101065338'><span style='mso-bookmark:_Toc102494877'></span></span></a><span\r
-style='mso-bookmark:_Toc101065338'><span style='mso-bookmark:_Toc102494877'></span></span></p>\r
-\r
-<p class=flag><span style='mso-bookmark:_Toc101065338'><span style='mso-bookmark:\r
-_Toc102494877'><a name="_Toc235958657"><span lang=AF>-evaluate_mode</span></a></span></span></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--evaluate_mode=&lt;t_coffee_fast,t_coffee_slow,t_coffee_non_extended &gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -evaluate_mode=t_coffee_fast</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>This flag indicates the mode used to\r
-normalize the t_coffee score when computing the reliability score. </span></p>\r
-\r
-<p class=flagdescription><i style='mso-bidi-font-style:normal'><span\r
-lang=EN-US>t_coffee_fast</span></i><span lang=EN-US>: Normalization is made\r
-using the highest score in the MSA. This evaluation mode was validated and in\r
-our hands, pairs of residues with a score of 5 or higher have 90 % chances to\r
-be correctly aligned to one another. </span></p>\r
-\r
-<p class=flagdescription><i style='mso-bidi-font-style:normal'><span\r
-lang=EN-US>t_coffee_slow:</span></i><span lang=EN-US> Normalization is made\r
-using the library. This usually results in lower score and a scoring scheme\r
-more sensitive to the number of sequences in the dataset. Note that this\r
-scoring scheme is not any more slower, thanks to the implementation of a faster\r
-heuristic algorithm. </span></p>\r
-\r
-<p class=flagdescription><i style='mso-bidi-font-style:normal'><span\r
-lang=EN-US>t_coffee_non_extended:</span></i><span lang=EN-US> the score of each\r
-residue is the ratio between the sum of its non extended scores with the column\r
-and the sum of all its possible non extended scores.</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>These modes will be useful when\r
-generating colored version of the output, with the <b style='mso-bidi-font-weight:\r
-normal'>\96output</b> flag:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee sample_seq1.fasta \96evaluate_mode t_coffee_slow \96output score_ascii,\r
-score_html </span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee sample_seq1.fasta \96evaluate_mode t_coffee_fast \96output score_ascii,\r
-score_html </span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee sample_seq1.fasta \96evaluate_mode t_coffee_non_extended \96output\r
-score_ascii, score_html </span></p>\r
-\r
-</div>\r
-\r
-<h2><a name="_Toc235958658"></a><a name="_Toc102494878"></a><a\r
-name="_Toc102494394"></a><a name="_Toc101065339"><span style='mso-bookmark:\r
-_Toc102494394'><span style='mso-bookmark:_Toc102494878'><span style='mso-bookmark:\r
-_Toc235958658'><span lang=EN-US>Generic Output</span></span></span></span></a></h2>\r
-\r
-<p class=flag><a name="_Toc235958659"></a><a name="_Toc102494879"><span\r
-style='mso-bookmark:_Toc235958659'><span lang=AF>-run_name</span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--run_name=&lt;your run name&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: no default set</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>This flag causes the prefix &lt;your\r
-sequences&gt; to be replaced by &lt;your run name&gt; when renaming the default\r
-output files.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958660"></a><a name="_Toc102494880"></a><a\r
-name="_Toc101065340"><span style='mso-bookmark:_Toc102494880'><span\r
-style='mso-bookmark:_Toc235958660'><span lang=AF>-quiet</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--quiet=&lt;stderr,stdout,file name OR nothing&gt;.<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default:-quiet=stderr</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Redirects the standard output to\r
-either a file. <b>-quiet</b> on its own redirect the output to /dev/null.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958661"></a><a name="_Toc102494881"><span\r
-style='mso-bookmark:_Toc235958661'><span lang=AF>-align [CW]</span></span></a></p>\r
-\r
-<p class=MyNormal><span lang=AF>This flag indicates that the program must\r
-produce the alignment. It is here for compatibility with ClustalW.</span></p>\r
-\r
-<h2><a name="_Toc235958662"><span lang=EN-US>APDB, iRMSD and tRMSD Parameters</span></a></h2>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.5pt;\r
-padding:0mm 0mm 0mm 0mm;background:#F7CBB7'>\r
-\r
-<p class=Warning><span lang=EN-US>Warning: These flags will only work within\r
-the APDB package that can be invoked via the \96other_pg parameter of T-Coffee:</span></p>\r
-\r
-<p class=Warning><span lang=EN-US><span style='mso-tab-count:2'>                               </span><span\r
-style='mso-spacerun:yes'> </span>t_coffee \96other_pg apdb \96aln &lt;your aln&gt;</span></p>\r
-\r
-<p class=Warning><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-</div>\r
-\r
-<p class=flag><a name="_Toc235958663"><span lang=AF>-quiet [Same as T-Coffee]</span></a></p>\r
-\r
-<p class=flag><a name="_Toc235958664"><span lang=AF>-run_name [Same as\r
-T-Coffee]</span></a></p>\r
-\r
-<p class=flag><a name="_Toc235958665"><span lang=AF>-aln</span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--aln=&lt;file_name&gt;.<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default:none</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Indicates the name of the file\r
-containing the sequences that need to be evaluated. The sequences whose\r
-structure is meant to be used must be named according to their PDB identifier. </span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>The format can be FASTA, CLUSTAL or\r
-any of the formats supported by T-Coffee. APDB only evaluates residues in\r
-capital and ignores those in lower case. If your sequences are in lower case,\r
-you can upper case them using seq_reformat:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee \96other_pg seq_reformat \96in 3d_sample4.aln \96action +upper \96output\r
-clustalw &gt; 3d_sample4.cw_aln</span></p>\r
-\r
-</div>\r
-\r
-<p class=flagdescription><span lang=EN-US>The alignment can then be evaluated\r
-using the defaultr of APDB:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee \96other_pg apdb \96aln 3d_sample4.aln</span></p>\r
-\r
-</div>\r
-\r
-<p class=flagdescription><span lang=EN-US>The alignment can contain as many\r
-structures as you wish.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958666"><span lang=AF>-n_excluded_nb</span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--n_excluded_nb=&lt;integer&gt;.<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default:1</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>When evaluating the local score of a\r
-pair of aligned residues, the residues immediately next to that column should\r
-not contribute to the measure. By default the first to the left and first to\r
-the right are excluded.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958667"><span lang=AF>-maximum_distance</span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--maximum_distance=&lt;float&gt;.<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default:10</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Size of the neighborhood considered\r
-around every residue. If .-local_mode is set to sphere, -maximum_distance is\r
-the radius of a sphere centered around each residue. If \96local_mode is set to\r
-window, then \96maximum_distance is the size of the half window (i.e.\r
-window_size=-maximum_distance*2+1).</span></p>\r
-\r
-<p class=flag><a name="_Toc235958668"><span lang=AF>-similarity_threshold</span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--similarity_threshold=&lt;integer&gt;.<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default:70</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Fraction of the neighborhood that\r
-must be supportive for a pair of residue to be considered correct in APDB. The\r
-neighborhood is a sphere defined by \96maximum_distance, and the support is\r
-defined by \96md_threshold.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958669"><span lang=AF>-local_mode</span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--local_mode=&lt;sphere,window&gt;.<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default:sphere</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Defines the shape of a neighborhood,\r
-either as a sphere or as a window.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958670"><span lang=AF>-filter</span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--filter=&lt;0.00-1.00&gt;.<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default:1.00</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Defines the centiles that should be\r
-kept when making the local measure. Foir instance, -filter=0.90 means that the\r
-the 10 last centiles will be removed from the evaluation. The filtration is\r
-carried out on the iRMSD values.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958671"><span lang=AF>-print_rapdb [Unsupported]</span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--print_rapdb (FLAG)<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default:off</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>This causes the prints out of the\r
-exact neighborhood of every considered pair of residues.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958672"><span lang=AF>-outfile [Same as T-Coffee]</span></a></p>\r
-\r
-<p class=MyNormal><span lang=AF>This flag is meant to control the output name\r
-of the colored APDB output. This file will either display the local APDB score\r
-or the local iRMD, depending on the value of \96color_mode. The default format is\r
-defined by \96ouptut and is score_html.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958673"><span lang=AF>-color_mode</span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--color_mode=&lt;apdb, irmsd&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default:apdb</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>This flag is meant to control the colored APDB\r
-output (local score). This file will either display the local APDB score or the\r
-local iRMD.</span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 3.0pt;\r
-padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0mm;margin-right:\r
-4.25pt'>\r
-\r
-<p class=ChapterTitle><a name="_Toc235958674"><span lang=EN-US>Building a\r
-Server</span></a></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF>We maintain a T-Coffee server (www.tcoffee.org).\r
-We will be pleased to provide anyone who wants to set up a similar service with\r
-the sources</span></p>\r
-\r
-<h3><a name="_Toc102494884"></a><a name="_Toc102494396"></a><a\r
-name="_Toc235958675"><span style='mso-bookmark:_Toc102494396'><span\r
-style='mso-bookmark:_Toc102494884'><span lang=EN-US>Environment Variables</span></span></span></a><span\r
-style='mso-bookmark:_Toc102494396'><span style='mso-bookmark:_Toc102494884'></span></span></h3>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc102494396'><span\r
-style='mso-bookmark:_Toc102494884'><span lang=AF>T-Coffee stores a lots of\r
-information in locations that may be unsuitable when running a server. </span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc102494396'><span\r
-style='mso-bookmark:_Toc102494884'><span lang=AF>By default, T-Coffee will\r
-generate and rely on the follwing directory structure:</span></span></span></p>\r
-\r
-<p class=example><span style='mso-bookmark:_Toc102494396'><span\r
-style='mso-bookmark:_Toc102494884'><span lang=EN-US>/home/youraccount/<span\r
-style='mso-tab-count:2'>         </span>#HOME_4_TCOFFEE</span></span></span></p>\r
-\r
-<p class=example><span style='mso-bookmark:_Toc102494396'><span\r
-style='mso-bookmark:_Toc102494884'><span lang=EN-US>HOME_4_TCOFFEE/.t_coffee/ <span\r
-style='mso-tab-count:1'> </span>#DIR_4_TCOFFEE</span></span></span></p>\r
-\r
-<p class=example><span style='mso-bookmark:_Toc102494396'><span\r
-style='mso-bookmark:_Toc102494884'><span lang=EN-US>DIR_4_TCOFFEE/cache<span\r
-style='mso-tab-count:2'>        </span>#CACHE_4_TCOFFEE</span></span></span></p>\r
-\r
-<p class=example><span style='mso-bookmark:_Toc102494396'><span\r
-style='mso-bookmark:_Toc102494884'><span lang=EN-US>DIR_4_TCOFFEE/tmp<span\r
-style='mso-tab-count:2'>          </span>#TMP_4_TCOFFEE</span></span></span></p>\r
-\r
-<p class=example><span style='mso-bookmark:_Toc102494396'><span\r
-style='mso-bookmark:_Toc102494884'><span lang=EN-US>DIR_4_TCOFFEE/methods<span\r
-style='mso-tab-count:2'>            </span>#METHOS_4_TCOFFEE</span></span></span></p>\r
-\r
-<p class=example><span style='mso-bookmark:_Toc102494396'><span\r
-style='mso-bookmark:_Toc102494884'><span lang=EN-US>DIR_4_TCOFFEE/mcoffee<span\r
-style='mso-tab-count:2'>            </span>#MCOFFEE_4_TCOFFEE</span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc102494396'><span\r
-style='mso-bookmark:_Toc102494884'><span lang=AF><o:p>&nbsp;</o:p></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc102494396'><span\r
-style='mso-bookmark:_Toc102494884'><span lang=AF>By default, all these\r
-directories are automatically created, following the dependencies suggested\r
-here. </span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc102494396'><span\r
-style='mso-bookmark:_Toc102494884'><span lang=AF>The first step is the\r
-determination of the HOME. By default the program tries to use HOME_4_TCOFFEE,\r
-then the HOME variable and TMP or TEMP if HOME is not set on your system or\r
-your account. It is your responsibility to make sure that one of these\r
-variables is set to some valid location where the T-Coffee process is allowed\r
-to read and write.</span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc102494396'><span\r
-style='mso-bookmark:_Toc102494884'><span lang=AF>If no valid location can be\r
-found for HOME_4_TCOFFEE, the program exits. If you are running T-Coffee on a\r
-server, we recommend to hard set the following locations, where your scratch is\r
-a valid location. </span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc102494396'><span\r
-style='mso-bookmark:_Toc102494884'><span lang=AF><o:p>&nbsp;</o:p></span></span></span></p>\r
-\r
-<p class=example><span style='mso-bookmark:_Toc102494396'><span\r
-style='mso-bookmark:_Toc102494884'><span lang=EN-US>HOME_4_TCOFFEE=\94your scratch\94</span></span></span></p>\r
-\r
-<p class=example><span style='mso-bookmark:_Toc102494396'><span\r
-style='mso-bookmark:_Toc102494884'><span lang=EN-US>TMP_4_TCOFFEE=\94your\r
-scratch\94</span></span></span></p>\r
-\r
-<p class=example><span style='mso-bookmark:_Toc102494396'><span\r
-style='mso-bookmark:_Toc102494884'><span lang=EN-US>DIR_4_TCOFFEE=\94your\r
-scratch\94</span></span></span></p>\r
-\r
-<p class=example><span style='mso-bookmark:_Toc102494396'><span\r
-style='mso-bookmark:_Toc102494884'><span lang=EN-US>CACHE_4_TCOFFEE=\94your\r
-scratch\94</span></span></span></p>\r
-\r
-<p class=example><span style='mso-bookmark:_Toc102494396'><span\r
-style='mso-bookmark:_Toc102494884'><span lang=EN-US>NO_ERROR_REPORT_4_TCOFFEE=1</span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc102494396'><span\r
-style='mso-bookmark:_Toc102494884'><span lang=AF>Note that<span\r
-style='mso-spacerun:yes'>  </span>it is a good idea to have a cron job that\r
-cleans up this scratch area, once in a while. </span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc102494396'><span\r
-style='mso-bookmark:_Toc102494884'><span lang=AF><o:p>&nbsp;</o:p></span></span></span></p>\r
-\r
-<h3><span style='mso-bookmark:_Toc102494396'><span style='mso-bookmark:_Toc102494884'><a\r
-name="_Toc235958676"><span lang=EN-US>Output of the .dnd file.</span></a></span></span></h3>\r
-\r
-<p class=MyNormal><span lang=AF>A common source of error when running a server:\r
-T-Coffee MUST output the .dnd file because it re-reads it to carry out the\r
-progressive alignment. By default T-Coffee outputs this file in the directory\r
-where the process is running. If the T-Coffee process does not have permission\r
-to write in that directory, the computation will abort...</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>To avoid this, simply specify the name of the\r
-output tree: </span></p>\r
-\r
-<p class=MyNormal><span lang=AF><span style='mso-tab-count:1'>         </span>-newtree=&lt;writable\r
-file (usually in /tmp)&gt;</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>Chose the name so that two processes may not\r
-over-write each other dnd file. </span></p>\r
-\r
-<h3><a name="_Toc235958677"></a><a name="_Toc102494885"></a><a\r
-name="_Toc102494397"><span style='mso-bookmark:_Toc102494885'><span\r
-style='mso-bookmark:_Toc235958677'><span lang=EN-US>Permissions</span></span></span></a></h3>\r
-\r
-<p class=MyNormal><span lang=AF>The t_coffee process MUST be allowed to write\r
-in some scratch area, even when it is ran by Mr nobody... Make sure the /tmp/\r
-partition is not protected.</span></p>\r
-\r
-<h3><a name="_Toc235958678"></a><a name="_Toc102494886"></a><a\r
-name="_Toc102494398"><span style='mso-bookmark:_Toc102494886'><span\r
-style='mso-bookmark:_Toc235958678'><span lang=EN-US>Other Programs</span></span></span></a></h3>\r
-\r
-<p class=MyNormal><span lang=AF>T-Coffee may call various programs while it\r
-runs (lalign2list by defaults). Make sure your process knows where to find\r
-these executables.</span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 3.0pt;\r
-padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0mm;margin-right:\r
-4.25pt'>\r
-\r
-<p class=ChapterTitle><a name="_Toc235958679"></a><a name="_Toc102494887"></a><a\r
-name="_Toc101065353"><span style='mso-bookmark:_Toc102494887'><span\r
-style='mso-bookmark:_Toc235958679'><span lang=EN-US>F</span></span></span></a><span\r
-style='mso-bookmark:_Toc235958679'><span lang=EN-US>ormats</span></span></p>\r
-\r
-</div>\r
-\r
-<h2><a name="_Toc235958680"></a><a name="_Toc102494888"></a><a\r
-name="_Toc102494399"></a><a name="_Toc101065354"><span style='mso-bookmark:\r
-_Toc102494399'><span style='mso-bookmark:_Toc102494888'><span style='mso-bookmark:\r
-_Toc235958680'><span lang=EN-US>Parameter files</span></span></span></span></a></h2>\r
-\r
-<p class=MyNormal><span lang=AF>Parameter files used with -parameters,\r
--t_coffee_defaults, -dali_defaults... Must contain a valid parameter string\r
-where line breaks are allowed. These files cannot contain any comment, the\r
-recommended format is one parameter per line:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span lang=EN-US><span style='mso-tab-count:1'>      </span>&lt;parameter\r
-name&gt;=&lt;value1&gt;,&lt;value2&gt;....</span></p>\r
-\r
-<p class=examplefileCxSpLast><span lang=EN-US><span style='mso-tab-count:1'>      </span>&lt;parameter\r
-name&gt;=.....</span></p>\r
-\r
-</div>\r
-\r
-<h2><a name="_Toc235958681"></a><a name="_Toc102494889"></a><a\r
-name="_Toc102494400"></a><a name="_Toc101065355"><span style='mso-bookmark:\r
-_Toc102494400'><span style='mso-bookmark:_Toc102494889'><span style='mso-bookmark:\r
-_Toc235958681'><span lang=EN-US>Sequence Name Handling</span></span></span></span></a></h2>\r
-\r
-<p class=MyNormal><span lang=AF>Sequence name handling is meant to be fully\r
-consistent with ClustalW (Version 1.75). This implies that in some cases the\r
-names of your sequences may be edited when coming out of the program. Five\r
-rules apply:</span></p>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 1.0pt 1.0pt 1.0pt'>\r
-\r
-<p class=Noteboxtitle style='border:none;mso-border-alt:solid windowtext .5pt;\r
-padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US>Naming\r
-Your Sequences the <st1:Street w:st="on"><st1:address w:st="on">Right Way</st1:address></st1:Street></span></p>\r
-\r
-<p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;\r
-padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US>1-No\r
-Space</span></p>\r
-\r
-<p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;\r
-padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US>Names\r
-that do contain spaces, for instance:</span></p>\r
-\r
-<p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;\r
-padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US><span\r
-style='mso-tab-count:1'>            </span>&gt;seq1 human_myc</span></p>\r
-\r
-<p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;\r
-padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US>will be\r
-turned into</span></p>\r
-\r
-<p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;\r
-padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US><span\r
-style='mso-tab-count:1'>            </span>&gt;seq1</span></p>\r
-\r
-<p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;\r
-padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US>It is\r
-your responsibility to make sure that the names you provide are not ambiguous\r
-after such an editing. This editing is consistent with Clustalw (Version 1.75)</span></p>\r
-\r
-<p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;\r
-padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;\r
-padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US>2-No\r
-Strange Character</span></p>\r
-\r
-<p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;\r
-padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US>Some non\r
-alphabetical characters are replaced with underscores. These are: ';:()'</span></p>\r
-\r
-<p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;\r
-padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US>Other\r
-characters are legal and will be kept unchanged. This editing is meant to keep\r
-in line with Clustalw (Version 1.75).</span></p>\r
-\r
-<p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;\r
-padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;\r
-padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US>3-&gt; is\r
-NEVER legal (except as a header token in a FASTA file)</span></p>\r
-\r
-<p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;\r
-padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;\r
-padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US>4-Name\r
-length must be below 100 characters, although 15 is recommended for\r
-compatibility with other programs.</span></p>\r
-\r
-<p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;\r
-padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US>5-Duplicated\r
-sequences will be renamed (i.e. sequences with the same name in the same\r
-dataset) are allowed but will be renamed according to their original order.\r
-When sequences come from multiple sources via the \96in flag, consistency of the\r
-renaming is not guaranteed. You should avoid duplicated sequences as they will\r
-cause your input to differ from your output thus making it difficult to track\r
-data.</span></p>\r
-\r
-</div>\r
-\r
-<h2><a name="_Toc235958682"></a><a name="_Toc102494890"></a><a\r
-name="_Toc102494401"></a><a name="_Toc101065356"><span style='mso-bookmark:\r
-_Toc102494401'><span style='mso-bookmark:_Toc102494890'><span style='mso-bookmark:\r
-_Toc235958682'><span lang=EN-US>Automatic Format Recognition</span></span></span></span></a></h2>\r
-\r
-<p class=MyNormal><span lang=AF>Most common formats are automatically\r
-recognized by t_coffee. See -in and the next section for more details. If your\r
-format is not recognized, use readseq or clustalw to switch to another format.\r
-We recommend Fasta.</span></p>\r
-\r
-<h2><a name="_Toc235958683"></a><a name="_Toc102494891"></a><a\r
-name="_Toc102494402"></a><a name="_Toc101065357"><span style='mso-bookmark:\r
-_Toc102494402'><span style='mso-bookmark:_Toc102494891'><span style='mso-bookmark:\r
-_Toc235958683'><span lang=EN-US>Structures</span></span></span></span></a></h2>\r
-\r
-<p class=MyNormal><span lang=AF>PDB format is recognized by T-Coffee. T-Coffee\r
-uses extract_from_pdb (cf \96other_pg flag). extract_from_pdb is a small embeded\r
-module that can be used on its own to extract information from pdb files.</span></p>\r
-\r
-<h2><a name="_Toc235958684"><span lang=EN-US>RNA Structures</span></a></h2>\r
-\r
-<p class=MyNormal><span lang=AF>RNA structures can either be coded as T-Coffee\r
-libraries, with each line indicating two paired residues, or as alifold output.\r
-The selex format is also partly supported (see the seq_reformat tutorial on RNA\r
-sequences handling).</span></p>\r
-\r
-<h2><a name="_Toc235958685"></a><a name="_Toc102494892"></a><a\r
-name="_Toc102494403"></a><a name="_Toc101065358"><span style='mso-bookmark:\r
-_Toc102494403'><span style='mso-bookmark:_Toc102494892'><span style='mso-bookmark:\r
-_Toc235958685'><span lang=EN-US>Sequences</span></span></span></span></a></h2>\r
-\r
-<p class=MyNormal><span lang=AF>Sequences can come in the following formats:\r
-fasta, pir, swiss-prot, clustal aln, msf aln and t_coffee aln. These formats\r
-are the one automatically recognized. Please replace the '*' sign sometimes\r
-used for stop codons with an X.</span></p>\r
-\r
-<h2><a name="_Toc235958686"></a><a name="_Toc102494893"></a><a\r
-name="_Toc102494404"></a><a name="_Toc101065359"><span style='mso-bookmark:\r
-_Toc102494404'><span style='mso-bookmark:_Toc102494893'><span style='mso-bookmark:\r
-_Toc235958686'><span lang=EN-US>Alignments</span></span></span></span></a></h2>\r
-\r
-<p class=MyNormal><span lang=AF>Alignments can come in the following formats:\r
-msf, ClustalW, Fasta, Pir and t_coffee. The t_coffee format is very similar to\r
-the ClustalW format, but slightly more flexible. Any interleaved format with\r
-sequence name on each line will be correctly parsed:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span lang=EN-US>&lt;empy line&gt; <span\r
-style='mso-tab-count:1'>      </span>[Facultative]n</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>&lt;line of text&gt; <span\r
-style='mso-tab-count:1'>   </span>[Required]</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>&lt;line of text&gt;<span\r
-style='mso-tab-count:3'>               </span>[Facultative]n</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>&lt;empty line&gt;<span\r
-style='mso-tab-count:3'>                 </span>[Required]</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>&lt;empty line&gt;<span\r
-style='mso-tab-count:3'>                 </span>[Facultative]n</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>&lt;seq1\r
-name&gt;&lt;space&gt;&lt;seq1&gt;</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>&lt;seq2\r
-name&gt;&lt;space&gt;&lt;seq2&gt;</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>&lt;seq3\r
-name&gt;&lt;space&gt;&lt;seq3&gt;</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>&lt;empty line&gt;<span\r
-style='mso-tab-count:3'>                 </span>[Required]</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>&lt;empty line&gt;<span\r
-style='mso-tab-count:3'>                 </span>[Facultative]n</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>&lt;seq1\r
-name&gt;&lt;space&gt;&lt;seq1&gt;</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>&lt;seq2\r
-name&gt;&lt;space&gt;&lt;seq2&gt;</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>&lt;seq3\r
-name&gt;&lt;space&gt;&lt;seq3&gt;</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>&lt;empty line&gt;<span\r
-style='mso-tab-count:3'>                 </span>[Required]</span></p>\r
-\r
-<p class=examplefileCxSpLast><span lang=EN-US>&lt;empty line&gt;<span\r
-style='mso-tab-count:3'>                 </span>[Facultative]n</span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF>An empty line is a line that does NOT contain\r
-amino-acid. A line that contains the ClustalW annotation (.:*) is empty.</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>Spaces are forbidden in the name. When the\r
-alignment is being read, non character signs are ignored in the sequence field\r
-(such as numbers, annotation\85).</span></p>\r
-\r
-<p class=Note><span lang=EN-US style='mso-ansi-language:EN-US'>Note: a\r
-different number of lines in the different blocks will cause the program to\r
-crash or hang.<o:p></o:p></span></p>\r
-\r
-<h2><a name="_Toc235958687"></a><a name="_Toc102494894"></a><a\r
-name="_Toc102494405"></a><a name="_Toc101065360"><span style='mso-bookmark:\r
-_Toc102494405'><span style='mso-bookmark:_Toc102494894'><span style='mso-bookmark:\r
-_Toc235958687'><span lang=EN-US>Libraries</span></span></span></span></a></h2>\r
-\r
-<h3><a name="_Toc235958688"></a><a name="_Toc102494895"></a><a\r
-name="_Toc102494406"><span style='mso-bookmark:_Toc102494895'><span\r
-style='mso-bookmark:_Toc235958688'><span lang=EN-US>T-COFFEE_LIB_FORMAT_01</span></span></span></a></h3>\r
-\r
-<p class=MyNormal><span lang=AF>This is currently the only supported format.</span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span lang=EN-US>!&lt;space&gt; TC_LIB_FORMAT_01</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>&lt;nseq&gt;</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>&lt;seq1 name&gt; &lt;seq1\r
-length&gt; &lt;seq1&gt;</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>&lt;seq2 name&gt; &lt;seq2\r
-length&gt; &lt;seq2&gt;</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>&lt;seq3 name&gt; &lt;seq3\r
-length&gt; &lt;seq3&gt;</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>!Comment</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>(!Comment)n</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>#Si1 Si2</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>Ri1 Ri2 V1 (V2, V3)</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>#1 2</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>12 13 99 (12/0 vs 13/1, weight\r
-99)</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>12 14 70</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>15 16 56</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>#1 3</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>12 13 99 </span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>12 14 70</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>15 16 56</span></p>\r
-\r
-<p class=examplefileCxSpLast><span lang=EN-US>!&lt;space&gt;SEQ_1_TO_N </span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF>Si1: index of Sequence 1</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>Ri1: index of residue 1 in seq1</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>V1: Integer Value: Weight</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>V2, V3: optional values</span></p>\r
-\r
-<p class=Note><span lang=EN-US style='mso-ansi-language:EN-US'>Note 1: There is\r
-a space between the ! And SEQ_1_TO_N<o:p></o:p></span></p>\r
-\r
-<p class=Note><span lang=EN-US style='mso-ansi-language:EN-US'>Note 2: The last\r
-line (! SEQ_1_TO_N) indicates that:<o:p></o:p></span></p>\r
-\r
-<p class=MyNormal><span lang=AF>Sequences and residues are numbered from 1 to\r
-N, unless the token SEQ_1_TO_N is omitted, in which case the sequences are\r
-numbered from 0 to N-1, and residues are from 1 to N.</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>Residues do not need to be sorted, and neither\r
-do the sequences. The same pair can appear several times in the library. For\r
-instance, the following file would be legal:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span lang=EN-US>#1 2</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>12 13 99</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>#1 2</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>15 16 99 </span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>#1 1</span></p>\r
-\r
-<p class=examplefileCxSpLast><span lang=EN-US>12 14 70</span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><a name="_Toc102494896"></a><a name="_Toc102494407"><span\r
-style='mso-bookmark:_Toc102494896'><span lang=AF>It is also poosible to declare\r
-ranges of resdues rather than single pairs. For instance, the following:</span></span></a></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc102494407'><span\r
-style='mso-bookmark:_Toc102494896'><span lang=EN-US>#0 1</span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494407'><span\r
-style='mso-bookmark:_Toc102494896'><span lang=EN-US>+BLOCK+<span\r
-style='mso-spacerun:yes'>  </span>10 12 14 99</span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494407'><span\r
-style='mso-bookmark:_Toc102494896'><span lang=EN-US>+BLOCK+<span\r
-style='mso-spacerun:yes'>  </span>15 30 40 99</span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494407'><span\r
-style='mso-bookmark:_Toc102494896'><span lang=EN-US>#0 2</span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494407'><span\r
-style='mso-bookmark:_Toc102494896'><span lang=EN-US>15 16 99 </span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494407'><span\r
-style='mso-bookmark:_Toc102494896'><span lang=EN-US>#0 1</span></span></span></p>\r
-\r
-<p class=examplefileCxSpLast><span style='mso-bookmark:_Toc102494407'><span\r
-style='mso-bookmark:_Toc102494896'><span lang=EN-US>12 14 70</span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc102494407'><span\r
-style='mso-bookmark:_Toc102494896'><span lang=AF>The first statement BLOCK\r
-declares a BLOCK of length 10, that starts on position 12 of sequence 1 and\r
-position 14 of sequence 2 and where each pair of residues within the block has\r
-a score of 99. The second BLOCK starts on residue 30 of 1, residue 40 of 2 and\r
-extends for 15 residues.</span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc102494407'><span\r
-style='mso-bookmark:_Toc102494896'><span lang=AF>Blocks can overalp and be\r
-incompatible with one another, just like single constraints.</span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc102494407'><span\r
-style='mso-bookmark:_Toc102494896'><span lang=AF><span\r
-style='mso-spacerun:yes'>  </span></span></span></span></p>\r
-\r
-<h3><span style='mso-bookmark:_Toc102494407'><span style='mso-bookmark:_Toc102494896'><a\r
-name="_Toc235958689"><span lang=EN-US>T-COFFEE_LIB_FORMAT_02</span></a></span></span></h3>\r
-\r
-<p class=MyNormal><span lang=AF>A simpler format is being developed, however it\r
-is not yet fully supported and is only mentioned here for development purpose.</span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span lang=EN-US>! TC_LIB_FORMAT_02</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>#S1 SEQ1 [OPTIONAL]</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>#S2 SEQ2 [OPTIONAL]</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>...</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>!comment [OPTIONAL]</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>S1 R1 Ri1 S2 R2 Ri2 V1 (V2 V3)</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>=&gt; <st1:place w:st="on">N R1</st1:place>\r
-Ri1 S2 R2 Ri2 V1 (V2 V3)</span></p>\r
-\r
-<p class=examplefileCxSpLast><span lang=EN-US>...</span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF>S1, S2: name of sequence 1 and 2</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>SEQ1: sequence of S1</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>Ri1, Ri2: index of the residues in their\r
-respective sequence</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>R1, R2: Residue type</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>V1, V2, V3: integer Values (V2 and V3 are\r
-optional)</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>Value1, Value 2 and Value3 are optional.</span></p>\r
-\r
-<h2><a name="_Toc101065361"></a><a name="_Toc235958690"></a><a\r
-name="_Toc102494897"></a><a name="_Toc102494408"><span style='mso-bookmark:\r
-_Toc102494897'><span style='mso-bookmark:_Toc235958690'><span style='mso-bookmark:\r
-_Toc101065361'><span lang=EN-US>Library List</span></span></span></span></a><span\r
-style='mso-bookmark:_Toc101065361'></span></h2>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065361'><span lang=AF>These\r
-are lists of pairs of sequences that must be used to compute a library. The\r
-format is:</span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc101065361'><span\r
-lang=EN-US>&lt;nseq&gt; &lt;S1&gt; &lt;S2&gt;</span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065361'><span\r
-lang=EN-US>2 hamg2 globav</span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065361'><span\r
-lang=EN-US>3 hamgw hemog singa</span></span></p>\r
-\r
-<p class=examplefileCxSpLast><span style='mso-bookmark:_Toc101065361'><span\r
-lang=EN-US>...</span></span></p>\r
-\r
-</div>\r
-\r
-<h2><span style='mso-bookmark:_Toc101065361'><a name="_Toc235958691"></a><a\r
-name="_Toc102494898"></a><a name="_Toc102494409"><span style='mso-bookmark:\r
-_Toc102494898'><span style='mso-bookmark:_Toc235958691'><span lang=EN-US>Substitution\r
-matrices.</span></span></span></a></span></h2>\r
-\r
-<p class=MyNormal><span lang=AF>If the required substitution matrix is not available,\r
-write your own in a file using the following format:</span></p>\r
-\r
-<h3><a name="_Toc235958692"></a><a name="_Toc102494899"></a><a\r
-name="_Toc102494410"></a><a name="_Toc101065362"><span style='mso-bookmark:\r
-_Toc102494410'><span style='mso-bookmark:_Toc102494899'><span style='mso-bookmark:\r
-_Toc235958692'><span lang=EN-US>ClustalW Style</span></span></span></span></a><span\r
-style='mso-bookmark:_Toc102494410'><span style='mso-bookmark:_Toc102494899'><span\r
-style='mso-bookmark:_Toc235958692'><span lang=EN-US> [Deprecated]</span></span></span></span></h3>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span lang=EN-US># CLUSTALW_MATRIX FORMAT</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>$</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>v1</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>v2 v3</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>v4 v5 v6</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>...</span></p>\r
-\r
-<p class=examplefileCxSpLast><span lang=EN-US>$</span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF>v1, v2... are integers, possibly negatives.</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>The order of the amino acids is:\r
-ABCDEFGHIKLMNQRSTVWXYZ, which means that v1 is the substitution value for A vs\r
-A, v2 for A vs B, v3 for B vs B, v4 for A vs C and so on.</span></p>\r
-\r
-<h3><a name="_Toc235958693"></a><a name="_Toc102494900"></a><a\r
-name="_Toc102494411"></a><a name="_Toc101065363"><span style='mso-bookmark:\r
-_Toc102494411'><span style='mso-bookmark:_Toc102494900'><span style='mso-bookmark:\r
-_Toc235958693'><span lang=EN-US>BLAST Format [Recommended]</span></span></span></span></a></h3>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span lang=EN-US># BLAST_MATRIX FORMAT</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US># ALPHABET=AGCT</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US><span\r
-style='mso-spacerun:yes'> </span>A G C T</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>A 0 1 2 3</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>G 0 2 3 4</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>C 1 1 2 3</span></p>\r
-\r
-<p class=examplefileCxSpLast><span lang=EN-US>...</span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF>The alphabet can be freely defined</span></p>\r
-\r
-<h2><a name="_Toc235958694"></a><a name="_Toc102494901"></a><a\r
-name="_Toc102494412"></a><a name="_Toc101065364"><span style='mso-bookmark:\r
-_Toc102494412'><span style='mso-bookmark:_Toc102494901'><span style='mso-bookmark:\r
-_Toc235958694'><span lang=EN-US>Sequences Weights</span></span></span></span></a></h2>\r
-\r
-<p class=MyNormal><span lang=AF>Create your own weight file, using the\r
--seq_weight flag:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span lang=EN-US># SINGLE_SEQ_WEIGHT_FORMAT_01</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>seq_name1 v1</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>seq_name2 v2</span></p>\r
-\r
-<p class=examplefileCxSpLast><span lang=EN-US>...</span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF>No duplicate allowed. Sequences not included in\r
-the set of sequences provided to t_coffee will be ignored. Order is free. V1 is\r
-a float. Un-weighted sequences will see their weight set to 1.</span></p>\r
-\r
-<span lang=AF style='font-size:11.0pt;font-family:"Times New Roman";mso-fareast-font-family:\r
-"Times New Roman";mso-bidi-font-family:"Courier New";mso-ansi-language:AF;\r
-mso-fareast-language:EN-US;mso-bidi-language:AR-SA'><br clear=all\r
-style='page-break-before:always'>\r
-</span>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 3.0pt;\r
-padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0mm;margin-right:\r
-4.25pt'>\r
-\r
-<p class=ChapterTitle><a name="_Toc235958695"><span lang=EN-US>Known Problems</span></a></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF>1-Sensitivity to sequence order: It is\r
-difficult to implement a MSA algorithm totally insensitive to the order of\r
-input of the sequences. In t_coffee, robustness is increased by sorting the\r
-sequences alphabetically before aligning them. Beware that this can result in\r
-confusing output where sequences with similar name are unexpectedly close to\r
-one another in the final alignment.</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>2-Nucleotides sequences with long stretches of\r
-Ns will cause problems to lalign, especially when using Mocca. To avoid any\r
-problem, filter out these nucleotides before running mocca.</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>3-Stop codons are sometimes coded with '*' in\r
-protein sequences. This will cause the program to crash or hang. Please replace\r
-the '*' signs with an X.</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>4-Results can differ from one architecture to\r
-another, due rounding differences. This is caused by the tree estimation\r
-procedcure. If you want to make sure an alignment is reproducible, you should\r
-keep the associated dendrogram.</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>5-Deploying the program on a </span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 3.0pt;\r
-padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0mm;margin-right:\r
-4.25pt'>\r
-\r
-<p class=ChapterTitle><a name="_Toc235958696"><span lang=EN-US>Technical Notes</span></a></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF>These notes are only meant for internal\r
-development.</span></p>\r
-\r
-<h2><a name="_Toc235958697"></a><a name="_Toc102494904"></a><a\r
-name="_Toc102494413"><span style='mso-bookmark:_Toc102494904'><span\r
-style='mso-bookmark:_Toc235958697'><span lang=EN-US>Development</span></span></span></a></h2>\r
-\r
-<p class=MyNormal><span lang=AF>The following examples are only meant for\r
-internal development, and are used to insure stability from release to release</span></p>\r
-\r
-<h4><span lang=AF>profile2list</span></h4>\r
-\r
-<p class=MyNormal><span lang=AF>prf1: profile containing one structure</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>prf2: profile containing one structure</span></p>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee<span style='mso-spacerun:yes'> \r
-</span>Rsample_profile1.aln,Rsample_profile2.aln -mode=3dcoffee\r
--outfile=aligned_prf.aln</span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-</div>\r
-\r
-<h3><a name="_Toc235958698"></a><a name="_Toc102494905"></a><a\r
-name="_Toc102494414"><span style='mso-bookmark:_Toc102494905'><span\r
-style='mso-bookmark:_Toc235958698'><span lang=EN-US>Command Line List</span></span></span></a></h3>\r
-\r
-<p class=MyNormal><span lang=AF>These command lines have been checked before\r
-every release (along with the other CL in this documentation:</span></p>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MyNormal><span lang=AF>-external methods;</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US><span\r
-style='mso-tab-count:1'>   </span>PROMPT: t_coffee sample_seq1.fasta \96in=Mclustalw_pair,Mclustalw_msa,Mslow_pair\r
-\96outfile=clustal_text</span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF>-fugue_client</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee \96in Ssample_seq5.fasta Pstruc4.pdb Mfugue_pair</span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF>-A list of command lines kindly provided by\r
-James Watson (used to crash the pg before version 3.40)</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee -in Sseq.fas P2PTC Mfugue_pair</span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee -in S2seqs.fas Mfugue_pair -template_file SELF_P_</span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee -mode 3dcoffee -in Sseq.fas P2PTC</span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee -mode 3dcoffee -in S2seqs.fas -template_file SELF_P_</span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF>-A list of command lines that crashed the\r
-program before 3.81</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee sample_seq6.fasta \96in Mfast_pair Msap_pair Mfugue_pair \96template_file\r
-template_file6.template </span></p>\r
-\r
-</div>\r
-\r
-<p class=MsoBodyText><span lang=EN-US><span style='mso-tab-count:1'>            </span>-A\r
-command line to read \93relaxed\94 pdb files...</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee \96in Msap_pair Ssample_seq7.fasta \96template_file\r
-template_file7.template \96weight 1001 \96out_lib test_lib7.tc_lib \96lib_only </span></p>\r
-\r
-</div>\r
-\r
-<p class=MsoBodyText><span lang=EN-US><span style='mso-tab-count:1'>            </span>-Parsing\r
-of MARNA libraries</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee \96in Lmarna.tc_lib \96outfile maran.test</span></p>\r
-\r
-</div>\r
-\r
-<p class=MsoBodyText><span lang=EN-US><span style='mso-tab-count:1'>            </span>-Parsing\r
-of long sequence lines:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee \96in Asample_aln5.aln \96outfile test.aln</span></p>\r
-\r
-</div>\r
-\r
-<p class=MsoBodyText><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 3.0pt;\r
-padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0mm;margin-right:\r
-4.25pt'>\r
-\r
-<p class=ChapterTitle><a name="_Toc235958699"></a><a name="_Toc102494906"><span\r
-style='mso-bookmark:_Toc235958699'><span lang=EN-US>To D</span></span></a><span\r
-style='mso-bookmark:_Toc235958699'><span lang=EN-US>o\85</span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF>-implement UPGMA tree computation</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>-implement seq2dpa_tree</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>-debug dpa</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>-Reconciliate sequences and template when\r
-reading the template</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>-Add the server command lines to the checking\r
-procedure</span></p>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MsoBodyText><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-</div>\r
-\r
-</body>\r
-\r
-</html>\r
+ /* Font Definitions */
+@font-face
+       {font-family:Arial;
+       panose-1:2 11 6 4 2 2 2 2 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Courier New";
+       panose-1:2 7 3 9 2 2 5 2 4 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Times;
+       panose-1:2 0 5 0 0 0 0 0 0 0;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Geneva;
+       panose-1:2 11 5 3 3 4 4 4 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Tms Rmn";
+       panose-1:0 0 0 0 0 0 0 0 0 0;
+       mso-font-charset:77;
+       mso-generic-font-family:roman;
+       mso-font-format:other;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Helv;
+       panose-1:0 0 0 0 0 0 0 0 0 0;
+       mso-font-charset:77;
+       mso-generic-font-family:swiss;
+       mso-font-format:other;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"MS Serif";
+       panose-1:0 0 0 0 0 0 0 0 0 0;
+       mso-font-charset:77;
+       mso-generic-font-family:roman;
+       mso-font-format:other;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"MS Sans Serif";
+       panose-1:0 0 0 0 0 0 0 0 0 0;
+       mso-font-charset:77;
+       mso-generic-font-family:swiss;
+       mso-font-format:other;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"New York";
+       panose-1:0 0 0 0 0 0 0 0 0 0;
+       mso-font-charset:77;
+       mso-generic-font-family:roman;
+       mso-font-format:other;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:System;
+       panose-1:0 0 0 0 0 0 0 0 0 0;
+       mso-font-charset:77;
+       mso-generic-font-family:swiss;
+       mso-font-format:other;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Wingdings;
+       panose-1:5 2 1 2 1 8 4 8 7 8;
+       mso-font-charset:2;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:0 0 65536 0 -2147483648 0;}
+@font-face
+       {font-family:"MS Mincho";
+       mso-font-charset:78;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16778247 0 131072 0;}
+@font-face
+       {font-family:Batang;
+       mso-font-charset:79;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16786438 0 524288 0;}
+@font-face
+       {font-family:SimSun;
+       mso-font-charset:80;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16778254 0 262144 0;}
+@font-face
+       {font-family:PMingLiU;
+       mso-font-charset:81;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16778248 0 1048576 0;}
+@font-face
+       {font-family:"MS Gothic";
+       mso-font-charset:78;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16778247 0 131072 0;}
+@font-face
+       {font-family:Century;
+       panose-1:2 4 6 4 5 5 5 2 3 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Verdana;
+       panose-1:2 11 6 4 3 5 4 4 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Calibri;
+       panose-1:2 15 5 2 2 2 4 3 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Cambria;
+       panose-1:2 4 5 3 5 4 6 3 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Cambria Math";
+       panose-1:0 0 0 0 0 0 0 0 0 0;
+       mso-font-charset:77;
+       mso-generic-font-family:roman;
+       mso-font-format:other;
+       mso-font-pitch:auto;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Tahoma;
+       panose-1:2 11 6 4 3 5 4 4 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"MS Mincho";
+       mso-font-alt:"MS Mincho";
+       mso-font-charset:128;
+       mso-generic-font-family:modern;
+       mso-font-pitch:fixed;
+       mso-font-signature:-536870145 1791491579 18 0 131231 0;}
+@font-face
+       {font-family:PMingLiU;
+       mso-font-alt:PMingLiU;
+       mso-font-charset:136;
+       mso-generic-font-family:roman;
+       mso-font-pitch:variable;
+       mso-font-signature:-1610611969 684719354 22 0 1048577 0;}
+@font-face
+       {font-family:"Trebuchet MS";
+       panose-1:2 11 6 3 2 2 2 2 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Century Schoolbook";
+       panose-1:2 4 6 4 5 5 5 2 3 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Wingdings 2";
+       panose-1:5 2 1 2 1 5 7 7 7 7;
+       mso-font-charset:2;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:0 0 65536 0 -2147483648 0;}
+@font-face
+       {font-family:Impact;
+       panose-1:2 11 8 6 3 9 2 5 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Arial Black";
+       panose-1:2 11 10 4 2 1 2 2 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Abadi MT Condensed Extra Bold";
+       panose-1:2 11 10 6 3 1 1 1 1 3;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Abadi MT Condensed Light";
+       panose-1:2 11 3 6 3 1 1 1 1 3;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"American Typewriter";
+       panose-1:2 9 6 4 2 0 4 2 3 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"American Typewriter Condensed";
+       panose-1:2 9 6 6 2 0 4 2 3 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"American Typewriter Light";
+       panose-1:2 9 3 4 2 0 4 2 3 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Andale Mono";
+       panose-1:2 11 5 9 0 0 0 0 0 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Apple Casual";
+       panose-1:0 1 4 0 0 0 0 0 0 0;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Apple Chancery";
+       panose-1:3 2 7 2 4 5 6 6 5 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Apple Symbols";
+       panose-1:2 0 0 0 0 0 0 0 0 0;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Arial Bold";
+       panose-1:2 11 7 4 2 2 2 2 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Arial Italic";
+       panose-1:2 11 6 4 2 2 2 9 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Arial Narrow";
+       panose-1:2 11 5 6 2 2 2 3 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Arial Narrow Bold";
+       panose-1:2 11 7 6 2 2 2 3 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Arial Narrow Bold Italic";
+       panose-1:2 11 7 6 2 2 2 10 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Arial Narrow Italic";
+       panose-1:2 11 6 6 2 2 2 10 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Arial Rounded MT Bold";
+       panose-1:2 15 7 4 3 5 4 3 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Arial Unicode MS";
+       panose-1:2 11 6 4 2 2 2 2 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Ayuthaya;
+       panose-1:0 0 4 0 0 0 0 0 0 0;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Baskerville;
+       panose-1:2 2 5 2 7 4 1 2 3 3;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Baskerville Old Face";
+       panose-1:2 2 6 2 8 5 5 2 3 3;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Baskerville Semibold";
+       panose-1:2 2 7 2 7 4 0 2 2 3;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Bauhaus 93";
+       panose-1:4 3 9 5 2 11 2 2 12 2;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Bell MT";
+       panose-1:2 2 5 3 6 3 5 2 3 3;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Bernard MT Condensed";
+       panose-1:2 5 8 6 6 9 5 2 4 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Big Caslon";
+       panose-1:2 0 6 3 9 0 0 2 0 3;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"BlairMdITC TT-Medium";
+       panose-1:0 0 5 0 0 0 0 0 0 0;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Book Antiqua";
+       panose-1:2 4 6 2 5 3 5 3 3 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Bookman Old Style";
+       panose-1:2 5 6 4 5 5 5 2 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Bookshelf Symbol 7";
+       panose-1:5 1 1 1 1 1 1 1 1 1;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Bordeaux Roman Bold LET";
+       panose-1:2 0 5 0 0 0 0 0 0 0;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Braggadocio;
+       panose-1:4 3 11 7 13 11 2 2 4 3;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Britannic Bold";
+       panose-1:2 11 9 3 6 7 3 2 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Brush Script MT Italic";
+       panose-1:3 6 8 2 4 4 6 7 3 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Calisto MT";
+       panose-1:2 4 6 3 5 5 5 3 3 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Candara;
+       panose-1:2 14 5 2 3 3 3 2 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Century Gothic";
+       panose-1:2 11 5 2 2 2 2 2 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Chalkboard;
+       panose-1:3 5 6 2 4 2 2 2 2 5;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Chalkduster;
+       panose-1:3 5 6 2 4 2 2 2 2 5;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Cochin;
+       panose-1:2 0 6 3 2 0 0 2 0 3;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Colonna MT";
+       panose-1:4 2 8 5 6 2 2 3 2 3;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Comic Sans MS";
+       panose-1:3 15 7 2 3 3 2 2 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Comic Sans MS Bold";
+       panose-1:3 15 9 2 3 3 2 2 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Consolas;
+       panose-1:2 11 6 9 2 2 4 3 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Constantia;
+       panose-1:2 3 6 2 5 3 6 3 3 3;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Cooper Black";
+       panose-1:2 8 9 4 4 3 11 2 4 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Copperplate;
+       panose-1:2 0 5 4 0 0 0 2 0 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Copperplate Gothic Bold";
+       panose-1:2 14 7 5 2 2 6 2 4 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Copperplate Gothic Light";
+       panose-1:2 14 5 7 2 2 6 2 4 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Copperplate Light";
+       panose-1:2 0 6 4 3 0 0 2 0 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Corbel;
+       panose-1:2 11 5 3 2 2 4 2 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Cracked;
+       panose-1:0 0 4 0 0 0 0 0 0 0;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Curlz MT";
+       panose-1:4 4 4 4 5 7 2 2 2 2;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Desdemona;
+       panose-1:4 2 5 5 2 14 3 4 5 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Didot;
+       panose-1:2 0 5 3 0 0 0 2 0 3;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Edwardian Script ITC";
+       panose-1:3 3 3 2 4 7 7 13 8 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Engravers MT";
+       panose-1:2 9 7 7 8 5 5 2 3 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Euphemia UCAS";
+       panose-1:2 11 5 3 4 1 2 2 1 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Eurostile;
+       panose-1:2 11 5 4 2 2 2 5 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Footlight MT Light";
+       panose-1:2 4 6 2 6 3 10 2 3 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Franklin Gothic Book";
+       panose-1:2 11 5 3 2 1 2 2 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Franklin Gothic Medium";
+       panose-1:2 11 6 3 2 1 2 2 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Futura;
+       panose-1:2 11 6 2 2 2 4 2 3 3;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Futura Condensed";
+       panose-1:2 11 5 6 2 2 4 3 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Garamond;
+       panose-1:2 2 4 4 3 3 1 1 8 3;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Georgia;
+       panose-1:2 4 5 2 5 4 5 2 3 3;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Gill Sans";
+       panose-1:2 11 5 2 2 1 4 2 2 3;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Gill Sans Light";
+       panose-1:2 11 3 2 2 1 4 2 2 3;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Gill Sans MT";
+       panose-1:2 11 5 2 2 1 4 2 2 3;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Gill Sans Ultra Bold";
+       panose-1:2 11 10 2 2 1 4 2 2 3;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Gloucester MT Extra Condensed";
+       panose-1:2 3 8 8 2 6 1 1 1 1;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Goudy Old Style";
+       panose-1:2 2 5 2 5 3 5 2 3 3;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Haettenschweiler;
+       panose-1:2 11 7 6 4 9 2 6 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Handwriting - Dakota";
+       panose-1:2 0 4 0 0 0 0 0 0 0;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Harrington;
+       panose-1:4 4 5 5 5 10 2 2 7 2;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Helvetica Neue";
+       panose-1:2 0 5 3 0 0 0 2 0 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Helvetica Neue Black Condensed";
+       panose-1:2 0 10 6 0 0 0 2 0 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Helvetica Neue Bold Condensed";
+       panose-1:2 0 8 6 0 0 0 2 0 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Helvetica Neue Light";
+       panose-1:2 0 4 3 0 0 0 2 0 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Helvetica Neue Medium";
+       panose-1:2 11 6 4 2 2 2 2 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Helvetica Neue UltraLight";
+       panose-1:2 0 2 6 0 0 0 2 0 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Herculanum;
+       panose-1:2 0 5 5 0 0 0 2 0 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Hoefler Text";
+       panose-1:2 3 6 2 5 5 6 2 2 3;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Hoefler Text Ornaments";
+       panose-1:0 0 0 0 0 0 0 0 0 0;
+       mso-font-charset:2;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:0 0 65536 0 -2147483648 0;}
+@font-face
+       {font-family:"Imprint MT Shadow";
+       panose-1:4 2 6 5 6 3 3 3 2 2;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:InaiMathi;
+       panose-1:2 0 5 0 0 0 0 0 0 0;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Kino MT";
+       panose-1:4 3 7 5 13 12 2 2 7 3;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Krungthep;
+       panose-1:2 0 4 0 0 0 0 0 0 0;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:KufiStandardGK;
+       panose-1:0 0 4 0 0 0 0 0 0 0;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Lucida Blackletter";
+       panose-1:0 0 0 0 0 0 0 0 0 0;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Lucida Bright";
+       panose-1:2 4 6 2 5 5 5 2 3 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Lucida Calligraphy";
+       panose-1:3 1 1 1 1 1 1 1 1 1;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Lucida Console";
+       panose-1:2 11 6 9 4 5 4 2 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Lucida Fax";
+       panose-1:2 6 6 2 5 5 5 2 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Lucida Grande";
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Lucida Handwriting";
+       panose-1:3 1 1 1 1 1 1 1 1 1;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Lucida Sans";
+       panose-1:2 11 6 2 3 5 4 2 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Lucida Sans Typewriter";
+       panose-1:2 11 5 9 3 5 4 3 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Lucida Sans Unicode";
+       panose-1:2 11 6 2 3 5 4 2 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Marker Felt";
+       panose-1:2 0 4 0 0 0 0 0 0 0;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Marlett;
+       panose-1:0 0 0 0 0 0 0 0 0 0;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Matura MT Script Capitals";
+       panose-1:3 2 8 2 6 6 2 7 2 2;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Menlo Bold";
+       panose-1:2 11 7 9 3 6 4 2 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Menlo Bold Italic";
+       panose-1:2 11 7 9 3 3 4 11 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Menlo Italic";
+       panose-1:2 11 6 9 3 3 4 11 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Menlo Regular";
+       panose-1:2 11 6 9 3 8 4 2 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Microsoft Sans Serif";
+       panose-1:2 11 6 4 2 2 2 2 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Mistral;
+       panose-1:3 9 7 2 3 4 7 2 4 3;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Modern No\. 20";
+       panose-1:2 7 7 4 7 5 5 2 3 3;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Monaco;
+       panose-1:2 0 5 0 0 0 0 0 0 0;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Monotype Corsiva";
+       panose-1:3 1 1 1 1 2 1 1 1 1;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Monotype Sorts";
+       panose-1:1 1 6 1 1 1 1 1 1 1;
+       mso-font-charset:2;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:0 0 65536 0 -2147483648 0;}
+@font-face
+       {font-family:"MS Reference Sans Serif";
+       panose-1:2 11 6 4 3 5 4 4 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"MS Reference Specialty";
+       panose-1:5 0 5 0 0 0 0 0 0 0;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"MT Extra";
+       panose-1:5 5 1 2 1 2 5 2 2 2;
+       mso-font-charset:2;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:0 0 65536 0 -2147483648 0;}
+@font-face
+       {font-family:"News Gothic MT";
+       panose-1:2 11 5 4 2 2 3 2 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Onyx;
+       panose-1:4 5 6 2 8 7 2 2 2 3;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Optima;
+       panose-1:2 0 5 3 6 0 0 2 0 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Optima ExtraBlack";
+       panose-1:2 0 11 3 0 0 0 2 0 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Palatino;
+       panose-1:2 0 5 0 0 0 0 0 0 0;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Papyrus;
+       panose-1:2 11 6 2 4 2 0 2 3 3;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Papyrus Condensed";
+       panose-1:2 11 6 2 4 2 0 2 3 3;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Perpetua;
+       panose-1:2 2 5 2 6 4 1 2 3 3;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Perpetua Titling MT";
+       panose-1:2 2 5 2 6 5 5 2 8 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Plantagenet Cherokee";
+       panose-1:2 2 0 0 0 0 0 0 0 0;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Playbill;
+       panose-1:4 5 6 3 10 6 2 2 2 2;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"PortagoITC TT";
+       panose-1:0 0 4 0 0 0 0 0 0 0;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Rockwell;
+       panose-1:2 6 6 3 2 2 5 2 4 3;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Rockwell Extra Bold";
+       panose-1:2 6 9 3 4 5 5 2 4 3;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Sathu;
+       panose-1:0 0 4 0 0 0 0 0 0 0;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Silom;
+       panose-1:0 0 4 0 0 0 0 0 0 0;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Skia;
+       panose-1:2 13 5 2 2 2 4 2 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Stencil;
+       panose-1:4 4 9 5 13 8 2 2 4 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Tahoma Bold";
+       panose-1:2 11 8 4 3 5 4 4 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Thonburi;
+       panose-1:0 0 4 0 0 0 0 0 0 0;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Times New Roman Bold Italic";
+       panose-1:2 2 7 3 6 5 5 9 3 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Trebuchet MS Bold";
+       panose-1:2 11 7 3 2 2 2 2 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Trebuchet MS Bold Italic";
+       panose-1:2 11 7 3 2 2 2 9 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Trebuchet MS Italic";
+       panose-1:2 11 6 3 2 2 2 9 2 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Tw Cen MT";
+       panose-1:2 11 6 2 2 1 4 2 6 3;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Webdings;
+       panose-1:5 3 1 2 1 5 9 6 7 3;
+       mso-font-charset:2;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:0 0 65536 0 -2147483648 0;}
+@font-face
+       {font-family:"Wide Latin";
+       panose-1:2 10 10 7 5 5 5 2 4 4;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Wingdings 3";
+       panose-1:5 4 1 2 1 8 7 7 7 7;
+       mso-font-charset:2;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:0 0 65536 0 -2147483648 0;}
+@font-face
+       {font-family:"Zapf Dingbats";
+       panose-1:5 2 1 2 1 7 4 2 6 9;
+       mso-font-charset:2;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:0 0 65536 0 -2147483648 0;}
+@font-face
+       {font-family:Zapfino;
+       panose-1:3 3 3 0 4 7 7 7 12 3;
+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Lucida Grande CE";
+       panose-1:2 11 6 0 4 5 2 2 2 4;
+       mso-font-charset:88;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:5 0 0 0 2 0;}
+@font-face
+       {font-family:"Charcoal CY";
+       panose-1:0 0 4 0 0 0 0 0 0 0;
+       mso-font-charset:89;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:513 0 0 0 4 0;}
+@font-face
+       {font-family:"Geneva CY";
+       panose-1:0 0 4 0 0 0 0 0 0 0;
+       mso-font-charset:89;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:513 0 0 0 4 0;}
+@font-face
+       {font-family:"Helvetica CY";
+       panose-1:0 0 4 0 0 0 0 0 0 0;
+       mso-font-charset:89;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:513 0 0 0 4 0;}
+@font-face
+       {font-family:"Lucida Grande CY";
+       panose-1:2 11 6 0 4 5 2 2 2 4;
+       mso-font-charset:89;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:513 0 0 0 4 0;}
+@font-face
+       {font-family:"Apple LiGothic Medium";
+       panose-1:2 0 5 0 0 0 0 0 0 0;
+       mso-font-charset:81;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16778248 0 1048576 0;}
+@font-face
+       {font-family:"Apple LiSung Light";
+       panose-1:2 0 5 0 0 0 0 0 0 0;
+       mso-font-charset:81;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16778248 0 1048576 0;}
+@font-face
+       {font-family:BiauKai;
+       panose-1:2 1 6 1 0 1 1 1 1 1;
+       mso-font-charset:81;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16778248 0 1048576 0;}
+@font-face
+       {font-family:"Heiti TC Light";
+       panose-1:2 0 0 0 0 0 0 0 0 0;
+       mso-font-charset:81;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16778248 0 1048576 0;}
+@font-face
+       {font-family:"Heiti TC Medium";
+       panose-1:0 0 0 0 0 0 0 0 0 0;
+       mso-font-charset:81;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16778248 0 1048576 0;}
+@font-face
+       {font-family:"\5137\5B8B Pro";
+       mso-font-charset:81;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16778248 0 1048576 0;}
+@font-face
+       {font-family:"\5137\9ED1 Pro";
+       mso-font-charset:81;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16778248 0 1048576 0;}
+@font-face
+       {font-family:"GB18030 Bitmap";
+       mso-font-charset:80;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16778254 0 262144 0;}
+@font-face
+       {font-family:Hei;
+       panose-1:2 0 5 0 0 0 0 0 0 0;
+       mso-font-charset:80;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16778254 0 262144 0;}
+@font-face
+       {font-family:"Heiti SC Light";
+       panose-1:2 0 0 0 0 0 0 0 0 0;
+       mso-font-charset:80;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16778254 0 262144 0;}
+@font-face
+       {font-family:"Heiti SC Medium";
+       panose-1:0 0 0 0 0 0 0 0 0 0;
+       mso-font-charset:80;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16778254 0 262144 0;}
+@font-face
+       {font-family:"Hiragino Sans GB W3";
+       panose-1:2 11 3 0 0 0 0 0 0 0;
+       mso-font-charset:80;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16778254 0 262144 0;}
+@font-face
+       {font-family:"Hiragino Sans GB W6";
+       panose-1:2 11 6 0 0 0 0 0 0 0;
+       mso-font-charset:80;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16778254 0 262144 0;}
+@font-face
+       {font-family:Kai;
+       panose-1:2 0 5 0 0 0 0 0 0 0;
+       mso-font-charset:80;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16778254 0 262144 0;}
+@font-face
+       {font-family:\534E\6587\4EFF\5B8B;
+       mso-font-charset:80;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16778254 0 262144 0;}
+@font-face
+       {font-family:\534E\6587\9ED1\4F53;
+       mso-font-charset:80;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16778254 0 262144 0;}
+@font-face
+       {font-family:\534E\6587\6977\4F53;
+       mso-font-charset:80;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16778254 0 262144 0;}
+@font-face
+       {font-family:\534E\6587\5B8B\4F53;
+       mso-font-charset:80;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16778254 0 262144 0;}
+@font-face
+       {font-family:\534E\6587\7EC6\9ED1;
+       mso-font-charset:80;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16778254 0 262144 0;}
+@font-face
+       {font-family:"MS PGothic";
+       mso-font-charset:78;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16778247 0 131072 0;}
+@font-face
+       {font-family:"MS PMincho";
+       mso-font-charset:78;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16778247 0 131072 0;}
+@font-face
+       {font-family:Osaka;
+       panose-1:2 11 6 0 0 0 0 0 0 0;
+       mso-font-charset:78;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16778247 0 131072 0;}
+@font-face
+       {font-family:Osaka\2212\7B49\5E45;
+       mso-font-charset:78;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16778247 0 131072 0;}
+@font-face
+       {font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 Pro W3";
+       mso-font-charset:78;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16778247 0 131072 0;}
+@font-face
+       {font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 Pro W6";
+       mso-font-charset:78;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16778247 0 131072 0;}
+@font-face
+       {font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 ProN W3";
+       mso-font-charset:78;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16778247 0 131072 0;}
+@font-face
+       {font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 ProN W6";
+       mso-font-charset:78;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16778247 0 131072 0;}
+@font-face
+       {font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 Std W8";
+       mso-font-charset:78;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16778247 0 131072 0;}
+@font-face
+       {font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 StdN W8";
+       mso-font-charset:78;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16778247 0 131072 0;}
+@font-face
+       {font-family:"\30D2\30E9\30AE\30CE\4E38\30B4 Pro W4";
+       mso-font-charset:78;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16778247 0 131072 0;}
+@font-face
+       {font-family:"\30D2\30E9\30AE\30CE\4E38\30B4 ProN W4";
+       mso-font-charset:78;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16778247 0 131072 0;}
+@font-face
+       {font-family:"\30D2\30E9\30AE\30CE\660E\671D Pro W3";
+       mso-font-charset:78;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16778247 0 131072 0;}
+@font-face
+       {font-family:"\30D2\30E9\30AE\30CE\660E\671D Pro W6";
+       mso-font-charset:78;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16778247 0 131072 0;}
+@font-face
+       {font-family:"\30D2\30E9\30AE\30CE\660E\671D ProN W3";
+       mso-font-charset:78;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16778247 0 131072 0;}
+@font-face
+       {font-family:"\30D2\30E9\30AE\30CE\660E\671D ProN W6";
+       mso-font-charset:78;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16778247 0 131072 0;}
+@font-face
+       {font-family:\30E1\30A4\30EA\30AA;
+       mso-font-charset:78;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16778247 0 131072 0;}
+@font-face
+       {font-family:AppleGothic;
+       panose-1:2 0 5 0 0 0 0 0 0 0;
+       mso-font-charset:79;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16786438 0 524288 0;}
+@font-face
+       {font-family:AppleMyungjo;
+       panose-1:2 0 5 0 0 0 0 0 0 0;
+       mso-font-charset:79;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16786438 0 524288 0;}
+@font-face
+       {font-family:PC\BA85\C870;
+       mso-font-charset:79;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16786438 0 524288 0;}
+@font-face
+       {font-family:\AD74\B9BC;
+       mso-font-charset:79;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16786438 0 524288 0;}
+@font-face
+       {font-family:"FE Modern font face";
+       mso-font-charset:79;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16786438 0 524288 0;}
+@font-face
+       {font-family:\D544\AE30\CCB4;
+       mso-font-charset:79;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16786438 0 524288 0;}
+@font-face
+       {font-family:\D5E4\B4DC\B77C\C778A;
+       mso-font-charset:79;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:1 0 16786438 0 524288 0;}
+@font-face
+       {font-family:starbats;
+       mso-font-charset:2;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:0 0 0 0 0 0;}
+@font-face
+       {font-family:Minion-Bold;
+       panose-1:0 0 0 0 0 0 0 0 0 0;
+       mso-font-alt:Cambria;
+       mso-font-charset:77;
+       mso-generic-font-family:roman;
+       mso-font-format:other;
+       mso-font-pitch:auto;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Minion-Regular;
+       panose-1:0 0 0 0 0 0 0 0 0 0;
+       mso-font-charset:77;
+       mso-generic-font-family:roman;
+       mso-font-format:other;
+       mso-font-pitch:auto;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Minion-Italic;
+       panose-1:0 0 0 0 0 0 0 0 0 0;
+       mso-font-charset:77;
+       mso-generic-font-family:roman;
+       mso-font-format:other;
+       mso-font-pitch:auto;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:OfficinaSerif-Bold;
+       panose-1:0 0 0 0 0 0 0 0 0 0;
+       mso-font-charset:77;
+       mso-generic-font-family:roman;
+       mso-font-format:other;
+       mso-font-pitch:auto;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Minion-Semibold;
+       panose-1:0 0 0 0 0 0 0 0 0 0;
+       mso-font-charset:77;
+       mso-generic-font-family:roman;
+       mso-font-format:other;
+       mso-font-pitch:auto;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:OfficinaSans-Book;
+       panose-1:0 0 0 0 0 0 0 0 0 0;
+       mso-font-charset:77;
+       mso-generic-font-family:swiss;
+       mso-font-format:other;
+       mso-font-pitch:auto;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:OfficinaSans-Bold;
+       panose-1:0 0 0 0 0 0 0 0 0 0;
+       mso-font-charset:77;
+       mso-generic-font-family:swiss;
+       mso-font-format:other;
+       mso-font-pitch:auto;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:Helvetica-Bold;
+       panose-1:0 0 0 0 0 0 0 0 0 0;
+       mso-font-charset:77;
+       mso-generic-font-family:swiss;
+       mso-font-format:other;
+       mso-font-pitch:auto;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:OfficinaSerif-Book;
+       panose-1:0 0 0 0 0 0 0 0 0 0;
+       mso-font-charset:77;
+       mso-generic-font-family:roman;
+       mso-font-format:other;
+       mso-font-pitch:auto;
+       mso-font-signature:3 0 0 0 1 0;}
+ /* Style Definitions */
+p.MsoNormal, li.MsoNormal, div.MsoNormal
+       {mso-style-parent:"";
+       margin:0cm;
+       margin-bottom:.0001pt;
+       mso-pagination:widow-orphan;
+       font-size:8.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Garamond;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";}
+h1
+       {mso-style-link:"Heading 1 Char";
+       mso-style-next:"Body Text";
+       margin-top:12.0pt;
+       margin-right:0cm;
+       margin-bottom:6.0pt;
+       margin-left:0cm;
+       mso-pagination:widow-orphan;
+       page-break-after:avoid;
+       mso-outline-level:1;
+       font-size:16.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Arial Black";
+       color:gray;
+       letter-spacing:-1.25pt;
+       mso-font-kerning:14.0pt;
+       font-weight:normal;}
+h2
+       {mso-style-update:auto;
+       mso-style-parent:"Heading 1";
+       mso-style-next:"Body Text";
+       margin-top:12.0pt;
+       margin-right:0cm;
+       margin-bottom:6.0pt;
+       margin-left:0cm;
+       mso-line-height-alt:12.0pt;
+       mso-pagination:widow-orphan;
+       page-break-after:avoid;
+       mso-outline-level:2;
+       font-size:16.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Arial Black";
+       color:gray;
+       letter-spacing:-.5pt;
+       mso-font-kerning:14.0pt;
+       font-weight:normal;}
+h3
+       {mso-style-update:auto;
+       mso-style-next:Normal;
+       margin-top:6.0pt;
+       margin-right:0cm;
+       margin-bottom:6.0pt;
+       margin-left:18.0pt;
+       text-align:justify;
+       mso-pagination:none;
+       page-break-after:avoid;
+       mso-outline-level:3;
+       mso-hyphenate:none;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:14.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Arial Black";
+       mso-hansi-font-family:Symbol;
+       font-weight:normal;}
+h4
+       {mso-style-update:auto;
+       mso-style-parent:MyNormal;
+       mso-style-next:Normal;
+       margin-top:2.0pt;
+       margin-right:0cm;
+       margin-bottom:12.0pt;
+       margin-left:1.0cm;
+       mso-pagination:none;
+       page-break-after:avoid;
+       mso-outline-level:4;
+       mso-hyphenate:none;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:11.0pt;
+       font-family:"Times New Roman";
+       mso-bidi-font-family:"Courier New";
+       text-transform:uppercase;
+       letter-spacing:1.5pt;
+       mso-ansi-language:AF;
+       font-weight:normal;}
+h5
+       {mso-style-next:"Body Text";
+       margin-top:2.0pt;
+       margin-right:0cm;
+       margin-bottom:12.0pt;
+       margin-left:0cm;
+       mso-pagination:widow-orphan;
+       page-break-after:avoid;
+       mso-outline-level:5;
+       mso-element:frame;
+       mso-element-frame-width:90.0pt;
+       mso-element-wrap:around;
+       mso-element-anchor-vertical:paragraph;
+       mso-element-anchor-horizontal:page;
+       mso-element-left:60.05pt;
+       mso-element-top:.05pt;
+       mso-height-rule:exactly;
+       font-size:9.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Arial Black";
+       letter-spacing:-.25pt;
+       font-weight:normal;}
+h6
+       {mso-style-next:"Body Text";
+       margin:0cm;
+       margin-bottom:.0001pt;
+       mso-pagination:widow-orphan;
+       page-break-after:avoid;
+       mso-outline-level:6;
+       mso-element:frame;
+       mso-element-frame-width:90.0pt;
+       mso-element-wrap:around;
+       mso-element-anchor-vertical:paragraph;
+       mso-element-anchor-horizontal:page;
+       mso-element-left:60.05pt;
+       mso-element-top:.05pt;
+       mso-height-rule:exactly;
+       font-size:8.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Garamond;
+       font-weight:normal;}
+p.MsoHeading7, li.MsoHeading7, div.MsoHeading7
+       {mso-style-next:"Body Text";
+       margin-top:3.0pt;
+       margin-right:0cm;
+       margin-bottom:0cm;
+       margin-left:0cm;
+       margin-bottom:.0001pt;
+       mso-pagination:widow-orphan;
+       mso-outline-level:7;
+       background:#F2F2F2;
+       mso-shading:windowtext;
+       mso-pattern:gray-5 auto;
+       border:none;
+       mso-border-alt:solid white .75pt;
+       padding:0cm;
+       mso-padding-alt:12.0pt 12.0pt 12.0pt 12.0pt;
+       mso-element:frame;
+       mso-element-frame-width:189.0pt;
+       mso-element-frame-hspace:12.0pt;
+       mso-element-wrap:around;
+       mso-element-anchor-vertical:paragraph;
+       mso-element-anchor-horizontal:page;
+       mso-element-left:74.45pt;
+       mso-element-top:.05pt;
+       mso-height-rule:exactly;
+       font-size:14.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Garamond;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       letter-spacing:-.25pt;
+       font-style:italic;
+       mso-bidi-font-style:normal;}
+p.MsoHeading8, li.MsoHeading8, div.MsoHeading8
+       {mso-style-next:"Body Text";
+       margin-top:3.0pt;
+       margin-right:0cm;
+       margin-bottom:0cm;
+       margin-left:0cm;
+       margin-bottom:.0001pt;
+       text-align:center;
+       line-height:16.0pt;
+       mso-line-height-rule:exactly;
+       mso-pagination:widow-orphan;
+       page-break-after:avoid;
+       mso-outline-level:8;
+       border:none;
+       mso-border-top-alt:solid windowtext 3.0pt;
+       mso-border-bottom-alt:solid windowtext .75pt;
+       padding:0cm;
+       mso-padding-alt:0cm 0cm 0cm 0cm;
+       mso-element:frame;
+       mso-element-frame-width:93.0pt;
+       mso-element-wrap:around;
+       mso-element-anchor-vertical:paragraph;
+       mso-element-anchor-horizontal:page;
+       mso-element-left:60.05pt;
+       mso-element-top:.05pt;
+       mso-height-rule:exactly;
+       font-size:7.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Arial Black";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       text-transform:uppercase;
+       letter-spacing:3.0pt;}
+p.MsoHeading9, li.MsoHeading9, div.MsoHeading9
+       {mso-style-next:"Body Text";
+       margin-top:4.0pt;
+       margin-right:0cm;
+       margin-bottom:3.0pt;
+       margin-left:0cm;
+       mso-pagination:widow-orphan;
+       page-break-after:avoid;
+       mso-outline-level:9;
+       font-size:8.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Garamond;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       mso-font-kerning:14.0pt;
+       font-weight:bold;
+       mso-bidi-font-weight:normal;
+       font-style:italic;
+       mso-bidi-font-style:normal;}
+p.MsoIndex1, li.MsoIndex1, div.MsoIndex1
+       {mso-style-update:auto;
+       mso-style-noshow:yes;
+       mso-style-next:Normal;
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:0cm;
+       margin-left:8.0pt;
+       margin-bottom:.0001pt;
+       text-indent:-8.0pt;
+       mso-pagination:widow-orphan;
+       font-size:8.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Garamond;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";}
+p.MsoToc1, li.MsoToc1, div.MsoToc1
+       {mso-style-noshow:yes;
+       margin-top:6.0pt;
+       margin-right:0cm;
+       margin-bottom:0cm;
+       margin-left:0cm;
+       margin-bottom:.0001pt;
+       mso-pagination:widow-orphan;
+       font-size:12.0pt;
+       font-family:Cambria;
+       mso-ascii-font-family:Cambria;
+       mso-ascii-theme-font:minor-latin;
+       mso-fareast-font-family:"Times New Roman";
+       mso-hansi-font-family:Cambria;
+       mso-hansi-theme-font:minor-latin;
+       mso-bidi-font-family:"Times New Roman";
+       font-weight:bold;
+       mso-bidi-font-weight:normal;}
+p.MsoToc2, li.MsoToc2, div.MsoToc2
+       {mso-style-noshow:yes;
+       mso-style-parent:"TOC 1";
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:0cm;
+       margin-left:8.0pt;
+       margin-bottom:.0001pt;
+       mso-pagination:widow-orphan;
+       font-size:11.0pt;
+       font-family:Cambria;
+       mso-ascii-font-family:Cambria;
+       mso-ascii-theme-font:minor-latin;
+       mso-fareast-font-family:"Times New Roman";
+       mso-hansi-font-family:Cambria;
+       mso-hansi-theme-font:minor-latin;
+       mso-bidi-font-family:"Times New Roman";
+       font-weight:bold;
+       mso-bidi-font-weight:normal;}
+p.MsoToc3, li.MsoToc3, div.MsoToc3
+       {mso-style-noshow:yes;
+       mso-style-next:Normal;
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:0cm;
+       margin-left:16.0pt;
+       margin-bottom:.0001pt;
+       mso-pagination:widow-orphan;
+       font-size:11.0pt;
+       font-family:Cambria;
+       mso-ascii-font-family:Cambria;
+       mso-ascii-theme-font:minor-latin;
+       mso-fareast-font-family:"Times New Roman";
+       mso-hansi-font-family:Cambria;
+       mso-hansi-theme-font:minor-latin;
+       mso-bidi-font-family:"Times New Roman";}
+p.MsoToc4, li.MsoToc4, div.MsoToc4
+       {mso-style-noshow:yes;
+       mso-style-next:Normal;
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:0cm;
+       margin-left:24.0pt;
+       margin-bottom:.0001pt;
+       mso-pagination:widow-orphan;
+       font-size:10.0pt;
+       font-family:Cambria;
+       mso-ascii-font-family:Cambria;
+       mso-ascii-theme-font:minor-latin;
+       mso-fareast-font-family:"Times New Roman";
+       mso-hansi-font-family:Cambria;
+       mso-hansi-theme-font:minor-latin;
+       mso-bidi-font-family:"Times New Roman";}
+p.MsoToc5, li.MsoToc5, div.MsoToc5
+       {mso-style-update:auto;
+       mso-style-noshow:yes;
+       mso-style-next:Normal;
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:0cm;
+       margin-left:32.0pt;
+       margin-bottom:.0001pt;
+       mso-pagination:widow-orphan;
+       font-size:10.0pt;
+       font-family:Cambria;
+       mso-ascii-font-family:Cambria;
+       mso-ascii-theme-font:minor-latin;
+       mso-fareast-font-family:"Times New Roman";
+       mso-hansi-font-family:Cambria;
+       mso-hansi-theme-font:minor-latin;
+       mso-bidi-font-family:"Times New Roman";}
+p.MsoToc6, li.MsoToc6, div.MsoToc6
+       {mso-style-update:auto;
+       mso-style-noshow:yes;
+       mso-style-next:Normal;
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:0cm;
+       margin-left:40.0pt;
+       margin-bottom:.0001pt;
+       mso-pagination:widow-orphan;
+       font-size:10.0pt;
+       font-family:Cambria;
+       mso-ascii-font-family:Cambria;
+       mso-ascii-theme-font:minor-latin;
+       mso-fareast-font-family:"Times New Roman";
+       mso-hansi-font-family:Cambria;
+       mso-hansi-theme-font:minor-latin;
+       mso-bidi-font-family:"Times New Roman";}
+p.MsoToc7, li.MsoToc7, div.MsoToc7
+       {mso-style-update:auto;
+       mso-style-noshow:yes;
+       mso-style-next:Normal;
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:0cm;
+       margin-left:48.0pt;
+       margin-bottom:.0001pt;
+       mso-pagination:widow-orphan;
+       font-size:10.0pt;
+       font-family:Cambria;
+       mso-ascii-font-family:Cambria;
+       mso-ascii-theme-font:minor-latin;
+       mso-fareast-font-family:"Times New Roman";
+       mso-hansi-font-family:Cambria;
+       mso-hansi-theme-font:minor-latin;
+       mso-bidi-font-family:"Times New Roman";}
+p.MsoToc8, li.MsoToc8, div.MsoToc8
+       {mso-style-update:auto;
+       mso-style-noshow:yes;
+       mso-style-next:Normal;
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:0cm;
+       margin-left:56.0pt;
+       margin-bottom:.0001pt;
+       mso-pagination:widow-orphan;
+       font-size:10.0pt;
+       font-family:Cambria;
+       mso-ascii-font-family:Cambria;
+       mso-ascii-theme-font:minor-latin;
+       mso-fareast-font-family:"Times New Roman";
+       mso-hansi-font-family:Cambria;
+       mso-hansi-theme-font:minor-latin;
+       mso-bidi-font-family:"Times New Roman";}
+p.MsoToc9, li.MsoToc9, div.MsoToc9
+       {mso-style-update:auto;
+       mso-style-noshow:yes;
+       mso-style-next:Normal;
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:0cm;
+       margin-left:64.0pt;
+       margin-bottom:.0001pt;
+       mso-pagination:widow-orphan;
+       font-size:10.0pt;
+       font-family:Cambria;
+       mso-ascii-font-family:Cambria;
+       mso-ascii-theme-font:minor-latin;
+       mso-fareast-font-family:"Times New Roman";
+       mso-hansi-font-family:Cambria;
+       mso-hansi-theme-font:minor-latin;
+       mso-bidi-font-family:"Times New Roman";}
+p.MsoHeader, li.MsoHeader, div.MsoHeader
+       {margin:0cm;
+       margin-bottom:.0001pt;
+       mso-pagination:widow-orphan lines-together;
+       tab-stops:center 216.0pt right 432.0pt;
+       font-size:7.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Arial Black";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       text-transform:uppercase;
+       letter-spacing:3.0pt;}
+p.MsoFooter, li.MsoFooter, div.MsoFooter
+       {margin:0cm;
+       margin-bottom:.0001pt;
+       text-align:center;
+       mso-pagination:widow-orphan lines-together;
+       tab-stops:center 216.0pt right 432.0pt;
+       border:none;
+       mso-border-top-alt:solid windowtext .75pt;
+       padding:0cm;
+       mso-padding-alt:3.0pt 0cm 0cm 0cm;
+       font-size:8.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Arial Black";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";}
+p.MsoCaption, li.MsoCaption, div.MsoCaption
+       {mso-style-next:"Body Text";
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:12.0pt;
+       margin-left:0cm;
+       mso-pagination:widow-orphan;
+       font-size:8.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Garamond;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       letter-spacing:-.25pt;}
+span.MsoCommentReference
+       {mso-style-noshow:yes;
+       mso-style-parent:"";
+       mso-ansi-font-size:8.0pt;}
+span.MsoLineNumber
+       {mso-style-parent:"";
+       mso-ansi-font-size:9.0pt;
+       font-family:Arial;
+       mso-ascii-font-family:Arial;
+       mso-hansi-font-family:Arial;
+       mso-bidi-font-family:Arial;}
+span.MsoPageNumber
+       {mso-style-parent:"";
+       font-weight:bold;
+       mso-bidi-font-weight:normal;}
+p.MsoList, li.MsoList, div.MsoList
+       {mso-style-parent:"Body Text";
+       mso-style-link:"List Char";
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:12.0pt;
+       margin-left:18.0pt;
+       text-align:justify;
+       mso-pagination:widow-orphan;
+       tab-stops:36.0pt;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Garamond;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       letter-spacing:-.25pt;}
+p.MsoListBullet, li.MsoListBullet, div.MsoListBullet
+       {mso-style-parent:List;
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:12.0pt;
+       margin-left:18.0pt;
+       text-align:justify;
+       text-indent:0cm;
+       mso-pagination:widow-orphan;
+       mso-list:l25 level1 lfo5;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Garamond;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       letter-spacing:-.25pt;}
+p.MsoListNumber, li.MsoListNumber, div.MsoListNumber
+       {mso-style-parent:List;
+       margin-top:0cm;
+       margin-right:18.0pt;
+       margin-bottom:12.0pt;
+       margin-left:36.0pt;
+       text-align:justify;
+       text-indent:-18.0pt;
+       mso-pagination:widow-orphan;
+       mso-list:l8 level1 lfo7;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Garamond;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       letter-spacing:-.25pt;}
+p.MsoList2, li.MsoList2, div.MsoList2
+       {mso-style-parent:List;
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:12.0pt;
+       margin-left:54.0pt;
+       text-align:justify;
+       mso-pagination:widow-orphan;
+       tab-stops:54.0pt;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Garamond;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       letter-spacing:-.25pt;}
+p.MsoList3, li.MsoList3, div.MsoList3
+       {mso-style-parent:List;
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:12.0pt;
+       margin-left:72.0pt;
+       text-align:justify;
+       mso-pagination:widow-orphan;
+       tab-stops:72.0pt;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Garamond;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       letter-spacing:-.25pt;}
+p.MsoList4, li.MsoList4, div.MsoList4
+       {mso-style-parent:List;
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:12.0pt;
+       margin-left:90.0pt;
+       text-align:justify;
+       mso-pagination:widow-orphan;
+       tab-stops:90.0pt;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Garamond;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       letter-spacing:-.25pt;}
+p.MsoList5, li.MsoList5, div.MsoList5
+       {mso-style-parent:List;
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:12.0pt;
+       margin-left:108.0pt;
+       text-align:justify;
+       mso-pagination:widow-orphan;
+       tab-stops:108.0pt;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Garamond;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       letter-spacing:-.25pt;}
+p.MsoListBullet2, li.MsoListBullet2, div.MsoListBullet2
+       {mso-style-parent:"List Bullet";
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:12.0pt;
+       margin-left:54.0pt;
+       text-align:justify;
+       text-indent:0cm;
+       mso-pagination:widow-orphan;
+       mso-list:l7 level1 lfo8;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Garamond;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       letter-spacing:-.25pt;}
+p.MsoListBullet3, li.MsoListBullet3, div.MsoListBullet3
+       {mso-style-parent:"List Bullet";
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:12.0pt;
+       margin-left:72.0pt;
+       text-align:justify;
+       text-indent:0cm;
+       mso-pagination:widow-orphan;
+       mso-list:l6 level1 lfo9;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Garamond;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       letter-spacing:-.25pt;}
+p.MsoListBullet4, li.MsoListBullet4, div.MsoListBullet4
+       {mso-style-parent:"List Bullet";
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:12.0pt;
+       margin-left:90.0pt;
+       text-align:justify;
+       text-indent:0cm;
+       mso-pagination:widow-orphan;
+       mso-list:l5 level1 lfo10;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Garamond;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       letter-spacing:-.25pt;}
+p.MsoListBullet5, li.MsoListBullet5, div.MsoListBullet5
+       {margin-top:0cm;
+       margin-right:18.0pt;
+       margin-bottom:0cm;
+       margin-left:18.0pt;
+       margin-bottom:.0001pt;
+       text-indent:-18.0pt;
+       line-height:16.0pt;
+       mso-line-height-rule:exactly;
+       mso-pagination:widow-orphan;
+       mso-list:l22 level1 lfo12;
+       tab-stops:list 18.0pt;
+       border:none;
+       mso-border-bottom-alt:solid windowtext .75pt;
+       padding:0cm;
+       mso-padding-alt:0cm 0cm 0cm 0cm;
+       mso-element:frame;
+       mso-element-frame-width:93.0pt;
+       mso-element-wrap:around;
+       mso-element-anchor-vertical:paragraph;
+       mso-element-anchor-horizontal:page;
+       mso-element-left:60.05pt;
+       mso-element-top:.05pt;
+       mso-height-rule:exactly;
+       font-size:9.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Garamond;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";}
+p.MsoListNumber2, li.MsoListNumber2, div.MsoListNumber2
+       {mso-style-parent:"List Number";
+       margin-top:0cm;
+       margin-right:18.0pt;
+       margin-bottom:12.0pt;
+       margin-left:54.0pt;
+       text-align:justify;
+       text-indent:-18.0pt;
+       mso-pagination:widow-orphan;
+       mso-list:l3 level1 lfo14;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Garamond;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       letter-spacing:-.25pt;}
+p.MsoListNumber3, li.MsoListNumber3, div.MsoListNumber3
+       {mso-style-parent:"List Number";
+       margin-top:0cm;
+       margin-right:18.0pt;
+       margin-bottom:12.0pt;
+       margin-left:72.0pt;
+       text-align:justify;
+       text-indent:-18.0pt;
+       mso-pagination:widow-orphan;
+       mso-list:l2 level1 lfo15;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Garamond;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       letter-spacing:-.25pt;}
+p.MsoListNumber4, li.MsoListNumber4, div.MsoListNumber4
+       {mso-style-parent:"List Number";
+       margin-top:0cm;
+       margin-right:18.0pt;
+       margin-bottom:12.0pt;
+       margin-left:90.0pt;
+       text-align:justify;
+       text-indent:-18.0pt;
+       mso-pagination:widow-orphan;
+       mso-list:l1 level1 lfo16;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Garamond;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       letter-spacing:-.25pt;}
+p.MsoListNumber5, li.MsoListNumber5, div.MsoListNumber5
+       {mso-style-parent:"List Number";
+       margin-top:0cm;
+       margin-right:18.0pt;
+       margin-bottom:12.0pt;
+       margin-left:108.0pt;
+       text-align:justify;
+       text-indent:-18.0pt;
+       mso-pagination:widow-orphan;
+       mso-list:l0 level1 lfo17;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Garamond;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       letter-spacing:-.25pt;}
+p.MsoTitle, li.MsoTitle, div.MsoTitle
+       {mso-style-parent:"Heading Base";
+       margin-top:5.0pt;
+       margin-right:0cm;
+       margin-bottom:180.0pt;
+       margin-left:0cm;
+       text-align:center;
+       line-height:30.0pt;
+       mso-line-height-rule:exactly;
+       mso-pagination:widow-orphan;
+       page-break-after:avoid;
+       border:none;
+       mso-border-bottom-alt:solid gray .75pt;
+       padding:0cm;
+       mso-padding-alt:0cm 0cm 14.0pt 0cm;
+       font-size:24.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Arial Black";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       color:gray;
+       letter-spacing:-1.75pt;
+       mso-font-kerning:14.0pt;}
+p.MsoBodyText, li.MsoBodyText, div.MsoBodyText
+       {margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:12.0pt;
+       margin-left:0cm;
+       text-align:justify;
+       mso-pagination:widow-orphan;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Garamond;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       letter-spacing:-.25pt;}
+p.MsoBodyTextIndent, li.MsoBodyTextIndent, div.MsoBodyTextIndent
+       {mso-style-parent:"Body Text";
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:12.0pt;
+       margin-left:0cm;
+       text-align:justify;
+       text-indent:18.0pt;
+       mso-pagination:widow-orphan;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Garamond;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       letter-spacing:-.25pt;}
+p.MsoListContinue, li.MsoListContinue, div.MsoListContinue
+       {mso-style-parent:List;
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:8.0pt;
+       margin-left:18.0pt;
+       text-align:justify;
+       mso-pagination:widow-orphan;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Garamond;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       letter-spacing:-.25pt;}
+p.MsoListContinue2, li.MsoListContinue2, div.MsoListContinue2
+       {mso-style-parent:"List Continue";
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:8.0pt;
+       margin-left:54.0pt;
+       text-align:justify;
+       mso-pagination:widow-orphan;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Garamond;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       letter-spacing:-.25pt;}
+p.MsoListContinue3, li.MsoListContinue3, div.MsoListContinue3
+       {mso-style-parent:"List Continue";
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:8.0pt;
+       margin-left:72.0pt;
+       text-align:justify;
+       mso-pagination:widow-orphan;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Garamond;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       letter-spacing:-.25pt;}
+p.MsoListContinue4, li.MsoListContinue4, div.MsoListContinue4
+       {mso-style-parent:"List Continue";
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:8.0pt;
+       margin-left:90.0pt;
+       text-align:justify;
+       mso-pagination:widow-orphan;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Garamond;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       letter-spacing:-.25pt;}
+p.MsoListContinue5, li.MsoListContinue5, div.MsoListContinue5
+       {mso-style-parent:"List Continue";
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:8.0pt;
+       margin-left:108.0pt;
+       text-align:justify;
+       mso-pagination:widow-orphan;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Garamond;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       letter-spacing:-.25pt;}
+p.MsoSubtitle, li.MsoSubtitle, div.MsoSubtitle
+       {mso-style-parent:Title;
+       mso-style-next:"Body Text";
+       margin-top:97.0pt;
+       margin-right:0cm;
+       margin-bottom:0cm;
+       margin-left:0cm;
+       margin-bottom:.0001pt;
+       text-align:center;
+       line-height:10.0pt;
+       mso-pagination:widow-orphan;
+       page-break-after:avoid;
+       border:none;
+       mso-border-bottom-alt:solid gray .75pt;
+       padding:0cm;
+       mso-padding-alt:0cm 0cm 14.0pt 0cm;
+       font-size:9.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Garamond;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       color:gray;
+       text-transform:uppercase;
+       letter-spacing:1.5pt;
+       mso-font-kerning:14.0pt;
+       mso-bidi-font-weight:bold;}
+p.MsoDate, li.MsoDate, div.MsoDate
+       {mso-style-parent:"Body Text";
+       margin-top:24.0pt;
+       margin-right:0cm;
+       margin-bottom:8.0pt;
+       margin-left:0cm;
+       text-align:center;
+       mso-pagination:widow-orphan;
+       font-size:10.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       font-weight:bold;
+       mso-bidi-font-weight:normal;}
+a:link, span.MsoHyperlink
+       {color:blue;
+       text-decoration:underline;
+       text-underline:single;}
+a:visited, span.MsoHyperlinkFollowed
+       {color:purple;
+       text-decoration:underline;
+       text-underline:single;}
+em
+       {mso-style-parent:"";
+       mso-ansi-font-size:9.0pt;
+       font-family:"Arial Black";
+       mso-ascii-font-family:"Arial Black";
+       mso-hansi-font-family:"Arial Black";
+       font-style:normal;}
+p.MsoPlainText, li.MsoPlainText, div.MsoPlainText
+       {margin:0cm;
+       margin-bottom:.0001pt;
+       mso-pagination:widow-orphan;
+       font-size:10.0pt;
+       font-family:"Courier New";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Courier New";
+       mso-ansi-language:FR;
+       mso-fareast-language:FR;}
+code
+       {mso-bidi-font-size:10.0pt;
+       font-family:"Courier New";
+       mso-ascii-font-family:"Courier New";
+       mso-fareast-font-family:"MS Mincho";
+       mso-hansi-font-family:"Courier New";
+       mso-bidi-font-family:"Courier New";}
+span.Heading1Char
+       {mso-style-name:"Heading 1 Char";
+       mso-style-locked:yes;
+       mso-style-link:"Heading 1";
+       mso-ansi-font-size:16.0pt;
+       font-family:"Arial Black";
+       mso-ascii-font-family:"Arial Black";
+       mso-hansi-font-family:"Arial Black";
+       color:gray;
+       letter-spacing:-1.25pt;
+       mso-font-kerning:14.0pt;
+       mso-ansi-language:EN-US;
+       mso-fareast-language:EN-US;}
+p.MyNormal, li.MyNormal, div.MyNormal
+       {mso-style-name:MyNormal;
+       mso-style-update:auto;
+       mso-style-link:"MyNormal Char";
+       margin-top:2.0pt;
+       margin-right:0cm;
+       margin-bottom:6.0pt;
+       margin-left:42.55pt;
+       text-align:justify;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:11.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Courier New";
+       mso-ansi-language:AF;}
+span.MyNormalChar
+       {mso-style-name:"MyNormal Char";
+       mso-style-locked:yes;
+       mso-style-parent:"example Char";
+       mso-style-link:MyNormal;
+       mso-ansi-font-size:11.0pt;
+       mso-bidi-font-size:11.0pt;
+       font-family:"Courier New";
+       mso-ascii-font-family:"Courier New";
+       mso-hansi-font-family:"Courier New";
+       mso-bidi-font-family:"Courier New";
+       mso-ansi-language:AF;
+       mso-fareast-language:EN-US;}
+span.exampleChar
+       {mso-style-name:"example Char";
+       mso-style-locked:yes;
+       mso-style-link:example;
+       mso-ansi-font-size:8.0pt;
+       font-family:"Courier New";
+       mso-ascii-font-family:"Courier New";
+       mso-hansi-font-family:"Courier New";
+       mso-bidi-font-family:"Courier New";
+       mso-ansi-language:EN-US;
+       mso-fareast-language:EN-US;}
+p.example, li.example, div.example
+       {mso-style-name:example;
+       mso-style-update:auto;
+       mso-style-link:"example Char";
+       margin-top:6.0pt;
+       margin-right:0cm;
+       margin-bottom:6.0pt;
+       margin-left:0cm;
+       text-indent:36.0pt;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:8.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Courier New";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Courier New";}
+p.FAQ, li.FAQ, div.FAQ
+       {mso-style-name:FAQ;
+       mso-style-update:auto;
+       mso-style-parent:MyNormal;
+       margin-top:12.0pt;
+       margin-right:0cm;
+       margin-bottom:6.0pt;
+       margin-left:1.0cm;
+       text-align:justify;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:11.0pt;
+       mso-bidi-font-size:14.0pt;
+       font-family:"Comic Sans MS";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Courier New";
+       mso-ansi-language:EN-GB;
+       font-weight:bold;
+       mso-bidi-font-weight:normal;}
+span.ListChar
+       {mso-style-name:"List Char";
+       mso-style-locked:yes;
+       mso-style-parent:"Text body Char";
+       mso-style-link:List;
+       mso-ansi-font-size:12.0pt;
+       font-family:Garamond;
+       mso-ascii-font-family:Garamond;
+       mso-hansi-font-family:Garamond;
+       letter-spacing:-.25pt;
+       mso-ansi-language:EN-US;
+       mso-fareast-language:EN-US;}
+span.TextbodyChar
+       {mso-style-name:"Text body Char";
+       mso-style-locked:yes;
+       mso-style-link:"Text body";
+       mso-ansi-font-size:12.0pt;
+       mso-ansi-language:EN-US;
+       mso-fareast-language:EN-US;}
+p.Textbody, li.Textbody, div.Textbody
+       {mso-style-name:"Text body";
+       mso-style-link:"Text body Char";
+       margin:0cm;
+       margin-bottom:.0001pt;
+       text-align:justify;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";}
+p.HeadingBase, li.HeadingBase, div.HeadingBase
+       {mso-style-name:"Heading Base";
+       mso-style-next:"Body Text";
+       margin-top:12.0pt;
+       margin-right:0cm;
+       margin-bottom:6.0pt;
+       margin-left:0cm;
+       mso-pagination:widow-orphan;
+       page-break-after:avoid;
+       font-size:18.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Arial;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       mso-font-kerning:14.0pt;
+       font-weight:bold;
+       mso-bidi-font-weight:normal;}
+p.BlockQuotation, li.BlockQuotation, div.BlockQuotation
+       {mso-style-name:"Block Quotation";
+       mso-style-next:"Body Text";
+       margin-top:0cm;
+       margin-right:30.0pt;
+       margin-bottom:12.0pt;
+       margin-left:30.0pt;
+       text-align:justify;
+       mso-pagination:widow-orphan;
+       background:#484848;
+       mso-shading:windowtext;
+       mso-pattern:gray-10 gray;
+       border:none;
+       mso-border-alt:solid white .75pt;
+       padding:0cm;
+       mso-padding-alt:12.0pt 12.0pt 12.0pt 12.0pt;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Garamond;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       letter-spacing:-.25pt;}
+p.BlockQuotationFirst, li.BlockQuotationFirst, div.BlockQuotationFirst
+       {mso-style-name:"Block Quotation First";
+       mso-style-next:"Block Quotation";
+       margin-top:0cm;
+       margin-right:24.0pt;
+       margin-bottom:0cm;
+       margin-left:24.0pt;
+       margin-bottom:.0001pt;
+       text-indent:3.0pt;
+       mso-pagination:widow-orphan lines-together;
+       background:#E5E5E5;
+       mso-shading:windowtext;
+       mso-pattern:gray-10 auto;
+       border:none;
+       mso-border-top-alt:solid white .75pt;
+       mso-border-left-alt:solid white .75pt;
+       mso-border-right-alt:solid white .75pt;
+       padding:0cm;
+       mso-padding-alt:6.0pt 6.0pt 0cm 6.0pt;
+       font-size:10.5pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Arial Black";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       letter-spacing:-.5pt;}
+p.BlockQuotationLast, li.BlockQuotationLast, div.BlockQuotationLast
+       {mso-style-name:"Block Quotation Last";
+       mso-style-parent:"Block Quotation";
+       mso-style-next:"Body Text";
+       margin-top:0cm;
+       margin-right:36.0pt;
+       margin-bottom:12.0pt;
+       margin-left:36.0pt;
+       mso-pagination:widow-orphan lines-together;
+       font-size:10.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       font-style:italic;
+       mso-bidi-font-style:normal;}
+p.BodyTextKeep, li.BodyTextKeep, div.BodyTextKeep
+       {mso-style-name:"Body Text Keep";
+       mso-style-parent:"Body Text";
+       mso-style-next:"Body Text";
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:12.0pt;
+       margin-left:0cm;
+       text-align:justify;
+       mso-pagination:widow-orphan;
+       page-break-after:avoid;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Garamond;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       letter-spacing:-.25pt;}
+p.ChapterLabel, li.ChapterLabel, div.ChapterLabel
+       {mso-style-name:"Chapter Label";
+       mso-style-next:"Body Text";
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:12.0pt;
+       margin-left:0cm;
+       mso-pagination:widow-orphan;
+       page-break-after:avoid;
+       border:none;
+       mso-border-bottom-alt:solid windowtext .75pt;
+       padding:0cm;
+       mso-padding-alt:0cm 0cm 3.0pt 0cm;
+       font-size:7.5pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Arial Black";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       text-transform:uppercase;
+       letter-spacing:3.5pt;
+       mso-font-kerning:14.0pt;}
+p.ChapterSubtitle, li.ChapterSubtitle, div.ChapterSubtitle
+       {mso-style-name:"Chapter Subtitle";
+       mso-style-next:"Body Text";
+       margin-top:0cm;
+       margin-right:90.0pt;
+       margin-bottom:18.0pt;
+       margin-left:0cm;
+       mso-line-height-alt:12.0pt;
+       mso-pagination:widow-orphan lines-together;
+       page-break-after:avoid;
+       font-size:14.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Garamond;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       letter-spacing:-1.0pt;
+       mso-font-kerning:14.0pt;
+       font-style:italic;
+       mso-bidi-font-style:normal;}
+p.ChapterTitle, li.ChapterTitle, div.ChapterTitle
+       {mso-style-name:"Chapter Title";
+       mso-style-update:auto;
+       mso-style-link:"Chapter Title Char";
+       mso-style-next:"Chapter Subtitle";
+       margin-top:30.0pt;
+       margin-right:4.25pt;
+       margin-bottom:102.0pt;
+       margin-left:0cm;
+       text-align:center;
+       mso-line-height-alt:22.0pt;
+       page-break-before:always;
+       mso-pagination:widow-orphan lines-together;
+       page-break-after:avoid;
+       background:#CCCCCC;
+       border:none;
+       mso-border-alt:solid windowtext 3.0pt;
+       padding:0cm;
+       mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;
+       font-size:36.0pt;
+       mso-bidi-font-size:48.0pt;
+       font-family:"Arial Black";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       color:white;
+       letter-spacing:-1.75pt;
+       mso-font-kerning:14.0pt;}
+span.ChapterTitleChar
+       {mso-style-name:"Chapter Title Char";
+       mso-style-locked:yes;
+       mso-style-link:"Chapter Title";
+       mso-ansi-font-size:36.0pt;
+       mso-bidi-font-size:48.0pt;
+       font-family:"Arial Black";
+       mso-ascii-font-family:"Arial Black";
+       mso-hansi-font-family:"Arial Black";
+       color:white;
+       letter-spacing:-1.75pt;
+       mso-font-kerning:14.0pt;
+       mso-ansi-language:EN-US;
+       mso-fareast-language:EN-US;}
+p.CompanyName, li.CompanyName, div.CompanyName
+       {mso-style-name:"Company Name";
+       mso-style-next:Normal;
+       margin-top:21.0pt;
+       margin-right:0cm;
+       margin-bottom:3.0pt;
+       margin-left:0cm;
+       line-height:16.0pt;
+       mso-line-height-rule:exactly;
+       mso-pagination:widow-orphan;
+       font-size:19.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Garamond;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       text-transform:uppercase;
+       mso-font-kerning:18.0pt;}
+p.DocumentLabel, li.DocumentLabel, div.DocumentLabel
+       {mso-style-name:"Document Label";
+       margin-top:12.0pt;
+       margin-right:0cm;
+       margin-bottom:18.0pt;
+       margin-left:0cm;
+       mso-pagination:widow-orphan;
+       page-break-after:avoid;
+       font-size:18.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Garamond;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       mso-font-kerning:14.0pt;
+       font-weight:bold;
+       mso-bidi-font-weight:normal;}
+p.FooterEven, li.FooterEven, div.FooterEven
+       {mso-style-name:"Footer Even";
+       mso-style-parent:Footer;
+       margin:0cm;
+       margin-bottom:.0001pt;
+       text-align:center;
+       mso-pagination:widow-orphan lines-together;
+       tab-stops:center 216.0pt right 432.0pt;
+       border:none;
+       mso-border-top-alt:solid windowtext .75pt;
+       padding:0cm;
+       mso-padding-alt:3.0pt 0cm 0cm 0cm;
+       font-size:8.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Arial Black";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";}
+p.FooterFirst, li.FooterFirst, div.FooterFirst
+       {mso-style-name:"Footer First";
+       mso-style-parent:Footer;
+       margin:0cm;
+       margin-bottom:.0001pt;
+       text-align:center;
+       mso-pagination:widow-orphan lines-together;
+       tab-stops:center 216.0pt;
+       font-size:8.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Arial Black";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       letter-spacing:-.5pt;}
+p.FooterOdd, li.FooterOdd, div.FooterOdd
+       {mso-style-name:"Footer Odd";
+       mso-style-parent:Footer;
+       margin:0cm;
+       margin-bottom:.0001pt;
+       text-align:center;
+       mso-pagination:widow-orphan lines-together;
+       tab-stops:right 0cm center 216.0pt right 432.0pt;
+       border:none;
+       mso-border-top-alt:solid windowtext .75pt;
+       padding:0cm;
+       mso-padding-alt:3.0pt 0cm 0cm 0cm;
+       font-size:8.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Arial Black";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";}
+p.FootnoteBase, li.FootnoteBase, div.FootnoteBase
+       {mso-style-name:"Footnote Base";
+       margin-top:12.0pt;
+       margin-right:0cm;
+       margin-bottom:0cm;
+       margin-left:0cm;
+       margin-bottom:.0001pt;
+       mso-pagination:widow-orphan;
+       font-size:9.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Garamond;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";}
+p.HeaderBase, li.HeaderBase, div.HeaderBase
+       {mso-style-name:"Header Base";
+       margin:0cm;
+       margin-bottom:.0001pt;
+       mso-pagination:widow-orphan lines-together;
+       tab-stops:center 216.0pt right 432.0pt;
+       font-size:8.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Garamond;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";}
+p.HeaderEven, li.HeaderEven, div.HeaderEven
+       {mso-style-name:"Header Even";
+       mso-style-parent:Header;
+       margin:0cm;
+       margin-bottom:.0001pt;
+       mso-pagination:widow-orphan lines-together;
+       tab-stops:center 216.0pt right 432.0pt;
+       font-size:7.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Arial Black";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       text-transform:uppercase;
+       letter-spacing:3.0pt;}
+p.HeaderFirst, li.HeaderFirst, div.HeaderFirst
+       {mso-style-name:"Header First";
+       mso-style-parent:Header;
+       margin:0cm;
+       margin-bottom:.0001pt;
+       mso-pagination:widow-orphan lines-together;
+       tab-stops:center 216.0pt;
+       font-size:7.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Garamond;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       text-transform:uppercase;
+       letter-spacing:3.0pt;
+       font-weight:bold;
+       mso-bidi-font-weight:normal;}
+p.HeaderOdd, li.HeaderOdd, div.HeaderOdd
+       {mso-style-name:"Header Odd";
+       mso-style-parent:Header;
+       margin:0cm;
+       margin-bottom:.0001pt;
+       text-align:right;
+       mso-pagination:widow-orphan lines-together;
+       tab-stops:right 0cm center 216.0pt right 432.0pt;
+       font-size:7.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Arial Black";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       text-transform:uppercase;
+       letter-spacing:3.0pt;}
+p.Icon1, li.Icon1, div.Icon1
+       {mso-style-name:"Icon 1";
+       margin-top:3.0pt;
+       margin-right:0cm;
+       margin-bottom:0cm;
+       margin-left:0cm;
+       margin-bottom:.0001pt;
+       text-align:center;
+       line-height:72.0pt;
+       mso-line-height-rule:exactly;
+       mso-pagination:widow-orphan;
+       background:#E5E5E5;
+       mso-shading:windowtext;
+       mso-pattern:gray-10 auto;
+       mso-element:frame;
+       mso-element-frame-width:72.0pt;
+       mso-element-frame-hspace:9.35pt;
+       mso-element-wrap:around;
+       mso-element-anchor-vertical:paragraph;
+       mso-element-anchor-horizontal:margin;
+       mso-element-top:.05pt;
+       mso-height-rule:exactly;
+       font-size:80.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Wingdings;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       color:white;
+       letter-spacing:-.5pt;
+       font-weight:bold;
+       mso-bidi-font-weight:normal;}
+p.IndexBase, li.IndexBase, div.IndexBase
+       {mso-style-name:"Index Base";
+       margin:0cm;
+       margin-bottom:.0001pt;
+       line-height:12.0pt;
+       mso-pagination:widow-orphan;
+       tab-stops:right 198.0pt;
+       font-size:9.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Garamond;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";}
+p.ListBulletFirst, li.ListBulletFirst, div.ListBulletFirst
+       {mso-style-name:"List Bullet First";
+       mso-style-parent:"List Bullet";
+       mso-style-next:"List Bullet";
+       margin-top:4.0pt;
+       margin-right:0cm;
+       margin-bottom:8.0pt;
+       margin-left:18.0pt;
+       text-indent:0cm;
+       mso-pagination:widow-orphan;
+       mso-list:l25 level1 lfo5;
+       font-size:10.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";}
+p.ListBulletLast, li.ListBulletLast, div.ListBulletLast
+       {mso-style-name:"List Bullet Last";
+       mso-style-parent:"List Bullet";
+       mso-style-next:"Body Text";
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:12.0pt;
+       margin-left:18.0pt;
+       text-indent:0cm;
+       mso-pagination:widow-orphan;
+       mso-list:l25 level1 lfo5;
+       font-size:10.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";}
+p.ListFirst, li.ListFirst, div.ListFirst
+       {mso-style-name:"List First";
+       mso-style-parent:List;
+       mso-style-next:List;
+       margin-top:4.0pt;
+       margin-right:0cm;
+       margin-bottom:4.0pt;
+       margin-left:36.0pt;
+       text-indent:-18.0pt;
+       mso-pagination:widow-orphan;
+       tab-stops:36.0pt;
+       font-size:10.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";}
+p.ListLast, li.ListLast, div.ListLast
+       {mso-style-name:"List Last";
+       mso-style-parent:List;
+       mso-style-next:"Body Text";
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:12.0pt;
+       margin-left:36.0pt;
+       text-indent:-18.0pt;
+       mso-pagination:widow-orphan;
+       tab-stops:36.0pt;
+       font-size:10.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";}
+p.ListNumberFirst, li.ListNumberFirst, div.ListNumberFirst
+       {mso-style-name:"List Number First";
+       mso-style-parent:"List Number";
+       mso-style-next:"List Number";
+       margin-top:4.0pt;
+       margin-right:0cm;
+       margin-bottom:8.0pt;
+       margin-left:36.0pt;
+       text-indent:-18.0pt;
+       mso-pagination:widow-orphan;
+       mso-list:l8 level1 lfo7;
+       font-size:10.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";}
+p.ListNumberLast, li.ListNumberLast, div.ListNumberLast
+       {mso-style-name:"List Number Last";
+       mso-style-parent:"List Number";
+       mso-style-next:"Body Text";
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:12.0pt;
+       margin-left:36.0pt;
+       text-indent:-18.0pt;
+       mso-pagination:widow-orphan;
+       mso-list:l8 level1 lfo7;
+       font-size:10.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";}
+p.PartLabel, li.PartLabel, div.PartLabel
+       {mso-style-name:"Part Label";
+       mso-style-link:"Part Label Char";
+       mso-style-next:Normal;
+       margin-top:16.0pt;
+       margin-right:0cm;
+       margin-bottom:0cm;
+       margin-left:0cm;
+       margin-bottom:.0001pt;
+       text-align:center;
+       line-height:78.0pt;
+       mso-line-height-rule:exactly;
+       mso-pagination:widow-orphan;
+       background:#CCCCCC;
+       mso-shading:windowtext;
+       mso-pattern:gray-20 auto;
+       mso-element:frame;
+       mso-element-frame-width:102.25pt;
+       mso-element-frame-hspace:9.35pt;
+       mso-element-frame-vspace:9.35pt;
+       mso-element-wrap:no-wrap-beside;
+       mso-element-anchor-vertical:page;
+       mso-element-anchor-horizontal:margin;
+       mso-element-left:right;
+       mso-element-top:48.3pt;
+       mso-height-rule:exactly;
+       font-size:98.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Arial Black";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       color:white;}
+span.PartLabelChar
+       {mso-style-name:"Part Label Char";
+       mso-style-locked:yes;
+       mso-style-link:"Part Label";
+       mso-ansi-font-size:98.0pt;
+       font-family:"Arial Black";
+       mso-ascii-font-family:"Arial Black";
+       mso-hansi-font-family:"Arial Black";
+       color:white;
+       mso-ansi-language:EN-US;
+       mso-fareast-language:EN-US;}
+p.PartSubtitle, li.PartSubtitle, div.PartSubtitle
+       {mso-style-name:"Part Subtitle";
+       mso-style-next:"Body Text";
+       margin-top:18.0pt;
+       margin-right:0cm;
+       margin-bottom:6.0pt;
+       margin-left:0cm;
+       text-align:center;
+       mso-pagination:widow-orphan;
+       page-break-after:avoid;
+       font-size:16.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Arial;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       mso-font-kerning:14.0pt;
+       font-style:italic;
+       mso-bidi-font-style:normal;}
+p.PartTitle, li.PartTitle, div.PartTitle
+       {mso-style-name:"Part Title";
+       mso-style-next:"Part Label";
+       margin:0cm;
+       margin-bottom:.0001pt;
+       text-align:center;
+       line-height:24.0pt;
+       mso-line-height-rule:exactly;
+       page-break-before:always;
+       mso-pagination:widow-orphan;
+       page-break-after:avoid;
+       background:#CCCCCC;
+       mso-shading:windowtext;
+       mso-pattern:gray-20 auto;
+       mso-element:frame;
+       mso-element-frame-width:102.25pt;
+       mso-element-frame-hspace:9.35pt;
+       mso-element-frame-vspace:9.35pt;
+       mso-element-wrap:no-wrap-beside;
+       mso-element-anchor-vertical:page;
+       mso-element-anchor-horizontal:margin;
+       mso-element-left:right;
+       mso-element-top:48.3pt;
+       mso-height-rule:exactly;
+       font-size:18.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Arial Black";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       letter-spacing:-2.5pt;}
+p.Picture, li.Picture, div.Picture
+       {mso-style-name:Picture;
+       mso-style-parent:"Body Text";
+       mso-style-next:Caption;
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:12.0pt;
+       margin-left:0cm;
+       text-align:justify;
+       mso-pagination:widow-orphan;
+       page-break-after:avoid;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Garamond;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       letter-spacing:-.25pt;}
+p.ReturnAddress, li.ReturnAddress, div.ReturnAddress
+       {mso-style-name:"Return Address";
+       margin:0cm;
+       margin-bottom:.0001pt;
+       text-align:center;
+       mso-pagination:widow-orphan;
+       font-size:10.0pt;
+       font-family:Garamond;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       letter-spacing:-.15pt;}
+p.SectionHeading, li.SectionHeading, div.SectionHeading
+       {mso-style-name:"Section Heading";
+       mso-style-next:"Body Text";
+       margin:0cm;
+       margin-bottom:.0001pt;
+       line-height:32.0pt;
+       mso-pagination:widow-orphan;
+       font-size:7.5pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Arial Black";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       text-transform:uppercase;
+       letter-spacing:3.0pt;}
+p.SectionLabel, li.SectionLabel, div.SectionLabel
+       {mso-style-name:"Section Label";
+       mso-style-next:Normal;
+       margin-top:102.0pt;
+       margin-right:0cm;
+       margin-bottom:18.0pt;
+       margin-left:0cm;
+       line-height:24.0pt;
+       mso-pagination:widow-orphan;
+       font-size:24.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Arial Black";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       color:gray;
+       letter-spacing:-1.75pt;}
+p.SubtitleCover, li.SubtitleCover, div.SubtitleCover
+       {mso-style-name:"Subtitle Cover";
+       mso-style-next:Normal;
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:264.0pt;
+       margin-left:0cm;
+       line-height:24.0pt;
+       mso-line-height-rule:exactly;
+       mso-pagination:widow-orphan;
+       page-break-after:avoid;
+       border:none;
+       mso-border-top-alt:solid windowtext .75pt;
+       padding:0cm;
+       mso-padding-alt:1.0pt 0cm 0cm 0cm;
+       font-size:22.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Garamond;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       letter-spacing:-.75pt;
+       mso-font-kerning:14.0pt;}
+p.TitleCover, li.TitleCover, div.TitleCover
+       {mso-style-name:"Title Cover";
+       mso-style-parent:"Heading Base";
+       mso-style-next:"Subtitle Cover";
+       margin-top:0cm;
+       margin-right:30.0pt;
+       margin-bottom:0cm;
+       margin-left:30.0pt;
+       margin-bottom:.0001pt;
+       text-align:right;
+       line-height:72.0pt;
+       mso-line-height-rule:exactly;
+       mso-pagination:widow-orphan;
+       background:#E5E5E5;
+       mso-shading:windowtext;
+       mso-pattern:gray-10 auto;
+       border:none;
+       mso-border-alt:solid white .75pt;
+       padding:0cm;
+       mso-padding-alt:31.0pt 31.0pt 31.0pt 31.0pt;
+       font-size:72.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Garamond;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       letter-spacing:-3.5pt;
+       mso-font-kerning:14.0pt;}
+p.TOCBase, li.TOCBase, div.TOCBase
+       {mso-style-name:"TOC Base";
+       mso-style-parent:"TOC 2";
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:0cm;
+       margin-left:8.0pt;
+       margin-bottom:.0001pt;
+       mso-pagination:widow-orphan;
+       font-size:11.0pt;
+       font-family:Cambria;
+       mso-ascii-font-family:Cambria;
+       mso-ascii-theme-font:minor-latin;
+       mso-fareast-font-family:"Times New Roman";
+       mso-hansi-font-family:Cambria;
+       mso-hansi-theme-font:minor-latin;
+       mso-bidi-font-family:"Times New Roman";
+       font-weight:bold;
+       mso-bidi-font-weight:normal;}
+span.Lead-inEmphasis
+       {mso-style-name:"Lead-in Emphasis";
+       mso-style-parent:"";
+       mso-ansi-font-size:11.0pt;
+       text-transform:uppercase;}
+span.Superscript
+       {mso-style-name:Superscript;
+       mso-style-parent:"";
+       position:relative;
+       top:0pt;
+       mso-text-raise:0pt;
+       vertical-align:super;}
+p.Heading, li.Heading, div.Heading
+       {mso-style-name:Heading;
+       mso-style-next:Normal;
+       margin-top:12.0pt;
+       margin-right:0cm;
+       margin-bottom:6.0pt;
+       margin-left:0cm;
+       mso-pagination:none;
+       page-break-after:avoid;
+       mso-hyphenate:none;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:14.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Helvetica;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";}
+span.WW-Absatz-Standardschriftart
+       {mso-style-name:WW-Absatz-Standardschriftart;
+       mso-style-parent:"";
+       mso-ansi-font-size:12.0pt;}
+span.FootnoteSymbol
+       {mso-style-name:"Footnote Symbol";
+       mso-style-parent:WW-Absatz-Standardschriftart;
+       mso-ansi-font-size:12.0pt;
+       vertical-align:super;}
+span.WW-Absatz-Standardschriftart1
+       {mso-style-name:WW-Absatz-Standardschriftart1;
+       mso-style-parent:"";
+       mso-ansi-font-size:12.0pt;}
+span.WW-FootnoteSymbol
+       {mso-style-name:"WW-Footnote Symbol";
+       mso-style-parent:WW-Absatz-Standardschriftart1;
+       mso-ansi-font-size:12.0pt;
+       vertical-align:super;}
+span.WW-Absatz-Standardschriftart11
+       {mso-style-name:WW-Absatz-Standardschriftart11;
+       mso-style-parent:"";
+       mso-ansi-font-size:12.0pt;}
+span.WW-FootnoteSymbol1
+       {mso-style-name:"WW-Footnote Symbol1";
+       mso-style-parent:WW-Absatz-Standardschriftart11;
+       mso-ansi-font-size:12.0pt;
+       vertical-align:super;}
+span.WW-Absatz-Standardschriftart111
+       {mso-style-name:WW-Absatz-Standardschriftart111;
+       mso-style-parent:"";
+       mso-ansi-font-size:12.0pt;}
+span.WW-FootnoteSymbol11
+       {mso-style-name:"WW-Footnote Symbol11";
+       mso-style-parent:WW-Absatz-Standardschriftart111;
+       mso-ansi-font-size:12.0pt;
+       vertical-align:super;}
+span.WW-Absatz-Standardschriftart1111
+       {mso-style-name:WW-Absatz-Standardschriftart1111;
+       mso-style-parent:"";
+       mso-ansi-font-size:12.0pt;}
+span.WW-FootnoteSymbol111
+       {mso-style-name:"WW-Footnote Symbol111";
+       mso-style-parent:WW-Absatz-Standardschriftart1111;
+       mso-ansi-font-size:12.0pt;
+       vertical-align:super;}
+span.WW-Absatz-Standardschriftart11111
+       {mso-style-name:WW-Absatz-Standardschriftart11111;
+       mso-style-parent:"";
+       mso-ansi-font-size:12.0pt;}
+span.WW-FootnoteSymbol1111
+       {mso-style-name:"WW-Footnote Symbol1111";
+       mso-style-parent:WW-Absatz-Standardschriftart11111;
+       mso-ansi-font-size:12.0pt;
+       vertical-align:super;}
+span.WW-Absatz-Standardschriftart111111
+       {mso-style-name:WW-Absatz-Standardschriftart111111;
+       mso-style-parent:"";
+       mso-ansi-font-size:12.0pt;}
+span.WW-FootnoteSymbol11111
+       {mso-style-name:"WW-Footnote Symbol11111";
+       mso-style-parent:WW-Absatz-Standardschriftart111111;
+       mso-ansi-font-size:12.0pt;
+       vertical-align:super;}
+span.WW-Absatz-Standardschriftart1111111
+       {mso-style-name:WW-Absatz-Standardschriftart1111111;
+       mso-style-parent:"";
+       mso-ansi-font-size:12.0pt;}
+span.WW-FootnoteSymbol111111
+       {mso-style-name:"WW-Footnote Symbol111111";
+       mso-style-parent:WW-Absatz-Standardschriftart1111111;
+       mso-ansi-font-size:12.0pt;
+       vertical-align:super;}
+span.WW-Absatz-Standardschriftart11111111
+       {mso-style-name:WW-Absatz-Standardschriftart11111111;
+       mso-style-parent:"";
+       mso-ansi-font-size:12.0pt;}
+span.WW-FootnoteSymbol1111111
+       {mso-style-name:"WW-Footnote Symbol1111111";
+       mso-style-parent:WW-Absatz-Standardschriftart11111111;
+       mso-ansi-font-size:12.0pt;
+       vertical-align:super;}
+span.WW-Absatz-Standardschriftart111111111
+       {mso-style-name:WW-Absatz-Standardschriftart111111111;
+       mso-style-parent:"";
+       mso-ansi-font-size:12.0pt;}
+span.WW-FootnoteSymbol11111111
+       {mso-style-name:"WW-Footnote Symbol11111111";
+       mso-style-parent:WW-Absatz-Standardschriftart111111111;
+       mso-ansi-font-size:12.0pt;
+       vertical-align:super;}
+span.EndnoteSymbol
+       {mso-style-name:"Endnote Symbol";
+       mso-style-parent:"";
+       mso-ansi-font-size:12.0pt;}
+span.WW-EndnoteSymbol
+       {mso-style-name:"WW-Endnote Symbol";
+       mso-style-parent:"";
+       mso-ansi-font-size:12.0pt;}
+span.WW-EndnoteSymbol1
+       {mso-style-name:"WW-Endnote Symbol1";
+       mso-style-parent:"";
+       mso-ansi-font-size:12.0pt;}
+span.WW-EndnoteSymbol11
+       {mso-style-name:"WW-Endnote Symbol11";
+       mso-style-parent:"";
+       mso-ansi-font-size:12.0pt;}
+span.WW-EndnoteSymbol111
+       {mso-style-name:"WW-Endnote Symbol111";
+       mso-style-parent:"";
+       mso-ansi-font-size:12.0pt;}
+span.WW-EndnoteSymbol1111
+       {mso-style-name:"WW-Endnote Symbol1111";
+       mso-style-parent:"";
+       mso-ansi-font-size:12.0pt;}
+span.WW-EndnoteSymbol11111
+       {mso-style-name:"WW-Endnote Symbol11111";
+       mso-style-parent:"";
+       mso-ansi-font-size:12.0pt;}
+span.WW-EndnoteSymbol111111
+       {mso-style-name:"WW-Endnote Symbol111111";
+       mso-style-parent:"";
+       mso-ansi-font-size:12.0pt;}
+span.WW-EndnoteSymbol1111111
+       {mso-style-name:"WW-Endnote Symbol1111111";
+       mso-style-parent:"";
+       mso-ansi-font-size:12.0pt;}
+span.Internetlink
+       {mso-style-name:"Internet link";
+       mso-style-parent:"";
+       mso-ansi-font-size:12.0pt;
+       color:navy;
+       text-decoration:underline;
+       text-underline:single;}
+span.WW-Internetlink
+       {mso-style-name:"WW-Internet link";
+       mso-style-parent:"";
+       mso-ansi-font-size:12.0pt;
+       color:navy;
+       text-decoration:underline;
+       text-underline:single;}
+span.WW-Internetlink1
+       {mso-style-name:"WW-Internet link1";
+       mso-style-parent:"";
+       mso-ansi-font-size:12.0pt;
+       color:navy;
+       text-decoration:underline;
+       text-underline:single;}
+span.WW-Internetlink11
+       {mso-style-name:"WW-Internet link11";
+       mso-style-parent:"";
+       mso-ansi-font-size:12.0pt;
+       color:navy;
+       text-decoration:underline;
+       text-underline:single;}
+span.WW-Internetlink111
+       {mso-style-name:"WW-Internet link111";
+       mso-style-parent:"";
+       mso-ansi-font-size:12.0pt;
+       color:navy;
+       text-decoration:underline;
+       text-underline:single;}
+span.WW-Internetlink1111
+       {mso-style-name:"WW-Internet link1111";
+       mso-style-parent:"";
+       mso-ansi-font-size:12.0pt;
+       color:navy;
+       text-decoration:underline;
+       text-underline:single;}
+span.WW-Internetlink11111
+       {mso-style-name:"WW-Internet link11111";
+       mso-style-parent:"";
+       mso-ansi-font-size:12.0pt;
+       color:navy;
+       text-decoration:underline;
+       text-underline:single;}
+span.WW-Internetlink111111
+       {mso-style-name:"WW-Internet link111111";
+       mso-style-parent:"";
+       mso-ansi-font-size:12.0pt;
+       color:navy;
+       text-decoration:underline;
+       text-underline:single;}
+span.WW-Internetlink1111111
+       {mso-style-name:"WW-Internet link1111111";
+       mso-style-parent:"";
+       mso-ansi-font-size:12.0pt;
+       color:navy;
+       text-decoration:underline;
+       text-underline:single;}
+span.VisitedInternetLink
+       {mso-style-name:"Visited Internet Link";
+       mso-style-parent:"";
+       mso-ansi-font-size:12.0pt;
+       color:maroon;
+       text-decoration:underline;
+       text-underline:single;}
+span.WW-VisitedInternetLink
+       {mso-style-name:"WW-Visited Internet Link";
+       mso-style-parent:"";
+       mso-ansi-font-size:12.0pt;
+       color:maroon;
+       text-decoration:underline;
+       text-underline:single;}
+span.WW-VisitedInternetLink1
+       {mso-style-name:"WW-Visited Internet Link1";
+       mso-style-parent:"";
+       mso-ansi-font-size:12.0pt;
+       color:maroon;
+       text-decoration:underline;
+       text-underline:single;}
+span.WW-VisitedInternetLink11
+       {mso-style-name:"WW-Visited Internet Link11";
+       mso-style-parent:"";
+       mso-ansi-font-size:12.0pt;
+       color:maroon;
+       text-decoration:underline;
+       text-underline:single;}
+span.WW-VisitedInternetLink111
+       {mso-style-name:"WW-Visited Internet Link111";
+       mso-style-parent:"";
+       mso-ansi-font-size:12.0pt;
+       color:maroon;
+       text-decoration:underline;
+       text-underline:single;}
+span.WW-VisitedInternetLink1111
+       {mso-style-name:"WW-Visited Internet Link1111";
+       mso-style-parent:"";
+       mso-ansi-font-size:12.0pt;
+       color:maroon;
+       text-decoration:underline;
+       text-underline:single;}
+span.WW-VisitedInternetLink11111
+       {mso-style-name:"WW-Visited Internet Link11111";
+       mso-style-parent:"";
+       mso-ansi-font-size:12.0pt;
+       color:maroon;
+       text-decoration:underline;
+       text-underline:single;}
+span.WW-VisitedInternetLink111111
+       {mso-style-name:"WW-Visited Internet Link111111";
+       mso-style-parent:"";
+       mso-ansi-font-size:12.0pt;
+       color:maroon;
+       text-decoration:underline;
+       text-underline:single;}
+span.WW-VisitedInternetLink1111111
+       {mso-style-name:"WW-Visited Internet Link1111111";
+       mso-style-parent:"";
+       mso-ansi-font-size:12.0pt;
+       color:maroon;
+       text-decoration:underline;
+       text-underline:single;}
+span.NumberingSymbols
+       {mso-style-name:"Numbering Symbols";
+       mso-style-parent:"";
+       mso-ansi-font-size:12.0pt;}
+span.WW-NumberingSymbols
+       {mso-style-name:"WW-Numbering Symbols";
+       mso-style-parent:"";
+       mso-ansi-font-size:12.0pt;}
+span.WW-NumberingSymbols1
+       {mso-style-name:"WW-Numbering Symbols1";
+       mso-style-parent:"";
+       mso-ansi-font-size:12.0pt;}
+span.WW-NumberingSymbols11
+       {mso-style-name:"WW-Numbering Symbols11";
+       mso-style-parent:"";
+       mso-ansi-font-size:12.0pt;}
+span.WW-NumberingSymbols111
+       {mso-style-name:"WW-Numbering Symbols111";
+       mso-style-parent:"";
+       mso-ansi-font-size:12.0pt;}
+span.WW-NumberingSymbols1111
+       {mso-style-name:"WW-Numbering Symbols1111";
+       mso-style-parent:"";
+       mso-ansi-font-size:12.0pt;}
+span.WW-NumberingSymbols11111
+       {mso-style-name:"WW-Numbering Symbols11111";
+       mso-style-parent:"";
+       mso-ansi-font-size:12.0pt;}
+span.BulletSymbols
+       {mso-style-name:"Bullet Symbols";
+       mso-style-parent:"";
+       mso-ansi-font-size:9.0pt;
+       font-family:starbats;
+       mso-ascii-font-family:starbats;
+       mso-hansi-font-family:starbats;}
+span.WW-BulletSymbols
+       {mso-style-name:"WW-Bullet Symbols";
+       mso-style-parent:"";
+       mso-ansi-font-size:9.0pt;
+       font-family:starbats;
+       mso-ascii-font-family:starbats;
+       mso-hansi-font-family:starbats;}
+span.WW-BulletSymbols1
+       {mso-style-name:"WW-Bullet Symbols1";
+       mso-style-parent:"";
+       mso-ansi-font-size:9.0pt;
+       font-family:starbats;
+       mso-ascii-font-family:starbats;
+       mso-hansi-font-family:starbats;}
+span.WW-BulletSymbols11
+       {mso-style-name:"WW-Bullet Symbols11";
+       mso-style-parent:"";
+       mso-ansi-font-size:9.0pt;
+       font-family:starbats;
+       mso-ascii-font-family:starbats;
+       mso-hansi-font-family:starbats;}
+p.Index, li.Index, div.Index
+       {mso-style-name:Index;
+       margin:0cm;
+       margin-bottom:.0001pt;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";}
+p.ContentsHeading, li.ContentsHeading, div.ContentsHeading
+       {mso-style-name:"Contents Heading";
+       margin-top:12.0pt;
+       margin-right:0cm;
+       margin-bottom:6.0pt;
+       margin-left:0cm;
+       mso-pagination:none;
+       page-break-after:avoid;
+       mso-hyphenate:none;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:16.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Helvetica;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       font-weight:bold;
+       mso-bidi-font-weight:normal;}
+p.Tableofcontents6, li.Tableofcontents6, div.Tableofcontents6
+       {mso-style-name:"Table of contents 6";
+       mso-style-parent:Index;
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:0cm;
+       margin-left:70.75pt;
+       margin-bottom:.0001pt;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       tab-stops:right dotted 432.0pt;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";}
+p.Tableofcontents7, li.Tableofcontents7, div.Tableofcontents7
+       {mso-style-name:"Table of contents 7";
+       mso-style-parent:Index;
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:0cm;
+       margin-left:84.9pt;
+       margin-bottom:.0001pt;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       tab-stops:right dotted 432.0pt;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";}
+p.Tableofcontents8, li.Tableofcontents8, div.Tableofcontents8
+       {mso-style-name:"Table of contents 8";
+       mso-style-parent:Index;
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:0cm;
+       margin-left:99.05pt;
+       margin-bottom:.0001pt;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       tab-stops:right dotted 432.0pt;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";}
+p.Tableofcontents9, li.Tableofcontents9, div.Tableofcontents9
+       {mso-style-name:"Table of contents 9";
+       mso-style-parent:Index;
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:0cm;
+       margin-left:113.2pt;
+       margin-bottom:.0001pt;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       tab-stops:right dotted 432.0pt;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";}
+p.Tableofcontents10, li.Tableofcontents10, div.Tableofcontents10
+       {mso-style-name:"Table of contents 10";
+       mso-style-parent:Index;
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:0cm;
+       margin-left:127.35pt;
+       margin-bottom:.0001pt;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       tab-stops:right dotted 432.0pt;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";}
+p.Textbodyindent, li.Textbodyindent, div.Textbodyindent
+       {mso-style-name:"Text body indent";
+       mso-style-parent:"Text body";
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:0cm;
+       margin-left:14.15pt;
+       margin-bottom:.0001pt;
+       text-align:justify;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";}
+p.ListContents, li.ListContents, div.ListContents
+       {mso-style-name:"List Contents";
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:0cm;
+       margin-left:28.3pt;
+       margin-bottom:.0001pt;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";}
+p.FAQexample, li.FAQexample, div.FAQexample
+       {mso-style-name:FAQ_example;
+       mso-style-parent:example;
+       margin-top:12.0pt;
+       margin-right:0cm;
+       margin-bottom:12.0pt;
+       margin-left:1.0cm;
+       mso-add-space:auto;
+       line-height:200%;
+       mso-pagination:widow-orphan lines-together;
+       page-break-after:avoid;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:10.0pt;
+       font-family:"Courier New";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Courier New";
+       font-weight:bold;
+       mso-bidi-font-weight:normal;}
+p.FAQexampleCxSpFirst, li.FAQexampleCxSpFirst, div.FAQexampleCxSpFirst
+       {mso-style-name:FAQ_exampleCxSpFirst;
+       mso-style-parent:example;
+       mso-style-type:export-only;
+       margin-top:12.0pt;
+       margin-right:0cm;
+       margin-bottom:0cm;
+       margin-left:1.0cm;
+       margin-bottom:.0001pt;
+       mso-add-space:auto;
+       line-height:200%;
+       mso-pagination:widow-orphan lines-together;
+       page-break-after:avoid;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:10.0pt;
+       font-family:"Courier New";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Courier New";
+       font-weight:bold;
+       mso-bidi-font-weight:normal;}
+p.FAQexampleCxSpMiddle, li.FAQexampleCxSpMiddle, div.FAQexampleCxSpMiddle
+       {mso-style-name:FAQ_exampleCxSpMiddle;
+       mso-style-parent:example;
+       mso-style-type:export-only;
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:0cm;
+       margin-left:1.0cm;
+       margin-bottom:.0001pt;
+       mso-add-space:auto;
+       line-height:200%;
+       mso-pagination:widow-orphan lines-together;
+       page-break-after:avoid;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:10.0pt;
+       font-family:"Courier New";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Courier New";
+       font-weight:bold;
+       mso-bidi-font-weight:normal;}
+p.FAQexampleCxSpLast, li.FAQexampleCxSpLast, div.FAQexampleCxSpLast
+       {mso-style-name:FAQ_exampleCxSpLast;
+       mso-style-parent:example;
+       mso-style-type:export-only;
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:12.0pt;
+       margin-left:1.0cm;
+       mso-add-space:auto;
+       line-height:200%;
+       mso-pagination:widow-orphan lines-together;
+       page-break-after:avoid;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:10.0pt;
+       font-family:"Courier New";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Courier New";
+       font-weight:bold;
+       mso-bidi-font-weight:normal;}
+p.Firstlineindent, li.Firstlineindent, div.Firstlineindent
+       {mso-style-name:"First line indent";
+       mso-style-parent:"Text body";
+       margin:0cm;
+       margin-bottom:.0001pt;
+       text-align:justify;
+       text-indent:14.15pt;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";}
+p.Hangingindent, li.Hangingindent, div.Hangingindent
+       {mso-style-name:"Hanging indent";
+       mso-style-parent:"Text body";
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:0cm;
+       margin-left:1.0cm;
+       margin-bottom:.0001pt;
+       text-align:justify;
+       text-indent:-14.15pt;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       tab-stops:1.0cm;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";}
+p.Numbering3, li.Numbering3, div.Numbering3
+       {mso-style-name:"Numbering 3";
+       mso-style-parent:List;
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:6.0pt;
+       margin-left:42.45pt;
+       text-align:justify;
+       text-indent:-14.15pt;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";}
+p.TableContents, li.TableContents, div.TableContents
+       {mso-style-name:"Table Contents";
+       mso-style-parent:"Text body";
+       margin:0cm;
+       margin-bottom:.0001pt;
+       text-align:justify;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";}
+p.TableHeading, li.TableHeading, div.TableHeading
+       {mso-style-name:"Table Heading";
+       mso-style-parent:"Table Contents";
+       margin:0cm;
+       margin-bottom:.0001pt;
+       text-align:center;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       font-weight:bold;
+       mso-bidi-font-weight:normal;
+       font-style:italic;
+       mso-bidi-font-style:normal;}
+p.author, li.author, div.author
+       {mso-style-name:author;
+       margin:0cm;
+       margin-bottom:.0001pt;
+       text-align:justify;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       font-weight:bold;
+       mso-bidi-font-weight:normal;}
+p.numberedlist, li.numberedlist, div.numberedlist
+       {mso-style-name:"numbered list";
+       mso-style-update:auto;
+       mso-style-parent:"Heading 4";
+       margin-top:3.0pt;
+       margin-right:0cm;
+       margin-bottom:3.0pt;
+       margin-left:0cm;
+       mso-pagination:none;
+       page-break-after:avoid;
+       mso-outline-level:4;
+       mso-hyphenate:none;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:10.0pt;
+       mso-bidi-font-size:12.0pt;
+       font-family:"Arial Black";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Courier New";
+       letter-spacing:1.0pt;
+       mso-ansi-language:AF;
+       font-weight:bold;
+       mso-bidi-font-weight:normal;
+       font-style:italic;
+       mso-bidi-font-style:normal;}
+p.Noteboxtitle, li.Noteboxtitle, div.Noteboxtitle
+       {mso-style-name:"Notebox\.title";
+       margin:0cm;
+       margin-bottom:.0001pt;
+       text-align:center;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:18.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Arial;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:Arial;
+       font-weight:bold;}
+p.noteboxexample, li.noteboxexample, div.noteboxexample
+       {mso-style-name:"notebox\.example";
+       margin:0cm;
+       margin-bottom:.0001pt;
+       text-indent:36.0pt;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       font-weight:bold;}
+p.noteboxbody, li.noteboxbody, div.noteboxbody
+       {mso-style-name:"notebox\.body";
+       margin:0cm;
+       margin-bottom:.0001pt;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       font-style:italic;}
+p.Note, li.Note, div.Note
+       {mso-style-name:Note;
+       mso-style-update:auto;
+       mso-style-link:"Note Char";
+       margin-top:6.0pt;
+       margin-right:0cm;
+       margin-bottom:12.0pt;
+       margin-left:42.55pt;
+       text-align:justify;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       tab-stops:1.0cm;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:10.0pt;
+       mso-bidi-font-size:8.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       mso-ansi-language:EN-GB;
+       font-weight:bold;
+       mso-bidi-font-weight:normal;}
+span.NoteChar
+       {mso-style-name:"Note Char";
+       mso-style-locked:yes;
+       mso-style-link:Note;
+       mso-bidi-font-size:8.0pt;
+       mso-ansi-language:EN-GB;
+       mso-fareast-language:EN-US;
+       font-weight:bold;
+       mso-bidi-font-weight:normal;}
+p.Table, li.Table, div.Table
+       {mso-style-name:Table;
+       mso-style-parent:Index;
+       margin:0cm;
+       margin-bottom:.0001pt;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Courier New";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Courier New";}
+p.flag, li.flag, div.flag
+       {mso-style-name:flag;
+       mso-style-parent:"Heading 4";
+       margin-top:12.0pt;
+       margin-right:0cm;
+       margin-bottom:3.0pt;
+       margin-left:1.0cm;
+       mso-pagination:none;
+       page-break-after:avoid;
+       mso-outline-level:4;
+       mso-hyphenate:none;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:12.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Courier New";
+       letter-spacing:1.0pt;
+       mso-ansi-language:AF;
+       font-weight:bold;
+       mso-bidi-font-weight:normal;
+       font-style:italic;
+       mso-bidi-font-style:normal;}
+p.flagusage, li.flagusage, div.flagusage
+       {mso-style-name:"flag usage";
+       mso-style-update:auto;
+       mso-style-parent:example;
+       margin-top:3.0pt;
+       margin-right:0cm;
+       margin-bottom:3.0pt;
+       margin-left:0cm;
+       text-indent:36.0pt;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:13.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Courier New";
+       mso-ansi-language:FR;
+       font-weight:bold;
+       mso-bidi-font-weight:normal;}
+p.flagdefault, li.flagdefault, div.flagdefault
+       {mso-style-name:"flag default";
+       mso-style-parent:"Heading 5";
+       margin-top:3.0pt;
+       margin-right:0cm;
+       margin-bottom:3.0pt;
+       margin-left:18.0pt;
+       mso-pagination:none;
+       mso-outline-level:5;
+       mso-hyphenate:none;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:13.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       font-weight:bold;}
+p.flagdescription, li.flagdescription, div.flagdescription
+       {mso-style-name:"flag description";
+       mso-style-update:auto;
+       mso-style-link:"flag description Char";
+       margin-top:6.0pt;
+       margin-right:0cm;
+       margin-bottom:0cm;
+       margin-left:42.55pt;
+       margin-bottom:.0001pt;
+       text-align:justify;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:10.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";}
+span.flagdescriptionChar
+       {mso-style-name:"flag description Char";
+       mso-style-locked:yes;
+       mso-style-link:"flag description";
+       mso-ansi-language:EN-US;
+       mso-fareast-language:EN-US;}
+p.flagNote, li.flagNote, div.flagNote
+       {mso-style-name:"flag Note";
+       margin:0cm;
+       margin-bottom:.0001pt;
+       text-align:justify;
+       text-indent:.05pt;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       font-weight:bold;}
+p.flagdescriptionid1, li.flagdescriptionid1, div.flagdescriptionid1
+       {mso-style-name:"flag description id1";
+       mso-style-parent:"flag description";
+       margin-top:6.0pt;
+       margin-right:0cm;
+       margin-bottom:0cm;
+       margin-left:70.9pt;
+       margin-bottom:.0001pt;
+       text-align:justify;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:10.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";}
+p.output, li.output, div.output
+       {mso-style-name:output;
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:0cm;
+       margin-left:18.0pt;
+       margin-bottom:.0001pt;
+       text-align:justify;
+       text-indent:.05pt;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:8.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Courier;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";}
+p.instruction, li.instruction, div.instruction
+       {mso-style-name:instruction;
+       mso-style-update:auto;
+       mso-style-parent:example;
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:0cm;
+       margin-left:42.55pt;
+       margin-bottom:.0001pt;
+       line-height:200%;
+       mso-pagination:widow-orphan lines-together;
+       page-break-after:avoid;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:10.0pt;
+       font-family:"Courier New";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Courier New";
+       font-weight:bold;
+       mso-bidi-font-weight:normal;}
+p.Format, li.Format, div.Format
+       {mso-style-name:Format;
+       mso-style-parent:example;
+       margin-top:12.0pt;
+       margin-right:0cm;
+       margin-bottom:12.0pt;
+       margin-left:1.0cm;
+       mso-add-space:auto;
+       line-height:200%;
+       mso-pagination:widow-orphan lines-together;
+       page-break-after:avoid;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:10.0pt;
+       font-family:"Courier New";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Courier New";
+       mso-ansi-language:EN-GB;
+       font-weight:bold;
+       mso-bidi-font-weight:normal;}
+p.FormatCxSpFirst, li.FormatCxSpFirst, div.FormatCxSpFirst
+       {mso-style-name:FormatCxSpFirst;
+       mso-style-parent:example;
+       mso-style-type:export-only;
+       margin-top:12.0pt;
+       margin-right:0cm;
+       margin-bottom:0cm;
+       margin-left:1.0cm;
+       margin-bottom:.0001pt;
+       mso-add-space:auto;
+       line-height:200%;
+       mso-pagination:widow-orphan lines-together;
+       page-break-after:avoid;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:10.0pt;
+       font-family:"Courier New";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Courier New";
+       mso-ansi-language:EN-GB;
+       font-weight:bold;
+       mso-bidi-font-weight:normal;}
+p.FormatCxSpMiddle, li.FormatCxSpMiddle, div.FormatCxSpMiddle
+       {mso-style-name:FormatCxSpMiddle;
+       mso-style-parent:example;
+       mso-style-type:export-only;
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:0cm;
+       margin-left:1.0cm;
+       margin-bottom:.0001pt;
+       mso-add-space:auto;
+       line-height:200%;
+       mso-pagination:widow-orphan lines-together;
+       page-break-after:avoid;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:10.0pt;
+       font-family:"Courier New";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Courier New";
+       mso-ansi-language:EN-GB;
+       font-weight:bold;
+       mso-bidi-font-weight:normal;}
+p.FormatCxSpLast, li.FormatCxSpLast, div.FormatCxSpLast
+       {mso-style-name:FormatCxSpLast;
+       mso-style-parent:example;
+       mso-style-type:export-only;
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:12.0pt;
+       margin-left:1.0cm;
+       mso-add-space:auto;
+       line-height:200%;
+       mso-pagination:widow-orphan lines-together;
+       page-break-after:avoid;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:10.0pt;
+       font-family:"Courier New";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Courier New";
+       mso-ansi-language:EN-GB;
+       font-weight:bold;
+       mso-bidi-font-weight:normal;}
+p.ListinFlag, li.ListinFlag, div.ListinFlag
+       {mso-style-name:"List in Flag";
+       mso-style-parent:List;
+       margin:0cm;
+       margin-bottom:.0001pt;
+       text-align:justify;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";}
+p.example2, li.example2, div.example2
+       {mso-style-name:example2;
+       mso-style-parent:example;
+       margin-top:12.0pt;
+       margin-right:0cm;
+       margin-bottom:12.0pt;
+       margin-left:2.0cm;
+       mso-add-space:auto;
+       line-height:200%;
+       mso-pagination:widow-orphan lines-together;
+       page-break-after:avoid;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:10.0pt;
+       font-family:"Courier New";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Courier New";
+       font-weight:bold;
+       mso-bidi-font-weight:normal;}
+p.example2CxSpFirst, li.example2CxSpFirst, div.example2CxSpFirst
+       {mso-style-name:example2CxSpFirst;
+       mso-style-parent:example;
+       mso-style-type:export-only;
+       margin-top:12.0pt;
+       margin-right:0cm;
+       margin-bottom:0cm;
+       margin-left:2.0cm;
+       margin-bottom:.0001pt;
+       mso-add-space:auto;
+       line-height:200%;
+       mso-pagination:widow-orphan lines-together;
+       page-break-after:avoid;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:10.0pt;
+       font-family:"Courier New";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Courier New";
+       font-weight:bold;
+       mso-bidi-font-weight:normal;}
+p.example2CxSpMiddle, li.example2CxSpMiddle, div.example2CxSpMiddle
+       {mso-style-name:example2CxSpMiddle;
+       mso-style-parent:example;
+       mso-style-type:export-only;
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:0cm;
+       margin-left:2.0cm;
+       margin-bottom:.0001pt;
+       mso-add-space:auto;
+       line-height:200%;
+       mso-pagination:widow-orphan lines-together;
+       page-break-after:avoid;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:10.0pt;
+       font-family:"Courier New";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Courier New";
+       font-weight:bold;
+       mso-bidi-font-weight:normal;}
+p.example2CxSpLast, li.example2CxSpLast, div.example2CxSpLast
+       {mso-style-name:example2CxSpLast;
+       mso-style-parent:example;
+       mso-style-type:export-only;
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:12.0pt;
+       margin-left:2.0cm;
+       mso-add-space:auto;
+       line-height:200%;
+       mso-pagination:widow-orphan lines-together;
+       page-break-after:avoid;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:10.0pt;
+       font-family:"Courier New";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Courier New";
+       font-weight:bold;
+       mso-bidi-font-weight:normal;}
+p.StyleNote, li.StyleNote, div.StyleNote
+       {mso-style-name:"Style Note";
+       mso-style-parent:Note;
+       margin-top:6.0pt;
+       margin-right:0cm;
+       margin-bottom:12.0pt;
+       margin-left:-35.45pt;
+       text-align:justify;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       tab-stops:1.0cm;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:10.0pt;
+       mso-bidi-font-size:8.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       mso-ansi-language:EN-GB;
+       font-weight:bold;}
+p.examplefile, li.examplefile, div.examplefile
+       {mso-style-name:example_file;
+       mso-style-update:auto;
+       margin-top:6.0pt;
+       margin-right:0cm;
+       margin-bottom:6.0pt;
+       margin-left:0cm;
+       mso-add-space:auto;
+       text-align:justify;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       background:#E6E6E6;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       border:none;
+       mso-border-alt:solid windowtext .5pt;
+       padding:0cm;
+       mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;
+       font-size:10.0pt;
+       font-family:"Courier New";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Courier New";}
+p.examplefileCxSpFirst, li.examplefileCxSpFirst, div.examplefileCxSpFirst
+       {mso-style-name:example_fileCxSpFirst;
+       mso-style-update:auto;
+       mso-style-type:export-only;
+       margin-top:6.0pt;
+       margin-right:0cm;
+       margin-bottom:0cm;
+       margin-left:0cm;
+       margin-bottom:.0001pt;
+       mso-add-space:auto;
+       text-align:justify;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       background:#E6E6E6;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       border:none;
+       mso-border-alt:solid windowtext .5pt;
+       padding:0cm;
+       mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;
+       font-size:10.0pt;
+       font-family:"Courier New";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Courier New";}
+p.examplefileCxSpMiddle, li.examplefileCxSpMiddle, div.examplefileCxSpMiddle
+       {mso-style-name:example_fileCxSpMiddle;
+       mso-style-update:auto;
+       mso-style-type:export-only;
+       margin:0cm;
+       margin-bottom:.0001pt;
+       mso-add-space:auto;
+       text-align:justify;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       background:#E6E6E6;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       border:none;
+       mso-border-alt:solid windowtext .5pt;
+       padding:0cm;
+       mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;
+       font-size:10.0pt;
+       font-family:"Courier New";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Courier New";}
+p.examplefileCxSpLast, li.examplefileCxSpLast, div.examplefileCxSpLast
+       {mso-style-name:example_fileCxSpLast;
+       mso-style-update:auto;
+       mso-style-type:export-only;
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:6.0pt;
+       margin-left:0cm;
+       mso-add-space:auto;
+       text-align:justify;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       background:#E6E6E6;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       border:none;
+       mso-border-alt:solid windowtext .5pt;
+       padding:0cm;
+       mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;
+       font-size:10.0pt;
+       font-family:"Courier New";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Courier New";}
+p.Warning, li.Warning, div.Warning
+       {mso-style-name:Warning;
+       mso-style-update:auto;
+       mso-style-link:"Warning Char";
+       mso-margin-top-alt:auto;
+       margin-right:0cm;
+       mso-margin-bottom-alt:auto;
+       margin-left:0cm;
+       mso-pagination:widow-orphan;
+       background:#F7CBB7;
+       border:none;
+       mso-border-alt:solid windowtext 1.5pt;
+       padding:0cm;
+       mso-padding-alt:0cm 0cm 0cm 0cm;
+       font-size:10.0pt;
+       font-family:Garamond;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       font-weight:bold;
+       mso-bidi-font-weight:normal;}
+span.WarningChar
+       {mso-style-name:"Warning Char";
+       mso-style-locked:yes;
+       mso-style-parent:"Note Char";
+       mso-style-link:Warning;
+       mso-bidi-font-size:8.0pt;
+       font-family:Garamond;
+       mso-ascii-font-family:Garamond;
+       mso-hansi-font-family:Garamond;
+       mso-ansi-language:EN-US;
+       mso-fareast-language:EN-US;
+       font-weight:bold;
+       mso-bidi-font-weight:normal;}
+p.Heaing3, li.Heaing3, div.Heaing3
+       {mso-style-name:"Heaing 3";
+       mso-style-parent:Note;
+       margin-top:6.0pt;
+       margin-right:0cm;
+       margin-bottom:12.0pt;
+       margin-left:42.55pt;
+       text-align:justify;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       tab-stops:1.0cm;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:10.0pt;
+       mso-bidi-font-size:8.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       mso-ansi-language:EN-GB;
+       font-weight:bold;
+       mso-bidi-font-weight:normal;}
+p.NormalJustified, li.NormalJustified, div.NormalJustified
+       {mso-style-name:"Normal + Justified";
+       mso-style-link:"Normal + Justified Char";
+       margin:0cm;
+       margin-bottom:.0001pt;
+       text-align:justify;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       mso-ansi-language:EN-GB;}
+span.NormalJustifiedChar
+       {mso-style-name:"Normal + Justified Char";
+       mso-style-locked:yes;
+       mso-style-link:"Normal + Justified";
+       mso-ansi-font-size:12.0pt;
+       mso-ansi-language:EN-GB;
+       mso-fareast-language:EN-US;}
+p.MyNormalID, li.MyNormalID, div.MyNormalID
+       {mso-style-name:MyNormalID;
+       mso-style-update:auto;
+       mso-style-parent:"List Bullet";
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:0cm;
+       margin-left:31.2pt;
+       margin-bottom:.0001pt;
+       text-indent:0cm;
+       mso-pagination:none;
+       mso-list:l8 level1 lfo7;
+       mso-hyphenate:none;
+       tab-stops:list 18.0pt;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";}
+p.MyExample, li.MyExample, div.MyExample
+       {mso-style-name:MyExample;
+       mso-style-update:auto;
+       mso-margin-top-alt:auto;
+       margin-right:0cm;
+       mso-margin-bottom-alt:auto;
+       margin-left:2.0cm;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       background:#FFFFCC;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       border:none;
+       mso-border-top-alt:solid black .25pt;
+       mso-border-bottom-alt:solid black .25pt;
+       padding:0cm;
+       mso-padding-alt:10.0pt 0cm 10.0pt 0cm;
+       font-size:9.0pt;
+       font-family:"Courier New";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       font-weight:bold;
+       mso-bidi-font-weight:normal;}
+p.Style1, li.Style1, div.Style1
+       {mso-style-name:Style1;
+       mso-style-update:auto;
+       margin:0cm;
+       margin-bottom:.0001pt;
+       mso-pagination:widow-orphan;
+       font-size:8.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Garamond;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       mso-ansi-language:EN-GB;
+       font-weight:bold;
+       mso-bidi-font-weight:normal;}
+p.StyleHeading6Bold, li.StyleHeading6Bold, div.StyleHeading6Bold
+       {mso-style-name:"Style Heading 6 + Bold";
+       mso-style-update:auto;
+       mso-style-link:"Style Heading 6 + Bold Char";
+       margin:0cm;
+       margin-bottom:.0001pt;
+       mso-pagination:widow-orphan;
+       font-size:8.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:Garamond;
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       font-weight:bold;}
+span.StyleHeading6BoldChar
+       {mso-style-name:"Style Heading 6 + Bold Char";
+       mso-style-locked:yes;
+       mso-style-link:"Style Heading 6 + Bold";
+       mso-ansi-font-size:8.0pt;
+       font-family:Garamond;
+       mso-ascii-font-family:Garamond;
+       mso-hansi-font-family:Garamond;
+       mso-ansi-language:EN-US;
+       mso-fareast-language:EN-US;
+       font-weight:bold;}
+p.MyNormaBoldl, li.MyNormaBoldl, div.MyNormaBoldl
+       {mso-style-name:MyNormaBoldl;
+       mso-style-parent:MyNormal;
+       mso-style-link:"MyNormaBoldl Char";
+       margin-top:2.0pt;
+       margin-right:0cm;
+       margin-bottom:6.0pt;
+       margin-left:42.55pt;
+       text-align:justify;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:11.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Courier New";
+       mso-ansi-language:AF;}
+p.Mylist, li.Mylist, div.Mylist
+       {mso-style-name:Mylist;
+       mso-style-parent:MyNormal;
+       margin-top:2.0pt;
+       margin-right:0cm;
+       margin-bottom:6.0pt;
+       margin-left:128.7pt;
+       text-align:justify;
+       text-indent:-72.0pt;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:11.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Courier New";
+       mso-ansi-language:AF;
+       font-style:italic;
+       mso-bidi-font-style:normal;}
+p.MyNormalBold, li.MyNormalBold, div.MyNormalBold
+       {mso-style-name:MyNormalBold;
+       mso-style-parent:MyNormalID;
+       margin-top:6.0pt;
+       margin-right:0cm;
+       margin-bottom:12.0pt;
+       margin-left:31.2pt;
+       text-indent:0cm;
+       mso-pagination:lines-together;
+       mso-list:l8 level1 lfo7;
+       tab-stops:list 18.0pt;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";}
+p.StyleflagdescriptionBoldItalic, li.StyleflagdescriptionBoldItalic, div.StyleflagdescriptionBoldItalic
+       {mso-style-name:"Style flag description + Bold Italic";
+       mso-style-update:auto;
+       mso-style-parent:"flag description";
+       mso-style-link:"Style flag description + Bold Italic Char";
+       margin-top:3.0pt;
+       margin-right:0cm;
+       margin-bottom:3.0pt;
+       margin-left:42.55pt;
+       text-align:justify;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:10.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       font-weight:bold;
+       font-style:italic;}
+span.StyleflagdescriptionBoldItalicChar
+       {mso-style-name:"Style flag description + Bold Italic Char";
+       mso-style-locked:yes;
+       mso-style-parent:"flag description Char";
+       mso-style-link:"Style flag description + Bold Italic";
+       mso-ansi-language:EN-US;
+       mso-fareast-language:EN-US;
+       font-weight:bold;
+       font-style:italic;}
+p.Formula, li.Formula, div.Formula
+       {mso-style-name:Formula;
+       mso-style-parent:"flag description";
+       margin-top:6.0pt;
+       margin-right:0cm;
+       margin-bottom:0cm;
+       margin-left:42.55pt;
+       margin-bottom:.0001pt;
+       text-align:justify;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:10.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";}
+p.examplefilesmall, li.examplefilesmall, div.examplefilesmall
+       {mso-style-name:example_file_small;
+       mso-style-parent:example_file;
+       margin-top:6.0pt;
+       margin-right:1.0cm;
+       margin-bottom:6.0pt;
+       margin-left:0cm;
+       mso-add-space:auto;
+       text-align:justify;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       background:#E6E6E6;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       border:none;
+       mso-border-alt:solid windowtext .5pt;
+       padding:0cm;
+       mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;
+       font-size:8.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Courier New";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Courier New";}
+p.examplefilesmallCxSpFirst, li.examplefilesmallCxSpFirst, div.examplefilesmallCxSpFirst
+       {mso-style-name:example_file_smallCxSpFirst;
+       mso-style-parent:example_file;
+       mso-style-type:export-only;
+       margin-top:6.0pt;
+       margin-right:1.0cm;
+       margin-bottom:0cm;
+       margin-left:0cm;
+       margin-bottom:.0001pt;
+       mso-add-space:auto;
+       text-align:justify;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       background:#E6E6E6;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       border:none;
+       mso-border-alt:solid windowtext .5pt;
+       padding:0cm;
+       mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;
+       font-size:8.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Courier New";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Courier New";}
+p.examplefilesmallCxSpMiddle, li.examplefilesmallCxSpMiddle, div.examplefilesmallCxSpMiddle
+       {mso-style-name:example_file_smallCxSpMiddle;
+       mso-style-parent:example_file;
+       mso-style-type:export-only;
+       margin-top:0cm;
+       margin-right:1.0cm;
+       margin-bottom:0cm;
+       margin-left:0cm;
+       margin-bottom:.0001pt;
+       mso-add-space:auto;
+       text-align:justify;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       background:#E6E6E6;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       border:none;
+       mso-border-alt:solid windowtext .5pt;
+       padding:0cm;
+       mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;
+       font-size:8.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Courier New";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Courier New";}
+p.examplefilesmallCxSpLast, li.examplefilesmallCxSpLast, div.examplefilesmallCxSpLast
+       {mso-style-name:example_file_smallCxSpLast;
+       mso-style-parent:example_file;
+       mso-style-type:export-only;
+       margin-top:0cm;
+       margin-right:1.0cm;
+       margin-bottom:6.0pt;
+       margin-left:0cm;
+       mso-add-space:auto;
+       text-align:justify;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       background:#E6E6E6;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       border:none;
+       mso-border-alt:solid windowtext .5pt;
+       padding:0cm;
+       mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;
+       font-size:8.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Courier New";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Courier New";}
+p.StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut, li.StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut, div.StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut
+       {mso-style-name:"Style notebox\.body + Bold Not Italic Box\: \(Single solid line Aut\.\.\.";
+       mso-style-parent:"notebox\.body";
+       margin:0cm;
+       margin-bottom:.0001pt;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       background:#FFFF89;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       border:none;
+       mso-border-alt:solid windowtext 1.5pt;
+       padding:0cm;
+       mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;
+       font-size:12.0pt;
+       mso-bidi-font-size:10.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       font-weight:bold;}
+p.MyNormalJustified, li.MyNormalJustified, div.MyNormalJustified
+       {mso-style-name:MyNormalJustified;
+       mso-style-parent:MyNormal;
+       margin-top:2.0pt;
+       margin-right:0cm;
+       margin-bottom:6.0pt;
+       margin-left:42.55pt;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:11.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Courier New";}
+p.flagheading2, li.flagheading2, div.flagheading2
+       {mso-style-name:"flag heading 2";
+       mso-style-update:auto;
+       mso-style-parent:"flag description";
+       margin-top:6.0pt;
+       margin-right:0cm;
+       margin-bottom:0cm;
+       margin-left:45.0pt;
+       margin-bottom:.0001pt;
+       text-align:justify;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:10.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Times New Roman";
+       font-weight:bold;
+       mso-bidi-font-weight:normal;
+       font-style:italic;
+       mso-bidi-font-style:normal;
+       text-decoration:underline;
+       text-underline:single;}
+p.example1, li.example1, div.example1
+       {mso-style-name:example1;
+       mso-style-parent:example2;
+       margin-top:12.0pt;
+       margin-right:0cm;
+       margin-bottom:12.0pt;
+       margin-left:2.0cm;
+       mso-add-space:auto;
+       line-height:200%;
+       mso-pagination:widow-orphan lines-together;
+       page-break-after:avoid;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:10.0pt;
+       font-family:"Courier New";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Courier New";
+       font-weight:bold;
+       mso-bidi-font-weight:normal;}
+p.example1CxSpFirst, li.example1CxSpFirst, div.example1CxSpFirst
+       {mso-style-name:example1CxSpFirst;
+       mso-style-parent:example2;
+       mso-style-type:export-only;
+       margin-top:12.0pt;
+       margin-right:0cm;
+       margin-bottom:0cm;
+       margin-left:2.0cm;
+       margin-bottom:.0001pt;
+       mso-add-space:auto;
+       line-height:200%;
+       mso-pagination:widow-orphan lines-together;
+       page-break-after:avoid;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:10.0pt;
+       font-family:"Courier New";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Courier New";
+       font-weight:bold;
+       mso-bidi-font-weight:normal;}
+p.example1CxSpMiddle, li.example1CxSpMiddle, div.example1CxSpMiddle
+       {mso-style-name:example1CxSpMiddle;
+       mso-style-parent:example2;
+       mso-style-type:export-only;
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:0cm;
+       margin-left:2.0cm;
+       margin-bottom:.0001pt;
+       mso-add-space:auto;
+       line-height:200%;
+       mso-pagination:widow-orphan lines-together;
+       page-break-after:avoid;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:10.0pt;
+       font-family:"Courier New";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Courier New";
+       font-weight:bold;
+       mso-bidi-font-weight:normal;}
+p.example1CxSpLast, li.example1CxSpLast, div.example1CxSpLast
+       {mso-style-name:example1CxSpLast;
+       mso-style-parent:example2;
+       mso-style-type:export-only;
+       margin-top:0cm;
+       margin-right:0cm;
+       margin-bottom:12.0pt;
+       margin-left:2.0cm;
+       mso-add-space:auto;
+       line-height:200%;
+       mso-pagination:widow-orphan lines-together;
+       page-break-after:avoid;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:10.0pt;
+       font-family:"Courier New";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Courier New";
+       font-weight:bold;
+       mso-bidi-font-weight:normal;}
+span.MyNormaBoldlChar
+       {mso-style-name:"MyNormaBoldl Char";
+       mso-style-locked:yes;
+       mso-style-parent:"MyNormal Char";
+       mso-style-link:MyNormaBoldl;
+       mso-ansi-font-size:11.0pt;
+       mso-bidi-font-size:11.0pt;
+       font-family:"Courier New";
+       mso-ascii-font-family:"Courier New";
+       mso-hansi-font-family:"Courier New";
+       mso-bidi-font-family:"Courier New";
+       mso-ansi-language:AF;
+       mso-fareast-language:EN-US;}
+p.MyNormal2, li.MyNormal2, div.MyNormal2
+       {mso-style-name:MyNormal2;
+       mso-style-parent:MyNormal;
+       margin-top:2.0pt;
+       margin-right:0cm;
+       margin-bottom:6.0pt;
+       margin-left:42.55pt;
+       text-align:justify;
+       mso-pagination:none;
+       mso-hyphenate:none;
+       mso-layout-grid-align:none;
+       punctuation-wrap:simple;
+       text-autospace:none;
+       font-size:11.0pt;
+       font-family:"Times New Roman";
+       mso-fareast-font-family:"Times New Roman";
+       mso-bidi-font-family:"Courier New";
+       mso-ansi-language:AF;}
+span.msoIns
+       {mso-style-type:export-only;
+       mso-style-name:"";
+       text-decoration:underline;
+       text-underline:single;
+       color:teal;}
+span.msoDel
+       {mso-style-type:export-only;
+       mso-style-name:"";
+       text-decoration:line-through;
+       color:red;}
+span.msoChangeProp
+       {mso-style-type:export-only;
+       mso-style-name:"";
+       color:black;}
+ /* Page Definitions */
+@page
+       {mso-footnote-separator:url(":t_coffee_technical_files:header.htm") fs;
+       mso-footnote-continuation-separator:url(":t_coffee_technical_files:header.htm") fcs;
+       mso-endnote-separator:url(":t_coffee_technical_files:header.htm") es;
+       mso-endnote-continuation-separator:url(":t_coffee_technical_files:header.htm") ecs;}
+@page Section1
+       {size:21.0cm 842.0pt;
+       margin:48.0pt 48.0pt 48.0pt 48.0pt;
+       mso-header-margin:0cm;
+       mso-footer-margin:0cm;
+       mso-page-numbers:0;
+       mso-title-page:yes;
+       mso-footer:url(":t_coffee_technical_files:header.htm") f1;
+       mso-paper-source:0;}
+div.Section1
+       {page:Section1;}
+@page Section2
+       {size:21.0cm 842.0pt;
+       margin:90.0pt 60.0pt 90.0pt 60.0pt;
+       mso-header-margin:48.0pt;
+       mso-footer-margin:48.0pt;
+       mso-page-numbers:roman-lower 1;
+       mso-title-page:yes;
+       mso-footer:url(":t_coffee_technical_files:header.htm") f1;
+       mso-first-footer:url(":t_coffee_technical_files:header.htm") ff2;
+       mso-paper-source:0;}
+div.Section2
+       {page:Section2;}
+@page Section3
+       {size:21.0cm 842.0pt;
+       margin:90.0pt 60.0pt 90.0pt 60.0pt;
+       mso-header-margin:48.0pt;
+       mso-footer-margin:48.0pt;
+       mso-page-numbers:1;
+       mso-header:url(":t_coffee_technical_files:header.htm") h3;
+       mso-footer:url(":t_coffee_technical_files:header.htm") f3;
+       mso-first-header:url(":t_coffee_technical_files:header.htm") fh3;
+       mso-first-footer:url(":t_coffee_technical_files:header.htm") ff3;
+       mso-paper-source:0;}
+div.Section3
+       {page:Section3;}
+@page Section4
+       {size:21.0cm 842.0pt;
+       margin:72.0pt 90.0pt 72.0pt 90.0pt;
+       mso-header-margin:36.0pt;
+       mso-footer-margin:36.0pt;
+       mso-header:url(":t_coffee_technical_files:header.htm") h4;
+       mso-footer:url(":t_coffee_technical_files:header.htm") f4;
+       mso-first-header:url(":t_coffee_technical_files:header.htm") fh4;
+       mso-first-footer:url(":t_coffee_technical_files:header.htm") ff3;
+       mso-paper-source:0;}
+div.Section4
+       {page:Section4;}
+ /* List Definitions */
+@list l0
+       {mso-list-id:-132;
+       mso-list-type:simple;
+       mso-list-template-ids:243462170;}
+@list l0:level1
+       {mso-level-style-link:"List Number 3";
+       mso-level-tab-stop:90.0pt;
+       mso-level-number-position:left;
+       margin-left:90.0pt;
+       text-indent:-18.0pt;}
+@list l1
+       {mso-list-id:-131;
+       mso-list-type:simple;
+       mso-list-template-ids:579796312;}
+@list l1:level1
+       {mso-level-style-link:"List Number 2";
+       mso-level-tab-stop:72.0pt;
+       mso-level-number-position:left;
+       margin-left:72.0pt;
+       text-indent:-18.0pt;}
+@list l2
+       {mso-list-id:-130;
+       mso-list-type:simple;
+       mso-list-template-ids:-525153058;}
+@list l2:level1
+       {mso-level-style-link:"List Bullet 5";
+       mso-level-tab-stop:54.0pt;
+       mso-level-number-position:left;
+       margin-left:54.0pt;
+       text-indent:-18.0pt;}
+@list l3
+       {mso-list-id:-129;
+       mso-list-type:simple;
+       mso-list-template-ids:1970563230;}
+@list l3:level1
+       {mso-level-style-link:"List Bullet 4";
+       mso-level-tab-stop:36.0pt;
+       mso-level-number-position:left;
+       text-indent:-18.0pt;}
+@list l4
+       {mso-list-id:-128;
+       mso-list-type:simple;
+       mso-list-template-ids:-118980482;}
+@list l4:level1
+       {mso-level-number-format:bullet;
+       mso-level-style-link:"List Bullet 3";
+       mso-level-text:\F0B7;
+       mso-level-tab-stop:90.0pt;
+       mso-level-number-position:left;
+       margin-left:90.0pt;
+       text-indent:-18.0pt;
+       font-family:Symbol;}
+@list l5
+       {mso-list-id:-127;
+       mso-list-type:simple;
+       mso-list-template-ids:-1465100272;}
+@list l5:level1
+       {mso-level-number-format:bullet;
+       mso-level-style-link:"List Bullet 2";
+       mso-level-text:\F0B7;
+       mso-level-tab-stop:72.0pt;
+       mso-level-number-position:left;
+       margin-left:72.0pt;
+       text-indent:-18.0pt;
+       font-family:Symbol;}
+@list l6
+       {mso-list-id:-126;
+       mso-list-type:simple;
+       mso-list-template-ids:-368430812;}
+@list l6:level1
+       {mso-level-number-format:bullet;
+       mso-level-style-link:"List 5";
+       mso-level-text:\F0B7;
+       mso-level-tab-stop:54.0pt;
+       mso-level-number-position:left;
+       margin-left:54.0pt;
+       text-indent:-18.0pt;
+       font-family:Symbol;}
+@list l7
+       {mso-list-id:-125;
+       mso-list-type:simple;
+       mso-list-template-ids:-706941758;}
+@list l7:level1
+       {mso-level-number-format:bullet;
+       mso-level-style-link:"List 4";
+       mso-level-text:\F0B7;
+       mso-level-tab-stop:36.0pt;
+       mso-level-number-position:left;
+       text-indent:-18.0pt;
+       font-family:Symbol;}
+@list l8
+       {mso-list-id:-120;
+       mso-list-type:simple;
+       mso-list-template-ids:1576020400;}
+@list l8:level1
+       {mso-level-style-link:"Plain Text";
+       mso-level-tab-stop:18.0pt;
+       mso-level-number-position:left;
+       margin-left:18.0pt;
+       text-indent:-18.0pt;}
+@list l9
+       {mso-list-id:-119;
+       mso-list-type:simple;
+       mso-list-template-ids:96769246;}
+@list l9:level1
+       {mso-level-number-format:bullet;
+       mso-level-style-link:"Text body Char";
+       mso-level-text:\F0B7;
+       mso-level-tab-stop:18.0pt;
+       mso-level-number-position:left;
+       margin-left:18.0pt;
+       text-indent:-18.0pt;
+       font-family:Symbol;}
+@list l10
+       {mso-list-id:-5;
+       mso-list-template-ids:-1557078836;}
+@list l10:level1
+       {mso-level-number-format:none;
+       mso-level-suffix:none;
+       mso-level-text:"";
+       mso-level-tab-stop:none;
+       mso-level-number-position:left;
+       margin-left:0cm;
+       text-indent:0cm;}
+@list l10:level2
+       {mso-level-number-format:none;
+       mso-level-text:"";
+       mso-level-tab-stop:none;
+       mso-level-number-position:left;
+       mso-level-legacy:yes;
+       mso-level-legacy-indent:0cm;
+       mso-level-legacy-space:0cm;
+       margin-left:0cm;
+       text-indent:0cm;}
+@list l10:level3
+       {mso-level-number-format:none;
+       mso-level-text:"";
+       mso-level-tab-stop:none;
+       mso-level-number-position:left;
+       mso-level-legacy:yes;
+       mso-level-legacy-indent:0cm;
+       mso-level-legacy-space:0cm;
+       margin-left:0cm;
+       text-indent:0cm;}
+@list l10:level4
+       {mso-level-number-format:none;
+       mso-level-text:"";
+       mso-level-tab-stop:none;
+       mso-level-number-position:left;
+       mso-level-legacy:yes;
+       mso-level-legacy-indent:0cm;
+       mso-level-legacy-space:0cm;
+       margin-left:0cm;
+       text-indent:0cm;
+       mso-ansi-language:EN-GB;}
+@list l10:level5
+       {mso-level-start-at:0;
+       mso-level-number-format:none;
+       mso-level-text:"";
+       mso-level-tab-stop:none;
+       mso-level-number-position:left;
+       margin-left:0cm;
+       text-indent:0cm;}
+@list l10:level6
+       {mso-level-start-at:0;
+       mso-level-number-format:none;
+       mso-level-text:"";
+       mso-level-tab-stop:none;
+       mso-level-number-position:left;
+       margin-left:0cm;
+       text-indent:0cm;}
+@list l10:level7
+       {mso-level-start-at:0;
+       mso-level-number-format:none;
+       mso-level-text:"";
+       mso-level-tab-stop:none;
+       mso-level-number-position:left;
+       margin-left:0cm;
+       text-indent:0cm;}
+@list l10:level8
+       {mso-level-start-at:0;
+       mso-level-number-format:none;
+       mso-level-text:"";
+       mso-level-tab-stop:none;
+       mso-level-number-position:left;
+       margin-left:0cm;
+       text-indent:0cm;}
+@list l10:level9
+       {mso-level-start-at:0;
+       mso-level-number-format:none;
+       mso-level-text:"";
+       mso-level-tab-stop:none;
+       mso-level-number-position:left;
+       margin-left:0cm;
+       text-indent:0cm;}
+@list l11
+       {mso-list-id:-2;
+       mso-list-type:simple;
+       mso-list-template-ids:-1;}
+@list l11:level1
+       {mso-level-start-at:0;
+       mso-level-text:*;
+       mso-level-tab-stop:none;
+       mso-level-number-position:left;
+       margin-left:0cm;
+       text-indent:0cm;}
+@list l12
+       {mso-list-id:16198800;
+       mso-list-type:hybrid;
+       mso-list-template-ids:-1589361750 67895311 67895321 67895323 67895311 67895321 67895323 67895311 67895321 67895323;}
+@list l12:level1
+       {mso-level-tab-stop:78.55pt;
+       mso-level-number-position:left;
+       margin-left:78.55pt;
+       text-indent:-18.0pt;}
+@list l12:level2
+       {mso-level-number-format:alpha-lower;
+       mso-level-tab-stop:114.55pt;
+       mso-level-number-position:left;
+       margin-left:114.55pt;
+       text-indent:-18.0pt;}
+@list l13
+       {mso-list-id:31855817;
+       mso-list-type:hybrid;
+       mso-list-template-ids:1137623166 -1 -1 -1 -1 -1 -1 -1 -1 -1;}
+@list l13:level1
+       {mso-level-number-format:bullet;
+       mso-level-text:\F0A7;
+       mso-level-tab-stop:108.0pt;
+       mso-level-number-position:left;
+       margin-left:108.0pt;
+       text-indent:-18.0pt;
+       font-family:Wingdings;}
+@list l14
+       {mso-list-id:351080084;
+       mso-list-template-ids:1670832864;}
+@list l14:level1
+       {mso-level-number-format:bullet;
+       mso-level-text:\F0B7;
+       mso-level-tab-stop:36.0pt;
+       mso-level-number-position:left;
+       text-indent:-18.0pt;
+       mso-ansi-font-size:10.0pt;
+       font-family:Symbol;}
+@list l14:level2
+       {mso-level-tab-stop:72.0pt;
+       mso-level-number-position:left;
+       text-indent:-18.0pt;}
+@list l15
+       {mso-list-id:429860257;
+       mso-list-type:simple;
+       mso-list-template-ids:-1193904264;}
+@list l15:level1
+       {mso-level-tab-stop:none;
+       mso-level-number-position:left;
+       mso-level-legacy:yes;
+       mso-level-legacy-indent:18.0pt;
+       mso-level-legacy-space:0cm;
+       margin-right:36.0pt;
+       text-indent:-18.0pt;
+       mso-ansi-font-size:10.0pt;
+       mso-ascii-font-family:"Arial Black";
+       mso-hansi-font-family:"Arial Black";}
+@list l16
+       {mso-list-id:873344605;
+       mso-list-template-ids:1828727762;}
+@list l16:level1
+       {mso-level-number-format:bullet;
+       mso-level-text:\F0A7;
+       mso-level-tab-stop:18.0pt;
+       mso-level-number-position:left;
+       margin-left:18.0pt;
+       text-indent:-18.0pt;
+       font-family:Wingdings;}
+@list l16:level2
+       {mso-level-number-format:none;
+       mso-level-text:"";
+       mso-level-tab-stop:none;
+       mso-level-number-position:left;
+       mso-level-legacy:yes;
+       mso-level-legacy-indent:0cm;
+       mso-level-legacy-space:0cm;
+       margin-left:0cm;
+       text-indent:0cm;}
+@list l16:level3
+       {mso-level-number-format:none;
+       mso-level-text:"";
+       mso-level-tab-stop:none;
+       mso-level-number-position:left;
+       mso-level-legacy:yes;
+       mso-level-legacy-indent:0cm;
+       mso-level-legacy-space:0cm;
+       margin-left:0cm;
+       text-indent:0cm;}
+@list l16:level4
+       {mso-level-number-format:none;
+       mso-level-text:"";
+       mso-level-tab-stop:none;
+       mso-level-number-position:left;
+       mso-level-legacy:yes;
+       mso-level-legacy-indent:0cm;
+       mso-level-legacy-space:0cm;
+       margin-left:0cm;
+       text-indent:0cm;}
+@list l16:level5
+       {mso-level-start-at:0;
+       mso-level-number-format:none;
+       mso-level-text:"";
+       mso-level-tab-stop:none;
+       mso-level-number-position:left;
+       margin-left:0cm;
+       text-indent:0cm;}
+@list l16:level6
+       {mso-level-start-at:0;
+       mso-level-number-format:none;
+       mso-level-text:"";
+       mso-level-tab-stop:none;
+       mso-level-number-position:left;
+       margin-left:0cm;
+       text-indent:0cm;}
+@list l16:level7
+       {mso-level-start-at:0;
+       mso-level-number-format:none;
+       mso-level-text:"";
+       mso-level-tab-stop:none;
+       mso-level-number-position:left;
+       margin-left:0cm;
+       text-indent:0cm;}
+@list l16:level8
+       {mso-level-start-at:0;
+       mso-level-number-format:none;
+       mso-level-text:"";
+       mso-level-tab-stop:none;
+       mso-level-number-position:left;
+       margin-left:0cm;
+       text-indent:0cm;}
+@list l16:level9
+       {mso-level-start-at:0;
+       mso-level-number-format:none;
+       mso-level-text:"";
+       mso-level-tab-stop:none;
+       mso-level-number-position:left;
+       margin-left:0cm;
+       text-indent:0cm;}
+@list l17
+       {mso-list-id:934939961;
+       mso-list-type:hybrid;
+       mso-list-template-ids:-467735746 67895311 67895321 67895323 67895311 67895321 67895323 67895311 67895321 67895323;}
+@list l17:level1
+       {mso-level-tab-stop:78.55pt;
+       mso-level-number-position:left;
+       margin-left:78.55pt;
+       text-indent:-18.0pt;}
+@list l18
+       {mso-list-id:941451051;
+       mso-list-type:hybrid;
+       mso-list-template-ids:1232603580 67895311 67895321 67895323 67895311 67895321 67895323 67895311 67895321 67895323;}
+@list l18:level1
+       {mso-level-tab-stop:78.55pt;
+       mso-level-number-position:left;
+       margin-left:78.55pt;
+       text-indent:-18.0pt;}
+@list l19
+       {mso-list-id:964848167;
+       mso-list-template-ids:1912510992;}
+@list l19:level1
+       {mso-level-number-format:bullet;
+       mso-level-text:\F0B7;
+       mso-level-tab-stop:36.0pt;
+       mso-level-number-position:left;
+       text-indent:-18.0pt;
+       mso-ansi-font-size:10.0pt;
+       font-family:Symbol;}
+@list l19:level2
+       {mso-level-number-format:bullet;
+       mso-level-text:o;
+       mso-level-tab-stop:72.0pt;
+       mso-level-number-position:left;
+       text-indent:-18.0pt;
+       mso-ansi-font-size:10.0pt;
+       font-family:"Courier New";}
+@list l19:level3
+       {mso-level-number-format:bullet;
+       mso-level-text:\F0A7;
+       mso-level-tab-stop:108.0pt;
+       mso-level-number-position:left;
+       text-indent:-18.0pt;
+       mso-ansi-font-size:10.0pt;
+       font-family:Wingdings;}
+@list l20
+       {mso-list-id:976836001;
+       mso-list-type:hybrid;
+       mso-list-template-ids:-1213013906 67895311 67895321 67895323 67895311 67895321 67895323 67895311 67895321 67895323;}
+@list l20:level1
+       {mso-level-tab-stop:78.55pt;
+       mso-level-number-position:left;
+       margin-left:78.55pt;
+       text-indent:-18.0pt;}
+@list l21
+       {mso-list-id:1112475268;
+       mso-list-type:hybrid;
+       mso-list-template-ids:1170372944 67895311 67895321 67895323 67895311 67895321 67895323 67895311 67895321 67895323;}
+@list l21:level1
+       {mso-level-tab-stop:78.55pt;
+       mso-level-number-position:left;
+       margin-left:78.55pt;
+       text-indent:-18.0pt;}
+@list l22
+       {mso-list-id:1280378370;
+       mso-list-type:simple;
+       mso-list-template-ids:-247183560;}
+@list l22:level1
+       {mso-level-number-format:bullet;
+       mso-level-style-link:"List Bullet 3";
+       mso-level-text:\F0A7;
+       mso-level-tab-stop:18.0pt;
+       mso-level-number-position:left;
+       margin-top:0cm;
+       margin-right:18.0pt;
+       margin-bottom:0cm;
+       margin-left:18.0pt;
+       margin-bottom:.0001pt;
+       text-indent:-18.0pt;
+       font-family:Wingdings;}
+@list l23
+       {mso-list-id:1469779017;
+       mso-list-type:simple;
+       mso-list-template-ids:-1193904264;}
+@list l23:level1
+       {mso-level-tab-stop:none;
+       mso-level-number-position:left;
+       mso-level-legacy:yes;
+       mso-level-legacy-indent:18.0pt;
+       mso-level-legacy-space:0cm;
+       margin-right:36.0pt;
+       text-indent:-18.0pt;
+       mso-ansi-font-size:10.0pt;
+       mso-ascii-font-family:"Arial Black";
+       mso-hansi-font-family:"Arial Black";}
+@list l24
+       {mso-list-id:1589343465;
+       mso-list-template-ids:1670832864;}
+@list l24:level1
+       {mso-level-number-format:bullet;
+       mso-level-text:\F0B7;
+       mso-level-tab-stop:36.0pt;
+       mso-level-number-position:left;
+       text-indent:-18.0pt;
+       mso-ansi-font-size:10.0pt;
+       font-family:Symbol;}
+@list l24:level2
+       {mso-level-tab-stop:72.0pt;
+       mso-level-number-position:left;
+       text-indent:-18.0pt;}
+@list l25
+       {mso-list-id:1598251408;
+       mso-list-type:simple;
+       mso-list-template-ids:-674336410;}
+@list l25:level1
+       {mso-level-number-format:bullet;
+       mso-level-style-link:"Text body Char";
+       mso-level-text:\F0A7;
+       mso-level-tab-stop:18.0pt;
+       mso-level-number-position:left;
+       margin-top:0cm;
+       margin-right:18.0pt;
+       margin-bottom:0cm;
+       margin-left:18.0pt;
+       margin-bottom:.0001pt;
+       text-indent:-18.0pt;
+       font-family:Wingdings;}
+@list l26
+       {mso-list-id:1649675689;
+       mso-list-type:simple;
+       mso-list-template-ids:-1193904264;}
+@list l26:level1
+       {mso-level-tab-stop:none;
+       mso-level-number-position:left;
+       mso-level-legacy:yes;
+       mso-level-legacy-indent:18.0pt;
+       mso-level-legacy-space:0cm;
+       margin-right:36.0pt;
+       text-indent:-18.0pt;
+       mso-ansi-font-size:10.0pt;
+       mso-ascii-font-family:"Arial Black";
+       mso-hansi-font-family:"Arial Black";}
+@list l27
+       {mso-list-id:2072076493;
+       mso-list-type:hybrid;
+       mso-list-template-ids:-1431952502 67895311 67895321 67895323 67895311 67895321 67895323 67895311 67895321 67895323;}
+@list l27:level1
+       {mso-level-tab-stop:78.55pt;
+       mso-level-number-position:left;
+       margin-left:78.55pt;
+       text-indent:-18.0pt;}
+@list l11:level1 lfo19
+       {mso-level-number-format:bullet;
+       mso-level-numbering:continue;
+       mso-level-text:\F031;
+       mso-level-tab-stop:none;
+       mso-level-number-position:left;
+       mso-level-legacy:yes;
+       mso-level-legacy-indent:18.0pt;
+       mso-level-legacy-space:0cm;
+       margin-top:0cm;
+       margin-right:18.0pt;
+       margin-bottom:0cm;
+       margin-left:18.0pt;
+       margin-bottom:.0001pt;
+       text-indent:-18.0pt;
+       mso-ansi-font-size:11.0pt;
+       mso-ascii-font-family:Wingdings;
+       mso-hansi-font-family:Wingdings;}
+@list l11:level1 lfo20
+       {mso-level-number-format:bullet;
+       mso-level-numbering:continue;
+       mso-level-text:\F021;
+       mso-level-tab-stop:none;
+       mso-level-number-position:left;
+       mso-level-legacy:yes;
+       mso-level-legacy-indent:18.0pt;
+       mso-level-legacy-space:0cm;
+       margin-top:0cm;
+       margin-right:18.0pt;
+       margin-bottom:0cm;
+       margin-left:18.0pt;
+       margin-bottom:.0001pt;
+       text-indent:-18.0pt;
+       mso-ansi-font-size:12.0pt;
+       mso-ascii-font-family:Wingdings;
+       mso-hansi-font-family:Wingdings;}
+@list l11:level1 lfo21
+       {mso-level-number-format:bullet;
+       mso-level-numbering:continue;
+       mso-level-text:\F03A;
+       mso-level-tab-stop:none;
+       mso-level-number-position:left;
+       mso-level-legacy:yes;
+       mso-level-legacy-indent:18.0pt;
+       mso-level-legacy-space:0cm;
+       margin-top:0cm;
+       margin-right:18.0pt;
+       margin-bottom:0cm;
+       margin-left:18.0pt;
+       margin-bottom:.0001pt;
+       text-indent:-18.0pt;
+       mso-ansi-font-size:11.0pt;
+       mso-ascii-font-family:Wingdings;
+       mso-hansi-font-family:Wingdings;}
+@list l11:level1 lfo22
+       {mso-level-number-format:bullet;
+       mso-level-numbering:continue;
+       mso-level-text:\F026;
+       mso-level-tab-stop:none;
+       mso-level-number-position:left;
+       mso-level-legacy:yes;
+       mso-level-legacy-indent:18.0pt;
+       mso-level-legacy-space:0cm;
+       margin-top:0cm;
+       margin-right:18.0pt;
+       margin-bottom:0cm;
+       margin-left:18.0pt;
+       margin-bottom:.0001pt;
+       text-indent:-18.0pt;
+       mso-ansi-font-size:10.0pt;
+       mso-ascii-font-family:Wingdings;
+       mso-hansi-font-family:Wingdings;}
+@list l11:level1 lfo23
+       {mso-level-number-format:bullet;
+       mso-level-numbering:continue;
+       mso-level-text:\F0B7;
+       mso-level-tab-stop:none;
+       mso-level-number-position:left;
+       mso-level-legacy:yes;
+       mso-level-legacy-indent:18.0pt;
+       mso-level-legacy-space:0cm;
+       margin-top:0cm;
+       margin-right:36.0pt;
+       margin-bottom:0cm;
+       margin-left:0cm;
+       margin-bottom:.0001pt;
+       text-indent:-18.0pt;
+       mso-ansi-font-size:14.0pt;
+       mso-ascii-font-family:Symbol;
+       mso-hansi-font-family:Symbol;}
+@list l11:level1 lfo24
+       {mso-level-number-format:bullet;
+       mso-level-numbering:continue;
+       mso-level-text:\F0B7;
+       mso-level-tab-stop:none;
+       mso-level-number-position:left;
+       mso-level-legacy:yes;
+       mso-level-legacy-indent:18.0pt;
+       mso-level-legacy-space:0cm;
+       margin-top:0cm;
+       margin-right:36.0pt;
+       margin-bottom:0cm;
+       margin-left:0cm;
+       margin-bottom:.0001pt;
+       text-indent:-18.0pt;
+       mso-ansi-font-size:14.0pt;
+       mso-ascii-font-family:Symbol;
+       mso-hansi-font-family:Symbol;}
+ol
+       {margin-bottom:0cm;}
+ul
+       {margin-bottom:0cm;}
+-->
+</style>
+<!--[if gte mso 10]>
+<style>
+ /* Style Definitions */
+table.MsoNormalTable
+       {mso-style-name:"Table Normal";
+       mso-tstyle-rowband-size:0;
+       mso-tstyle-colband-size:0;
+       mso-style-noshow:yes;
+       mso-style-parent:"";
+       mso-padding-alt:0cm 5.4pt 0cm 5.4pt;
+       mso-para-margin:0cm;
+       mso-para-margin-bottom:.0001pt;
+       mso-pagination:widow-orphan;
+       font-size:10.0pt;
+       font-family:"Times New Roman";}
+</style>
+<![endif]--><!--[if gte mso 9]><xml>
+ <o:shapedefaults v:ext="edit" spidmax="2050"/>
+</xml><![endif]--><!--[if gte mso 9]><xml>
+ <o:shapelayout v:ext="edit">
+  <o:idmap v:ext="edit" data="1"/>
+ </o:shapelayout></xml><![endif]-->
+</head>
+
+<body lang=EN-US link=blue vlink=purple style='tab-interval:35.4pt'>
+
+<div class=Section1>
+
+<div style='mso-element:frame;mso-element-wrap:no-wrap-beside;mso-height-rule:
+exactly'>
+
+<table cellspacing=0 cellpadding=0 hspace=0 vspace=0 width=112 align=right>
+ <tr>
+  <td valign=top style='padding-top:9.35pt;padding-right:9.35pt;padding-bottom:
+  9.35pt;padding-left:9.35pt'>
+  <p class=PartTitle>Technical</p>
+  </td>
+ </tr>
+</table>
+
+</div>
+
+<![if !supportTextWrap]><br clear=ALL>
+<![endif]>
+
+<p class=CompanyName><span style='font-size:14.0pt'>Centre National De LA
+Recherche scientifique (France)<br>
+CeNTRO De REGULACIO GENOMICA (SPAIN)<o:p></o:p></span></p>
+
+<div style='mso-element:para-border-div;border:none;border-top:solid windowtext 1.0pt;
+mso-border-top-alt:solid windowtext .75pt;padding:1.0pt 0cm 0cm 0cm'>
+
+<p class=SubtitleCover>Cédric Notredame<br>
+www.tcoffee.org</p>
+
+</div>
+
+<div style='mso-element:para-border-div;border:solid white 1.0pt;mso-border-alt:
+solid white .75pt;padding:31.0pt 31.0pt 31.0pt 31.0pt;background:#E5E5E5;
+mso-shading:windowtext;mso-pattern:gray-10 auto'>
+
+<p class=TitleCover style='margin:0cm;margin-bottom:.0001pt;background:#E5E5E5;
+mso-shading:windowtext;mso-pattern:gray-10 auto'>T-Coffee:<br>
+Technical Documentation</p>
+
+</div>
+
+<div style='mso-element:para-border-div;border:none;border-top:solid windowtext 1.0pt;
+mso-border-top-alt:solid windowtext .75pt;padding:1.0pt 0cm 0cm 0cm'>
+
+<p class=SubtitleCover><o:p>&nbsp;</o:p></p>
+
+</div>
+
+</div>
+
+<span style='font-size:72.0pt;mso-bidi-font-size:10.0pt;font-family:Garamond;
+mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman";
+letter-spacing:-3.5pt;mso-font-kerning:14.0pt;mso-ansi-language:EN-US;
+mso-fareast-language:EN-US'><br clear=ALL style='page-break-before:always;
+mso-break-type:section-break'>
+</span>
+
+<div class=Section2>
+
+<div style='mso-element:para-border-div;border:none;border-bottom:solid gray 1.0pt;
+mso-border-bottom-alt:solid gray .75pt;padding:0cm 0cm 14.0pt 0cm'>
+
+<p class=MsoTitle>T-Coffee Technical Documentation<br>
+(Version 8.96, July 2010)<br>
+www.tcoffee.org<br>
+<br>
+T-Coffee, seq_reformat<br>
+<span style="mso-spacerun: yes">&nbsp;</span>PSI-Coffee, 3D-Coffee, Expresso, M-Coffee,
+R-Coffee, APDB, iRMSD, T-RMSD</p>
+
+</div>
+
+<p class=ReturnAddress><span style='font-family:Symbol;mso-ascii-font-family:
+Garamond;mso-hansi-font-family:Garamond;mso-char-type:symbol;mso-symbol-font-family:
+Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:Symbol'>ã</span></span>
+Cédric Notredame, Centro de Regulacio Genomica, Centre National de la Recherche
+Scientifique, France<span style='letter-spacing:0pt'><o:p></o:p></span></p>
+
+</div>
+
+<span style='font-size:8.0pt;mso-bidi-font-size:10.0pt;font-family:Garamond;
+mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman";
+mso-ansi-language:EN-US;mso-fareast-language:EN-US'><br clear=ALL
+style='page-break-before:always;mso-break-type:section-break'>
+</span>
+
+<div class=Section3>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><!--[if supportFields]><span
+style='mso-element:field-begin'></span><span style="mso-spacerun:
+yes">&nbsp;</span>TOC <span style='mso-element:field-separator'></span><![endif]--><span
+style='mso-no-proof:yes'>T-Coffee is distributed under the Gnu Public License<span
+style='mso-tab-count:1 dotted'>................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732187
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>6<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003100380037000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>T-Coffee code can be re-used freely<span
+style='mso-tab-count:1 dotted'>............................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732188
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>6<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003100380038000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>T-Coffee can be incorporated in most pipelines:
+Plug-in/Plug-out\85<span style='mso-tab-count:1 dotted'>......................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732189
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>6<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003100380039000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Contributors<span style='mso-tab-count:1 dotted'>................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732190
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>7<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003100390030000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Addresses<span style='mso-tab-count:1 dotted'>....................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732191
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>7<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003100390031000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>T-Coffee<span style='mso-tab-count:1 dotted'>.......................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732192
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>8<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003100390032000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Mocca<span style='mso-tab-count:1 dotted'>............................................................................................................................................ </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732193
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>10<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003100390033000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>CORE<span style='mso-tab-count:1 dotted'>............................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732194
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>10<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003100390034000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Other Contributions<span style='mso-tab-count:1 dotted'>.................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732195
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>10<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003100390035000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Bug Reports and Feedback<span style='mso-tab-count:
+1 dotted'>......................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732196
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>10<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003100390036000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Third Party Packages and On Demand Installations<span
+style='mso-tab-count:1 dotted'>................................................................ </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732197
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>11<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003100390037000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Standard Installation of T-Coffee<span
+style='mso-tab-count:1 dotted'>............................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732198
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>11<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003100390038000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-hansi-font-family:"Arial Black";mso-no-proof:yes'>Automated
+Installation</span><span style='mso-no-proof:yes'><span style='mso-tab-count:
+1 dotted'>......................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732199
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>11<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003100390039000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Mac-OsX<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................................ </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732200
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>11<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200300030000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Unix<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732201
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>11<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200300031000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-hansi-font-family:"Arial Black";mso-no-proof:yes'>Unix</span><span
+style='mso-no-proof:yes'><span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732202
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>12<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200300032000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Microsoft Windows/Cygwin<span style='mso-tab-count:
+1 dotted'>............................................................................................................................................................ </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732203
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>13<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200300033000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>MAC osX, Linux<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732204
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>13<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200300034000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>CLUSTER Installation<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732205
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>13<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200300035000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>If you have PDB installed:<span style='mso-tab-count:
+1 dotted'>.................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732206
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>14<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200300036000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Installing BLAST for T-Coffee<span style='mso-tab-count:
+1 dotted'>...................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732207
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>14<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200300037000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Why Do I need BLAST with T-Coffee?<span
+style='mso-tab-count:1 dotted'>......................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732208
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>14<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200300038000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Using the EBI BLAST Client<span style='mso-tab-count:
+1 dotted'>................................................................................................................................................................ </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732209
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>15<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200300039000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Using the NCBI BLAST Client<span style='mso-tab-count:
+1 dotted'>............................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732210
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>15<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200310030000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Using another Client<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................ </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732211
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>16<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200310031000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Using a BLAST local version on UNIX<span
+style='mso-tab-count:1 dotted'>.......................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732212
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>16<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200310032000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Using a BLAST local version on Windows/cygwin<span
+style='mso-tab-count:1 dotted'>............................................................................................................ </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732213
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>17<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200310033000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>BLAST+<span style='mso-tab-count:1 dotted'>.......................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732214
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>17<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200310034000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>ORIGINAL NCBI BLAST<span style='mso-tab-count:1 dotted'>.......................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732215
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>17<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200310035000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Installing Other Companion Packages<span
+style='mso-tab-count:1 dotted'>....................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732216
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>17<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200310036000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Installation of PSI-Coffee and Expresso<span
+style='mso-tab-count:1 dotted'>..................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732217
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>19<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200310037000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Installation of M-Coffee<span style='mso-tab-count:
+1 dotted'>............................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732218
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>19<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200310038000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Automated Installation<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732219
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>20<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200310039000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Manual Installation<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732220
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>20<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200320030000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Installation of APDB and iRMSD<span style='mso-tab-count:
+1 dotted'>.................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732221
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>22<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200320031000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Installation of tRMSD<span style='mso-tab-count:1 dotted'>................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732222
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>22<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200320032000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Installation of seq_reformat<span style='mso-tab-count:
+1 dotted'>........................................................................................................ </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732223
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>23<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200320033000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Installation of extract_from_pdb<span
+style='mso-tab-count:1 dotted'>................................................................................................ </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732224
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>23<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200320034000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Installation of 3D-Coffee/Expresso<span
+style='mso-tab-count:1 dotted'>............................................................................................ </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732225
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>23<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200320035000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Automated Installation<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732226
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>23<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200320036000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Manual Installation<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732227
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>23<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200320037000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Installing Fugue for T-Coffee<span style='mso-tab-count:
+1 dotted'>............................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732228
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>24<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200320038000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Installation of R-Coffee<span style='mso-tab-count:
+1 dotted'>................................................................................................................ </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732229
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>24<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200320039000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Automated Installation<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732230
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>24<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200330030000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Manual Installation<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732231
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>25<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200330031000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Installing ProbbonsRNA for R-Coffee<span
+style='mso-tab-count:1 dotted'>.......................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732232
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>25<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200330032000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Installing Consan for R-Coffee<span style='mso-tab-count:
+1 dotted'>.......................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732233
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>25<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200330033000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>T-COFFEE<span style='mso-tab-count:1 dotted'>...................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732234
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>26<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200330034000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>M-Coffee<span style='mso-tab-count:1 dotted'>....................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732235
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>26<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200330035000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Expresso<span style='mso-tab-count:1 dotted'>....................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732236
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>27<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200330036000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>R-Coffee<span style='mso-tab-count:1 dotted'>........................................................................................................................................ </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732237
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>27<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200330037000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>iRMSD and APDB<span style='mso-tab-count:1 dotted'>.......................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732238
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>28<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200330038000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>tRMSD<span style='mso-tab-count:1 dotted'>........................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732239
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>28<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200330039000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>MOCCA<span style='mso-tab-count:1 dotted'>.......................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732240
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>29<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200340030000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Environment Variables<span style='mso-tab-count:1 dotted'>............................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732241
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>31<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200340031000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>http_proxy_4_TCOFFEE<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................ </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732242
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>31<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200340032000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>email_4_TCOFFEE<span style='mso-tab-count:1 dotted'>..................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732243
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>32<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200340033000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>DIR_4_TCOFFEE<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732244
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>32<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200340034000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>TMP_4_TCOFFEE<span style='mso-tab-count:1 dotted'>....................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732245
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>32<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200340035000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>CACHE_4_TCOFFEE<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732246
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>32<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200340036000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>PLUGINS_4_TCOFFEE<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732247
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>32<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200340037000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>NO_ERROR_REPORT_4_TCOFFEE<span style='mso-tab-count:
+1 dotted'>.................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732248
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>32<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200340038000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>PDB_DIR<span style='mso-tab-count:1 dotted'>.......................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732249
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>32<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200340039000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>NO_WARNING_4_TCOFFEE<span style='mso-tab-count:1 dotted'>................................................................................................................................................................ </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732250
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>32<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200350030000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>UNIQUE_DIR_4_TCOFFEE<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732251
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>32<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200350031000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Setting up the T-Coffee environment variables<span
+style='mso-tab-count:1 dotted'>........................................................................ </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732252
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>32<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200350032000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Well Behaved Parameters<span style='mso-tab-count:
+1 dotted'>.......................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732253
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>33<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200350033000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Separation<span style='mso-tab-count:1 dotted'>...................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732254
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>33<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200350034000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Posix<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732255
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>33<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200350035000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Entering the right parameters<span style='mso-tab-count:
+1 dotted'>.......................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732256
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>33<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200350036000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Parameters Syntax<span style='mso-tab-count:1 dotted'>...................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732257
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>34<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200350037000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>No Flag<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732258
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>34<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200350038000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-parameters<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732259
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>34<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200350039000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-t_coffee_defaults<span style='mso-tab-count:1 dotted'>...................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732260
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>35<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200360030000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-mode<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732261
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>35<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200360031000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-score [Deprecated]<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................ </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732262
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>35<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200360032000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-evaluate<span style='mso-tab-count:1 dotted'>....................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732263
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>35<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200360033000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-convert [cw]<span style='mso-tab-count:1 dotted'>.............................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732264
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>36<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200360034000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-do_align [cw]<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................ </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732265
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>36<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200360035000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Special Parameters<span style='mso-tab-count:1 dotted'>...................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732266
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>36<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200360036000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-version<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732267
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>36<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200360037000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-proxy<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732268
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>36<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200360038000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-email<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732269
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>36<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200360039000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-check_configuration<span style='mso-tab-count:1 dotted'>.............................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732270
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>37<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200370030000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-cache<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732271
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>37<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200370031000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-update<span style='mso-tab-count:1 dotted'>.......................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732272
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>37<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200370032000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-full_log<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732273
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>37<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200370033000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-plugins<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732274
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>37<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200370034000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-other_pg<span style='mso-tab-count:1 dotted'>...................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732275
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>37<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200370035000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Input<span style='mso-tab-count:1 dotted'>............................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732276
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>38<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200370036000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Sequence Input<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732277
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>38<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200370037000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-infile [cw]<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732278
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>38<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200370038000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-in (Cf &#8211;in from the Method and Library Input
+section)<span style='mso-tab-count:1 dotted'>........................................................................................................ </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732279
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>38<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200370039000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-get_type<span style='mso-tab-count:1 dotted'>....................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732280
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>38<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200380030000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-type [cw]<span style='mso-tab-count:1 dotted'>..................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732281
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>38<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200380031000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-seq<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732282
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>38<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200380032000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-seq_source<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732283
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>38<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200380033000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Structure Input<span style='mso-tab-count:1 dotted'>.......................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732284
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>39<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200380034000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-pdb<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732285
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>39<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200380035000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Tree Input<span style='mso-tab-count:1 dotted'>...................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732286
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>39<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200380036000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-usetree<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732287
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>39<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200380037000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Structures, Sequences Methods and Library Input via
+the -in Flag<span style='mso-tab-count:1 dotted'>......................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732288
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>39<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200380038000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-in<span style='mso-tab-count:1 dotted'>..................................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732289
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>40<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200380039000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Profile Input<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732290
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>41<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200390030000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-profile<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732291
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>41<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200390031000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-profile1 [cw]<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732292
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>42<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200390032000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-profile2 [cw]<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732293
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>42<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200390033000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Alignment Computation<span style='mso-tab-count:1 dotted'>.............................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732294
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>42<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200390034000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Library Computation: Methods<span style='mso-tab-count:
+1 dotted'>...................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732295
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>42<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200390035000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-lalign_n_top<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732296
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>42<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200390036000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-align_pdb_param_file<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732297
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>42<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200390037000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-align_pdb_hasch_mode<span style='mso-tab-count:1 dotted'>....................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732298
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>42<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200390038000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Library Computation: Extension<span style='mso-tab-count:
+1 dotted'>.................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732299
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>43<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200390039000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-lib_list [Unsupported]<span style='mso-tab-count:
+1 dotted'>.......................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732300
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>43<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300300030000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-do_normalise<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................ </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732301
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>43<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300300031000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-extend<span style='mso-tab-count:1 dotted'>.......................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732302
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>43<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300300032000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-extend_mode<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................ </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732303
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>43<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300300033000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-max_n_pair<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................ </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732304
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>44<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300300034000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-seq_name_for_quadruplet<span style='mso-tab-count:
+1 dotted'>.................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732305
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>44<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300300035000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-compact<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................................ </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732306
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>44<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300300036000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-clean<span style='mso-tab-count:1 dotted'>.............................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732307
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>44<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300300037000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-maximise<span style='mso-tab-count:1 dotted'>..................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732308
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>44<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300300038000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-do_self<span style='mso-tab-count:1 dotted'>.......................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732309
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>44<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300300039000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-seq_name_for_quadruplet<span style='mso-tab-count:
+1 dotted'>.................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732310
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>44<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300310030000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-weight<span style='mso-tab-count:1 dotted'>.......................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732311
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>44<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300310031000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Tree Computation<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732312
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>45<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300310032000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-distance_matrix_mode<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732313
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>45<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300310033000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-quicktree [CW]<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732314
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>45<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300310034000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Pair-wise Alignment Computation<span style='mso-tab-count:
+1 dotted'>................................................................................................................................................ </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732315
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>46<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300310035000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-dp_mode<span style='mso-tab-count:1 dotted'>..................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732316
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>46<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300310036000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-ktuple<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732317
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>47<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300310037000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-ndiag<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732318
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>47<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300310038000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-diag_mode<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732319
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>47<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300310039000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-diag_threshold<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732320
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>47<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300320030000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-sim_matrix<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732321
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>47<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300320031000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-matrix [CW]<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732322
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>48<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300320032000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-nomatch<span style='mso-tab-count:1 dotted'>....................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732323
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>48<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300320033000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-gapopen<span style='mso-tab-count:1 dotted'>...................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732324
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>48<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300320034000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-gapext<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732325
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>48<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300320035000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-fgapopen<span style='mso-tab-count:1 dotted'>..................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732326
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>48<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300320036000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-fgapext<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732327
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>49<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300320037000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-cosmetic_penalty<span style='mso-tab-count:1 dotted'>..................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732328
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>49<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300320038000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-tg_mode<span style='mso-tab-count:1 dotted'>....................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732329
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>49<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300320039000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Weighting Schemes<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732330
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>49<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300330030000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-seq_weight<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732331
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>49<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300330031000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Multiple Alignment Computation<span style='mso-tab-count:
+1 dotted'>................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732332
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>50<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300330032000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-msa_mode<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732333
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>50<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300330033000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-one2all<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732334
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>50<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300330034000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-profile_comparison<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................ </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732335
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>50<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300330035000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-profile_mode<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732336
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>50<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300330036000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Alignment Post-Processing<span style='mso-tab-count:
+1 dotted'>................................................................................................................................................................ </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732337
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>51<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300330037000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-clean_aln<span style='mso-tab-count:1 dotted'>..................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732338
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>51<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300330038000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-clean_threshold<span style='mso-tab-count:1 dotted'>....................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732339
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>51<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300330039000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-clean_iteration<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732340
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>51<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300340030000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-clean_evaluation_mode<span style='mso-tab-count:1 dotted'>....................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732341
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>51<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300340031000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-iterate<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732342
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>51<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300340032000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>BLAST Template Selection Parameters<span
+style='mso-tab-count:1 dotted'>...................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732343
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>51<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300340033000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-blast_server<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................ </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732344
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>52<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300340034000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-prot_min_sim<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................ </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732345
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>52<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300340035000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-prot_max_sim<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................ </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732346
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>52<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300340036000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-prot_min_cov<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732347
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>52<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300340037000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-protein_db<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732348
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>52<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300340038000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-pdb_min_sim<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732349
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>52<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300340039000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-pdb_max_sim<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................ </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732350
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>52<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300350030000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-pdb_min_cov<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732351
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>53<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300350031000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-pdb_db<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732352
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>53<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300350032000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-pdb_type<span style='mso-tab-count:1 dotted'>..................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732353
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>53<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300350033000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>CPU Control<span style='mso-tab-count:1 dotted'>................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732354
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>53<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300350034000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Multithreading<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................ </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732355
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>53<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300350035000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-multi_core<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732356
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>53<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300350036000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-n_core<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732357
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>54<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300350037000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Limits<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................................ </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732358
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>54<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300350038000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-mem_mode<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732359
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>54<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300350039000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-ulimit<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................................ </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732360
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>54<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300360030000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-maxlen<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732361
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>54<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300360031000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Aligning more than 100 sequences with DPA<span
+style='mso-tab-count:1 dotted'>......................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732362
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>54<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300360032000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-maxnseq<span style='mso-tab-count:1 dotted'>...................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732363
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>54<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300360033000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-dpa_master_aln<span style='mso-tab-count:1 dotted'>....................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732364
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>55<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300360034000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-dpa_maxnseq<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................ </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732365
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>55<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300360035000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-dpa_min_score1<span style='mso-tab-count:1 dotted'>...................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732366
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>55<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300360036000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-dpa_min_score2<span style='mso-tab-count:1 dotted'>...................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732367
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>55<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300360037000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-dap_tree [NOT IMPLEMENTED]<span style='mso-tab-count:
+1 dotted'>.................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732368
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>55<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300360038000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Using Structures<span style='mso-tab-count:1 dotted'>.......................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732369
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>56<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300360039000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Generic<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732370
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>56<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300370030000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-mode<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732371
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>56<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300370031000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-check_pdb_status<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732372
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>56<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300370032000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>3D Coffee: Using SAP<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................ </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732373
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>56<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300370033000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Using/finding PDB templates for the Sequences<span
+style='mso-tab-count:1 dotted'>................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732374
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>57<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300370034000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-template_file<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732375
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>57<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300370035000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-struc_to_use<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732376
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>59<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300370036000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Multiple Local Alignments<span style='mso-tab-count:
+1 dotted'>........................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732377
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>59<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300370037000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-domain/-mocca<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................ </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732378
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>59<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300370038000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-start<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................................ </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732379
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>59<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300370039000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-len<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732380
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>60<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300380030000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-scale<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732381
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>60<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300380031000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-domain_interactive [Examples]<span style='mso-tab-count:
+1 dotted'>...................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732382
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>60<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300380032000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Output Control<span style='mso-tab-count:1 dotted'>............................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732383
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>61<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300380033000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Generic<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732384
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>61<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300380034000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Conventions Regarding Filenames<span style='mso-tab-count:
+1 dotted'>................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732385
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>61<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300380035000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Identifying the Output files automatically<span
+style='mso-tab-count:1 dotted'>.................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732386
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>61<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300380036000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-no_warning<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732387
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>61<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300380037000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Alignments<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732388
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>61<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300380038000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-outfile<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732389
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>61<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300380039000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-output<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732390
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>61<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300390030000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-outseqweight<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................ </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732391
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>62<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300390031000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-case<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................................ </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732392
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>62<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300390032000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-cpu<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732393
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>63<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300390033000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-outseqweight<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................ </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732394
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>63<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300390034000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-outorder [cw]<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732395
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>63<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300390035000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-inorder [cw]<span style='mso-tab-count:1 dotted'>.............................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732396
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>63<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300390036000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-seqnos<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732397
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>63<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300390037000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Libraries<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732398
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>63<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300390038000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-out_lib<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732399
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>64<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300390039000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-lib_only<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................................ </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732400
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>64<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400300030000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Trees<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732401
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>64<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400300031000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-newtree<span style='mso-tab-count:1 dotted'>....................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732402
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>64<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400300032000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Reliability Estimation<span style='mso-tab-count:1 dotted'>................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732403
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>64<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400300033000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>CORE Computation<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732404
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>64<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400300034000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-evaluate_mode<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732405
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>64<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400300035000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Generic Output<span style='mso-tab-count:1 dotted'>............................................................................................................................ </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732406
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>65<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400300036000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-run_name<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732407
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>65<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400300037000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-quiet<span style='mso-tab-count:1 dotted'>.............................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732408
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>65<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400300038000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-align [CW]<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732409
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>65<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400300039000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>APDB, iRMSD and tRMSD Parameters<span
+style='mso-tab-count:1 dotted'>........................................................................................ </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732410
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>65<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400310030000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-quiet [Same as T-Coffee]<span style='mso-tab-count:
+1 dotted'>..................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732411
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>66<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400310031000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-run_name [Same as T-Coffee]<span style='mso-tab-count:
+1 dotted'>.......................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732412
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>66<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400310032000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-aln<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732413
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>66<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400310033000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-n_excluded_nb<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732414
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>66<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400310034000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-maximum_distance<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................ </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732415
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>66<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400310035000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-similarity_threshold<span style='mso-tab-count:1 dotted'>.............................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732416
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>66<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400310036000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-local_mode<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732417
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>67<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400310037000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-filter<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732418
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>67<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400310038000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-print_rapdb [Unsupported]<span style='mso-tab-count:
+1 dotted'>.............................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732419
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>67<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400310039000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-outfile [Same as T-Coffee]<span style='mso-tab-count:
+1 dotted'>.................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732420
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>67<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400320030000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>-color_mode<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732421
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>67<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400320031000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Environment Variables<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732422
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>68<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400320032000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Output of the .dnd file.<span style='mso-tab-count:
+1 dotted'>............................................................................................................................................................................ </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732423
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>69<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400320033000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Permissions<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732424
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>69<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400320034000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Other Programs<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732425
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>69<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400320035000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Parameter files<span style='mso-tab-count:1 dotted'>............................................................................................................................ </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732426
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>70<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400320036000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Sequence Name Handling<span style='mso-tab-count:1 dotted'>........................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732427
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>70<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400320037000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Automatic Format Recognition<span style='mso-tab-count:
+1 dotted'>................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732428
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>71<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400320038000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Structures<span style='mso-tab-count:1 dotted'>.................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732429
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>71<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400320039000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>RNA Structures<span style='mso-tab-count:1 dotted'>............................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732430
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>71<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400330030000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Sequences<span style='mso-tab-count:1 dotted'>.................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732431
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>71<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400330031000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Alignments<span style='mso-tab-count:1 dotted'>................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732432
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>71<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400330032000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Libraries<span style='mso-tab-count:1 dotted'>....................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732433
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>72<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400330033000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>T-COFFEE_LIB_FORMAT_01<span style='mso-tab-count:1 dotted'>............................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732434
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>72<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400330034000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>T-COFFEE_LIB_FORMAT_02<span style='mso-tab-count:1 dotted'>............................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732435
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>73<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400330035000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Library List<span style='mso-tab-count:1 dotted'>................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732436
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>73<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400330036000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Substitution matrices.<span style='mso-tab-count:1 dotted'>................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732437
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>73<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400330037000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>ClustalW Style [Deprecated]<span style='mso-tab-count:
+1 dotted'>.............................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732438
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>73<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400330038000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>BLAST Format [Recommended]<span style='mso-tab-count:
+1 dotted'>..................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732439
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>74<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400330039000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Sequences Weights<span style='mso-tab-count:1 dotted'>..................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732440
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>74<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400340030000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Development<span style='mso-tab-count:1 dotted'>............................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732441
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>76<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400340031000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>profile2list<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732442
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>76<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400340032000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
+style='mso-no-proof:yes'>Command Line List<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................. </span></span><!--[if supportFields]><span
+style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732443
+\h <span style='mso-element:field-separator'></span></span><![endif]--><span
+style='mso-no-proof:yes'>76<!--[if gte mso 9]><xml>
+ <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400340033000000</w:data>
+</xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
+mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
+mso-no-proof:yes'><o:p></o:p></span></p>
+
+<p class=FAQ><!--[if supportFields]><span lang=EN-GB><span style='mso-element:
+field-end'></span></span><![endif]--></p>
+
+</div>
+
+<b style='mso-bidi-font-weight:normal'><span lang=EN-GB style='font-size:11.0pt;
+mso-bidi-font-size:14.0pt;font-family:"Comic Sans MS";mso-fareast-font-family:
+"Times New Roman";mso-bidi-font-family:"Courier New";mso-ansi-language:EN-GB;
+mso-fareast-language:EN-US'><br clear=ALL style='page-break-before:auto;
+mso-break-type:section-break'>
+</span></b>
+
+<div class=Section4>
+
+<div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
+padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0cm;margin-right:
+4.25pt'>
+
+<p class=ChapterTitle><a name="_Toc101065185"></a><a name="_Toc102494650"><span
+style='mso-bookmark:_Toc101065185'>License and Terms of Use</span></a></p>
+
+</div>
+
+<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
+
+<h2><a name="_Toc102494275"></a><a name="_Toc102494651"></a><a
+name="_Toc151732187"><span style='mso-bookmark:_Toc102494651'><span
+style='mso-bookmark:_Toc102494275'>T-Coffee is distributed under the Gnu Public
+License</span></span></a></h2>
+
+<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
+
+<p class=MyNormal><span lang=AF>Please make sure you have agreed with the terms
+of the license attached to the package before using the T-Coffee package or its
+documentation. T-Coffee is a freeware open source distributed under a GPL
+license. This means that there are very little restrictions to its use, either
+in an academic or a non academic environment.</span></p>
+
+<h2><a name="_Toc102494276"></a><a name="_Toc102494652"></a><a
+name="_Toc151732188"><span style='mso-bookmark:_Toc102494652'><span
+style='mso-bookmark:_Toc102494276'>T-Coffee code can be re-used freely</span></span></a></h2>
+
+<p class=MyNormal><span lang=AF>Our philosophy is that code is meant to be
+re-used, including ours. No permission is needed for the cut and paste of a few
+functions, although we are always happy to receive pieces of improved code.</span></p>
+
+<h2><a name="_Toc101065186"></a><a name="_Toc102494653"></a><a
+name="_Toc151732189"><span style='mso-bookmark:_Toc102494653'><span
+style='mso-bookmark:_Toc101065186'>T-Coffee can be incorporated in most
+pipelines: Plug-in/Plug-out\85</span></span></a><span style='mso-bookmark:_Toc102494653'><span
+style='mso-bookmark:_Toc101065186'></span></span></h2>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494653'><span
+style='mso-bookmark:_Toc101065186'><span lang=AF>Our philosophy is to insure
+that as many methods as possible can be used as plug-ins within T-Coffee.
+Likewise, we will give as much support as possible to anyone wishing to turn
+T-Coffee into a plug-in for another method. For more details on how to do this,
+see the plug-in and the plug-out sections of the Tutorial Manual.</span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494653'><span
+style='mso-bookmark:_Toc101065186'><span lang=AF>Again, you do not need our
+permission to either use T-Coffee (or your method as a plug-in/out) but if you
+let us know, we will insure the stability of T-Coffee within your system
+through future releases. </span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494653'><span
+style='mso-bookmark:_Toc101065186'><span lang=AF>The current license only
+allows for the incorporation of T-Coffee in non-commercial pipelines (i.e.
+where you do not sell the pipeline, or access to it). If your pipeline is
+commercial, please get in touch with us. </span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494653'><span
+style='mso-bookmark:_Toc101065186'><span lang=AF><o:p>&nbsp;</o:p></span></span></span></p>
+
+<div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
+padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0cm;margin-right:
+4.25pt'>
+
+<p class=ChapterTitle><span style='mso-bookmark:_Toc102494653'><span
+style='mso-bookmark:_Toc101065186'>Addresses and Contacts</span></span><span
+style='mso-bookmark:_Toc101065186'></span><span style='mso-bookmark:_Toc102494653'></span><span
+style='font-size:98.0pt;mso-bidi-font-size:48.0pt'><o:p></o:p></span></p>
+
+</div>
+
+<h2><a name="_Toc151732190">Contributors</a></h2>
+
+<p class=MsoBodyText>T-coffee is developed, maintained, monitored, used and
+debugged by a dedicated team that include or have included:</p>
+
+<p class=MsoBodyText><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Cédric
+Notredame, Paolo di Tomasso, Jean-François Taly, Cedrik Magis, Fabrice
+Armougom, Des Higgins, Sebastien Moretti, Orla O\92Sullivan. Eamon O\92Toole,
+Olivier Poirot, Karsten Suhre, Iain Wallace, Andreas Wilm</p>
+
+<h2><a name="_Toc151732191">Addresses</a></h2>
+
+<p class=MyNormal><span lang=AF>We are always very eager to get some user
+feedback. Please do not hesitate to drop us a line<span style="mso-spacerun:
+yes">&nbsp; </span>at: <a href="mailto:cedric.notredame@europe.com"><span
+lang=EN-US style='mso-ansi-language:EN-US'>cedric.notredame@europe.com</span></a>
+The latest updates of T-Coffee are always available<span style="mso-spacerun:
+yes">&nbsp; </span>on: www.tcoffee.org . On this address you will also find a
+link to some of the online T-Coffee servers, including Tcoffee@igs </span></p>
+
+<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
+
+<p class=MyNormal><span lang=AF>T-Coffee can be used to automatically check if
+an updated version is available, however the program will not update
+automatically, as this can cause endless reproducibility problems.</span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+&#8211;update</p>
+
+</div>
+
+<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
+
+<div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
+padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0cm;margin-right:
+4.25pt'>
+
+<p class=ChapterTitle><a name="_Toc101065187"></a><a name="_Toc102494654"><span
+style='mso-bookmark:_Toc101065187'>Citations</span></a></p>
+
+</div>
+
+<p class=MyNormal><span lang=AF>It is important that you cite T-Coffee when you
+use it. Citing us is (almost) like giving us money: it helps us convincing our
+institutions that what we do is useful and that they should keep paying our
+salaries and deliver Donuts to our offices from time to time (Not that they
+ever did it, but it would be nice anyway). </span></p>
+
+<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
+
+<p class=MyNormal><span lang=AF>Cite the server if you used it, otherwise, cite
+the original paper from 2000 (No, it was never named &quot;T-Coffee
+2000&quot;).</span></p>
+
+<table class=MsoNormalTable border=0 cellspacing=4 cellpadding=0 width="81%"
+ style='width:81.78%;mso-cellspacing:3.7pt;mso-padding-alt:0cm 0cm 0cm 0cm'>
+ <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>
+  <td width="53%" style='width:53.48%;padding:0cm 0cm 0cm 0cm'>
+  <p class=MyNormalJustified><a
+  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=10964570">Notredame
+  C, Higgins DG, Heringa J.</a><span style='mso-bidi-font-size:12.0pt;
+  color:black'><o:p></o:p></span></p>
+  </td>
+  <td width="43%" nowrap valign=top style='width:43.3%;padding:0cm 0cm 0cm 0cm'>
+  <p class=MyNormalJustified><a
+  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Display&amp;dopt=pubmed_pubmed&amp;from_uid=10964570"><span
+  style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <!--[if gte vml 1]><v:shapetype
+   id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
+   path="m@4@5l@4@11@9@11@9@5xe" filled="f" stroked="f">
+   <v:stroke joinstyle="miter"/>
+   <v:formulas>
+    <v:f eqn="if lineDrawn pixelLineWidth 0"/>
+    <v:f eqn="sum @0 1 0"/>
+    <v:f eqn="sum 0 0 @1"/>
+    <v:f eqn="prod @2 1 2"/>
+    <v:f eqn="prod @3 21600 pixelWidth"/>
+    <v:f eqn="prod @3 21600 pixelHeight"/>
+    <v:f eqn="sum @0 0 1"/>
+    <v:f eqn="prod @6 1 2"/>
+    <v:f eqn="prod @7 21600 pixelWidth"/>
+    <v:f eqn="sum @8 21600 0"/>
+    <v:f eqn="prod @7 21600 pixelHeight"/>
+    <v:f eqn="sum @10 21600 0"/>
+   </v:formulas>
+   <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
+   <o:lock v:ext="edit" aspectratio="t"/>
+  </v:shapetype><v:shape id="_x0000_i1025" type="#_x0000_t75" style='width:15pt;
+   height:11pt;visibility:hidden' print="f">
+   <v:imagedata src="t_coffee_technical_files/image001.png" o:title="&#37008;&#28494;&#28018;&#27745;&#36864;&#24902;x0&#37008;1"/>
+   <o:lock v:ext="edit" grouping="t"/>
+  </v:shape><![endif]--><!--[if gte vml 1]><v:shape id="_x0000_i1026" type="#_x0000_t75"
+   style='width:15pt;height:11pt;visibility:hidden' print="f">
+   <v:imagedata src="t_coffee_technical_files/image002.png" o:title="&#37008;&#28494;&#28018;&#27745;&#36864;&#24902;x0&#37008;1"/>
+   <o:lock v:ext="edit" grouping="t"/>
+  </v:shape><![endif]--><span style='mso-field-code:"HYPERLINK \0022javascript\:PopUpMenu2_Set\(Menu10964570\)\;\0022 \\t \0022_self\0022"'><span
+  class=MsoHyperlink><span style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></span></span>
+  <span style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
+  </td>
+ </tr>
+ <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>
+  <td width="97%" colspan=2 style='width:97.86%;padding:0cm 0cm 0cm 0cm'>
+  <p class=MyNormalJustified>T-Coffee: A novel method for fast and accurate
+  multiple sequence alignment.<br>
+  J Mol Biol. 2000 Sep 8;302(1):205-17. <br>
+  PMID: 10964570 [PubMed - indexed for MEDLINE]<span style='mso-bidi-font-size:
+  12.0pt;color:black'><o:p></o:p></span></p>
+  </td>
+ </tr>
+</table>
+
+<p class=MyNormal><span lang=AF>Other useful publications include:</span></p>
+
+<h2><a name="_Toc101065188"></a><a name="_Toc102494277"></a><a
+name="_Toc102494655"></a><a name="_Toc151732192"><span style='mso-bookmark:
+_Toc102494655'><span style='mso-bookmark:_Toc102494277'><span style='mso-bookmark:
+_Toc101065188'>T-Coffee</span></span></span></a></h2>
+
+<table class=MsoNormalTable border=0 cellspacing=4 cellpadding=0 width="81%"
+ style='width:81.78%;mso-cellspacing:3.7pt;mso-padding-alt:0cm 0cm 0cm 0cm'>
+ <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>
+  <td width="53%" style='width:53.48%;padding:0cm 0cm 0cm 0cm'>
+  <p class=MyNormalJustified><a
+  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=15215460">Claude
+  JB, Suhre K, Notredame C, Claverie JM, Abergel C.</a><span style='mso-bidi-font-size:
+  12.0pt;color:black'><o:p></o:p></span></p>
+  </td>
+  <td width="43%" nowrap valign=top style='width:43.3%;padding:0cm 0cm 0cm 0cm'>
+  <p class=MyNormalJustified><a
+  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Display&amp;dopt=pubmed_pubmed&amp;from_uid=15215460"><span
+  style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <!--[if gte vml 1]><v:shape
+   id="_x0000_i1027" type="#_x0000_t75" style='width:15pt;height:11pt;
+   visibility:hidden' print="f">
+   <v:imagedata src="t_coffee_technical_files/image003.png" o:title="&#37008;&#28494;&#28018;&#27745;&#36864;&#24902;x0&#37008;1"/>
+   <o:lock v:ext="edit" grouping="t"/>
+  </v:shape><![endif]--><!--[if gte vml 1]><v:shape id="_x0000_i1028" type="#_x0000_t75"
+   style='width:15pt;height:11pt;visibility:hidden' print="f">
+   <v:imagedata src="t_coffee_technical_files/image004.png" o:title="&#37008;&#28494;&#28018;&#27745;&#36864;&#24902;x0&#37008;1"/>
+   <o:lock v:ext="edit" grouping="t"/>
+  </v:shape><![endif]--><span style='mso-field-code:"HYPERLINK \0022javascript\:PopUpMenu2_Set\(Menu15215460\)\;\0022 \\t \0022_self\0022"'><span
+  class=MsoHyperlink><span style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></span></span>
+  <span style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
+  </td>
+ </tr>
+ <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>
+  <td width="97%" colspan=2 style='width:97.86%;padding:0cm 0cm 0cm 0cm'>
+  <p class=MyNormalJustified>CaspR: a web server for automated molecular
+  replacement using homology modelling.<br>
+  Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W606-9. <br>
+  PMID: 15215460 [PubMed - indexed for MEDLINE]<span style='mso-bidi-font-size:
+  12.0pt;color:black'><o:p></o:p></span></p>
+  </td>
+ </tr>
+</table>
+
+<p class=MyNormalJustified><o:p>&nbsp;</o:p></p>
+
+<table class=MsoNormalTable border=0 cellspacing=4 cellpadding=0 width="81%"
+ style='width:81.98%;mso-cellspacing:3.7pt;mso-padding-alt:0cm 0cm 0cm 0cm'>
+ <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>
+  <td width="53%" style='width:53.5%;padding:0cm 0cm 0cm 0cm'>
+  <p class=MyNormalJustified><a
+  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=15215345">Poirot
+  O, Suhre K, Abergel C, O'Toole E, Notredame C.</a><span style='mso-bidi-font-size:
+  12.0pt;color:black'><o:p></o:p></span></p>
+  </td>
+  <td nowrap valign=top style='padding:0cm 0cm 0cm 0cm'>
+  <p class=MyNormalJustified><a
+  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Display&amp;dopt=pubmed_pubmed&amp;from_uid=15215345"><span
+  style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <!--[if gte vml 1]><v:shape
+   id="_x0000_i1029" type="#_x0000_t75" style='width:15pt;height:11pt;
+   visibility:hidden' print="f">
+   <v:imagedata src="t_coffee_technical_files/image005.png" o:title="&#37008;&#28494;&#28018;&#27745;&#36864;&#24902;x0&#37008;1"/>
+   <o:lock v:ext="edit" grouping="t"/>
+  </v:shape><![endif]--><span style='mso-field-code:"HYPERLINK \0022javascript\:PopUpMenu2_Set\(Menu15215345\)\;\0022 \\t \0022_self\0022"'><span
+  class=MsoHyperlink><span style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></span></span>
+  <span style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
+  </td>
+ </tr>
+ <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>
+  <td colspan=2 style='padding:0cm 0cm 0cm 0cm'>
+  <p class=MyNormalJustified>3DCoffee@igs: a web server for combining sequences
+  and structures into a multiple sequence alignment.<br>
+  Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W37-40. <br>
+  PMID: 15215345 [PubMed - indexed for MEDLINE]<span style='mso-bidi-font-size:
+  12.0pt;color:black'><o:p></o:p></span></p>
+  </td>
+ </tr>
+</table>
+
+<p class=MyNormalJustified><o:p>&nbsp;</o:p></p>
+
+<table class=MsoNormalTable border=0 cellspacing=4 cellpadding=0 width="81%"
+ style='width:81.98%;mso-cellspacing:3.7pt;mso-padding-alt:0cm 0cm 0cm 0cm'>
+ <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>
+  <td width="53%" style='width:53.5%;padding:0cm 0cm 0cm 0cm'>
+  <p class=MyNormalJustified><a
+  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=15201059">O'Sullivan
+  O, Suhre K, Abergel C, Higgins DG, Notredame C.</a><span style='mso-bidi-font-size:
+  12.0pt;color:black'><o:p></o:p></span></p>
+  </td>
+  <td nowrap valign=top style='padding:0cm 0cm 0cm 0cm'>
+  <p class=MyNormalJustified><a
+  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Display&amp;dopt=pubmed_pubmed&amp;from_uid=15201059"><span
+  style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <!--[if gte vml 1]><v:shape
+   id="_x0000_i1030" type="#_x0000_t75" style='width:15pt;height:11pt;
+   visibility:hidden' print="f">
+   <v:imagedata src="t_coffee_technical_files/image006.png" o:title="&#37008;&#28494;&#28018;&#27745;&#36864;&#24902;x0&#37008;1"/>
+   <o:lock v:ext="edit" grouping="t"/>
+  </v:shape><![endif]--><span style='mso-field-code:"HYPERLINK \0022javascript\:PopUpMenu2_Set\(Menu15201059\)\;\0022 \\t \0022_self\0022"'><span
+  class=MsoHyperlink><span style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></span></span>
+  <span style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
+  </td>
+ </tr>
+ <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>
+  <td colspan=2 style='padding:0cm 0cm 0cm 0cm'>
+  <p class=MyNormalJustified>3DCoffee: combining protein sequences and
+  structures within multiple sequence alignments.<br>
+  J Mol Biol. 2004 Jul 2;340(2):385-95. <br>
+  PMID: 15201059 [PubMed - indexed for MEDLINE]<span style='mso-bidi-font-size:
+  12.0pt;color:black'><o:p></o:p></span></p>
+  </td>
+ </tr>
+</table>
+
+<p class=MyNormalJustified><o:p>&nbsp;</o:p></p>
+
+<table class=MsoNormalTable border=0 cellspacing=4 cellpadding=0 width="81%"
+ style='width:81.98%;mso-cellspacing:3.7pt;mso-padding-alt:0cm 0cm 0cm 0cm'>
+ <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>
+  <td width="53%" style='width:53.5%;padding:0cm 0cm 0cm 0cm'>
+  <p class=MyNormalJustified><a
+  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=12824354">Poirot
+  O, O'Toole E, Notredame C.</a><span style='mso-bidi-font-size:12.0pt;
+  color:black'><o:p></o:p></span></p>
+  </td>
+  <td nowrap valign=top style='padding:0cm 0cm 0cm 0cm'>
+  <p class=MyNormalJustified><a
+  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Display&amp;dopt=pubmed_pubmed&amp;from_uid=12824354"><span
+  style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <!--[if gte vml 1]><v:shape
+   id="_x0000_i1031" type="#_x0000_t75" style='width:15pt;height:11pt;
+   visibility:hidden' print="f">
+   <v:imagedata src="t_coffee_technical_files/image007.png" o:title="&#37008;&#28494;&#28018;&#27745;&#36864;&#24902;x0&#37008;1"/>
+   <o:lock v:ext="edit" grouping="t"/>
+  </v:shape><![endif]--><span style='mso-field-code:"HYPERLINK \0022javascript\:PopUpMenu2_Set\(Menu12824354\)\;\0022 \\t \0022_self\0022"'><span
+  class=MsoHyperlink><span style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></span></span>
+  <span style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
+  </td>
+ </tr>
+ <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>
+  <td colspan=2 style='padding:0cm 0cm 0cm 0cm'>
+  <p class=MyNormalJustified>Tcoffee@igs: A web server for computing,
+  evaluating and combining multiple sequence alignments.<br>
+  Nucleic Acids Res. 2003 Jul 1;31(13):3503-6. <br>
+  PMID: 12824354 [PubMed - indexed for MEDLINE]<span style='mso-bidi-font-size:
+  12.0pt;color:black'><o:p></o:p></span></p>
+  </td>
+ </tr>
+</table>
+
+<p class=MyNormalJustified><o:p>&nbsp;</o:p></p>
+
+<table class=MsoNormalTable border=0 cellspacing=4 cellpadding=0 width="81%"
+ style='width:81.98%;mso-cellspacing:3.7pt;mso-padding-alt:0cm 0cm 0cm 0cm'>
+ <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>
+  <td width="53%" style='width:53.5%;padding:0cm 0cm 0cm 0cm'>
+  <p class=MyNormalJustified><a
+  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=11301309">Notredame
+  C.</a><span style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
+  </td>
+  <td nowrap valign=top style='padding:0cm 0cm 0cm 0cm'>
+  <p class=MyNormalJustified><a
+  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Display&amp;dopt=pubmed_pubmed&amp;from_uid=11301309"><span
+  style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <!--[if gte vml 1]><v:shape
+   id="_x0000_i1032" type="#_x0000_t75" style='width:15pt;height:11pt;
+   visibility:hidden' print="f">
+   <v:imagedata src="t_coffee_technical_files/image008.png" o:title="&#37008;&#28494;&#28018;&#27745;&#36864;&#24902;x0&#37008;1"/>
+   <o:lock v:ext="edit" grouping="t"/>
+  </v:shape><![endif]--><span style='mso-field-code:"HYPERLINK \0022javascript\:PopUpMenu2_Set\(Menu11301309\)\;\0022 \\t \0022_self\0022"'><span
+  class=MsoHyperlink><span style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></span></span>
+  <span style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
+  </td>
+ </tr>
+ <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>
+  <td colspan=2 style='padding:0cm 0cm 0cm 0cm'>
+  <p class=MyNormalJustified>Mocca: semi-automatic method for domain hunting.<br>
+  Bioinformatics. 2001 Apr;17(4):373-4. <br>
+  PMID: 11301309 [PubMed - indexed for MEDLINE]<span style='mso-bidi-font-size:
+  12.0pt;color:black'><o:p></o:p></span></p>
+  </td>
+ </tr>
+</table>
+
+<p class=MyNormalJustified><o:p>&nbsp;</o:p></p>
+
+<table class=MsoNormalTable border=0 cellspacing=4 cellpadding=0 width="81%"
+ style='width:81.98%;mso-cellspacing:3.7pt;mso-padding-alt:0cm 0cm 0cm 0cm'>
+ <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>
+  <td width="53%" style='width:53.5%;padding:0cm 0cm 0cm 0cm'>
+  <p class=MyNormalJustified><a
+  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=10964570">Notredame
+  C, Higgins DG, Heringa J.</a><span style='mso-bidi-font-size:12.0pt;
+  color:black'><o:p></o:p></span></p>
+  </td>
+  <td nowrap valign=top style='padding:0cm 0cm 0cm 0cm'>
+  <p class=MyNormalJustified><a
+  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Display&amp;dopt=pubmed_pubmed&amp;from_uid=10964570"><span
+  style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <!--[if gte vml 1]><v:shape
+   id="_x0000_i1033" type="#_x0000_t75" style='width:15pt;height:11pt;
+   visibility:hidden' print="f">
+   <v:imagedata src="t_coffee_technical_files/image009.png" o:title="&#37008;&#28494;&#28018;&#27745;&#36864;&#24902;x0&#37008;1"/>
+   <o:lock v:ext="edit" grouping="t"/>
+  </v:shape><![endif]--><span style='mso-field-code:"HYPERLINK \0022javascript\:PopUpMenu2_Set\(Menu10964570\)\;\0022 \\t \0022_self\0022"'><span
+  class=MsoHyperlink><span style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></span></span>
+  <span style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
+  </td>
+ </tr>
+ <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>
+  <td colspan=2 style='padding:0cm 0cm 0cm 0cm'>
+  <p class=MyNormalJustified>T-Coffee: A novel method for fast and accurate
+  multiple sequence alignment.<br>
+  J Mol Biol. 2000 Sep 8;302(1):205-17. <br>
+  PMID: 10964570 [PubMed - indexed for MEDLINE]<span style='mso-bidi-font-size:
+  12.0pt;color:black'><o:p></o:p></span></p>
+  </td>
+ </tr>
+</table>
+
+<p class=MyNormalJustified><o:p>&nbsp;</o:p></p>
+
+<table class=MsoNormalTable border=0 cellspacing=4 cellpadding=0 width="81%"
+ style='width:81.98%;mso-cellspacing:3.7pt;mso-padding-alt:0cm 0cm 0cm 0cm'>
+ <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>
+  <td width="53%" style='width:53.5%;padding:0cm 0cm 0cm 0cm'>
+  <p class=MyNormalJustified><a
+  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=9682054">Notredame
+  C, Holm L, Higgins DG.</a><span style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
+  </td>
+  <td nowrap valign=top style='padding:0cm 0cm 0cm 0cm'>
+  <p class=MyNormalJustified><a
+  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Display&amp;dopt=pubmed_pubmed&amp;from_uid=9682054"><span
+  style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <!--[if gte vml 1]><v:shape
+   id="_x0000_i1034" type="#_x0000_t75" style='width:15pt;height:11pt;
+   visibility:hidden' print="f">
+   <v:imagedata src="t_coffee_technical_files/image010.png" o:title="&#37008;&#28494;&#28018;&#27745;&#36864;&#24902;x0&#37008;1"/>
+   <o:lock v:ext="edit" grouping="t"/>
+  </v:shape><![endif]--><span style='mso-field-code:"HYPERLINK \0022javascript\:PopUpMenu2_Set\(Menu9682054\)\;\0022 \\t \0022_self\0022"'><span
+  class=MsoHyperlink><span style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></span></span>
+  <span style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
+  </td>
+ </tr>
+ <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>
+  <td colspan=2 style='padding:0cm 0cm 0cm 0cm'>
+  <p class=MyNormalJustified>COFFEE: an objective function for multiple
+  sequence alignments.<br>
+  Bioinformatics. 1998 Jun;14(5):407-22. <br>
+  PMID: 9682054 [PubMed - indexed for MEDLINE]<span style='mso-bidi-font-size:
+  12.0pt;color:black'><o:p></o:p></span></p>
+  </td>
+ </tr>
+</table>
+
+<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
+
+<h2><a name="_Toc101065189"></a><a name="_Toc102494278"></a><a
+name="_Toc102494656"></a><a name="_Toc151732193"><span style='mso-bookmark:
+_Toc102494656'><span style='mso-bookmark:_Toc102494278'><span style='mso-bookmark:
+_Toc101065189'>Mocca</span></span></span></a></h2>
+
+<table class=MsoNormalTable border=0 cellspacing=4 cellpadding=0 width="81%"
+ style='width:81.98%;mso-cellspacing:3.7pt;mso-padding-alt:0cm 0cm 0cm 0cm'>
+ <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>
+  <td width="53%" style='width:53.5%;padding:0cm 0cm 0cm 0cm'>
+  <p class=MyNormal><span lang=AF><a
+  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=11301309"><span
+  lang=EN-US style='mso-ansi-language:EN-US'>Notredame C.</span></a></span><span
+  lang=AF style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
+  </td>
+  <td nowrap valign=top style='padding:0cm 0cm 0cm 0cm'>
+  <p class=MyNormal><span lang=AF><a
+  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Display&amp;dopt=pubmed_pubmed&amp;from_uid=11301309&amp;tool=ExternalSearch"><span
+  lang=EN-US style='mso-bidi-font-size:9.0pt;color:#336699;mso-ansi-language:
+  EN-US'>Related Articles,</span></a> <!--[if gte vml 1]><v:shape id="_x0000_i1035"
+   type="#_x0000_t75" style='width:15pt;height:11pt;visibility:hidden' print="f">
+   <v:imagedata src="t_coffee_technical_files/image011.png" o:title="&#37008;&#28494;&#28018;&#27745;&#36864;&#24902;x0&#37008;1"/>
+   <o:lock v:ext="edit" grouping="t"/>
+  </v:shape><![endif]--><span style='mso-field-code:"HYPERLINK \0022javascript\:PopUpMenu2_Set\(Menu11301309\)\;\0022 \\t \0022_self\0022"'><span
+  class=MsoHyperlink><span lang=EN-US style='mso-bidi-font-size:9.0pt;
+  color:#336699;mso-ansi-language:EN-US'>Links</span></span></span> </span><span
+  lang=AF style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
+  </td>
+ </tr>
+ <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>
+  <td colspan=2 style='padding:0cm 0cm 0cm 0cm'>
+  <p class=MyNormal><span lang=AF>Mocca: semi-automatic method for domain
+  hunting.<br>
+  Bioinformatics. 2001 Apr;17(4):373-4. <br>
+  PMID: 11301309 [PubMed - indexed for MEDLINE]</span><span lang=AF
+  style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
+  </td>
+ </tr>
+</table>
+
+<h2><a name="_Toc102494279"></a><a name="_Toc102494657"></a><a
+name="_Toc151732194"><span style='mso-bookmark:_Toc102494657'><span
+style='mso-bookmark:_Toc102494279'>CORE</span></span></a></h2>
+
+<p class=MyNormal><span lang=AF><a
+href="http://www.tcoffee.org/Publications/Pdf/core.pp.pdf"><span lang=EN-US
+style='mso-ansi-language:EN-US'>http://www.tcoffee.org/Publications/Pdf/core.pp.pdf<o:p></o:p></span></a></span></p>
+
+<h2><a name="_Toc101065367"></a><a name="_Toc102494280"></a><a
+name="_Toc102494658"><span style='mso-bookmark:_Toc102494280'><span
+style='mso-bookmark:_Toc101065367'></span></span></a><a name="_Toc151732195"><span
+style='mso-bookmark:_Toc101065367'><span style='mso-bookmark:_Toc102494280'><span
+style='mso-bookmark:_Toc102494658'>Other Contributions</span></span></span></a></h2>
+
+<p class=MyNormal><span lang=AF>We do not mean to steal code, but we will
+always try to re-use pre-existing code whenever that code exists, free of
+copyright, just like we expect people to do with our code. However, whenever
+this happens, we make a point at properly citing the source of the original
+contribution. If ever you recognize a piece of your code improperly cited,
+please drop us a note and we will be happy to correct that.</span></p>
+
+<p class=MyNormal><span lang=AF>In the mean time, here are some important
+pieces of code from other packages that have been incorporated within the
+T-Coffee package. These include: </span></p>
+
+<p class=MyNormal><span lang=AF><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>-The
+Sim algorithm of Huang and Miller that given two sequences computes the N best
+scoring local alignments.</span></p>
+
+<p class=MyNormal><span lang=AF><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>-The
+tree reading/computing routines are taken from the ClustalW Package, courtesy
+of Julie Thompson, Des Higgins and Toby Gibson (Thompson, Higgins, Gibson,
+1994, 4673-4680,vol. 22, Nucleic Acid Research).</span></p>
+
+<p class=MyNormal><span lang=AF><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>-The
+implementation of the algorithm for aligning two sequences in linear space was
+adapted from Myers and Miller, in CABIOS, 1988, 11-17, vol. 1)</span></p>
+
+<p class=MyNormal><span lang=AF><span style="mso-spacerun: yes">&nbsp;</span><span
+style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>-Various
+techniques and algorithms have been implemented. Whenever relevant, the source
+of the code/algorithm/idea is indicated in the corresponding function.</span></p>
+
+<p class=MyNormal><span lang=AF><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>-64
+Bits compliance was implemented by Benjamin Sohn, Performance Computing Center
+Stuttgart (HLRS), Germany</span></p>
+
+<p class=MyNormal><span lang=AF><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>-David
+Mathog (Caltech) provided many fixes and useful feedback for improving the code
+and making the whole soft behaving more rationally</span></p>
+
+<h2><a name="_Toc151732196">Bug Reports and Feedback</a></h2>
+
+<p class=MyNormal><span lang=AF><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>-Prof
+David Jones (UCL) reported and corrected the PDB1K bug (now t_coffee/sap can
+align PDB sequences longer than 1000 AA).</span></p>
+
+<p class=MyNormal><span lang=AF><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>-Johan
+Leckner reported several bugs related to the treatment of PDB structures,
+insuring a consistent behavior between version 1.37 and current ones.</span></p>
+
+<p class=MyNormal><span lang=AF><span style="mso-spacerun: yes">&nbsp;</span></span></p>
+
+<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
+
+<div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
+padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0cm;margin-right:
+4.25pt'>
+
+<p class=ChapterTitle><a name="_Toc101065204"></a><a name="_Toc102494673"><span
+style='mso-bookmark:_Toc101065204'>I</span></a>nstallation of The T-Coffee
+Packages</p>
+
+</div>
+
+<h2><a name="_Toc101065205"></a><a name="_Toc102494294"></a><a
+name="_Toc102494674"></a><a name="_Toc151732197"><span style='mso-bookmark:
+_Toc102494674'><span style='mso-bookmark:_Toc102494294'><span style='mso-bookmark:
+_Toc101065205'>Third Party Packages and On Demand Installations</span></span></span></a><span
+style='mso-bookmark:_Toc102494674'><span style='mso-bookmark:_Toc102494294'><span
+style='mso-bookmark:_Toc101065205'></span></span></span></h2>
+
+<p class=MyNormaBoldl><span style='mso-bookmark:_Toc102494674'><span
+style='mso-bookmark:_Toc102494294'><span style='mso-bookmark:_Toc101065205'><span
+lang=AF>T-Coffee is a complex package that interacts with many other third part
+software. If you only want a standalone version of T-Coffee, you may install
+that package on its own. If you want to use a most sophisticated flavor
+(3dcoffee, expresso, rcofeee, etc...), the installer will try to install all
+the third party packages required.</span></span></span></span></p>
+
+<p class=MyNormaBoldl><span style='mso-bookmark:_Toc102494674'><span
+style='mso-bookmark:_Toc102494294'><span style='mso-bookmark:_Toc101065205'><span
+lang=AF>Note that since version 7.56, T-Coffee will use 'on demand'
+installation and install the third party packages it needs *when* it needs
+them. This only works for packages not requiring specific licenses and that can
+be installed by the regular installer. Please let us know if you would like
+another third party package to be included. </span></span></span></span></p>
+
+<p class=MyNormaBoldl><span style='mso-bookmark:_Toc102494674'><span
+style='mso-bookmark:_Toc102494294'><span style='mso-bookmark:_Toc101065205'><span
+lang=AF>Whenver on-demand installation or automated installation fails because
+of unforessen system specificities, users should install the third party package
+manually. This documentation gives some tips we have found useful, but users
+are encouraged to check the original documentation.</span></span></span></span></p>
+
+<h2><span style='mso-bookmark:_Toc102494674'><span style='mso-bookmark:_Toc102494294'><span
+style='mso-bookmark:_Toc101065205'><a name="_Toc151732198">Standard
+Installation</a></span></span></span><span style='mso-bookmark:_Toc151732198'>
+of T-Coffee</span></h2>
+
+<h3><a name="_Toc151732199"><span style='mso-hansi-font-family:"Arial Black"'>Automated
+Installation</span></a><span style='mso-hansi-font-family:"Arial Black"'><o:p></o:p></span></h3>
+
+<p class=MyNormaBoldl><span lang=AF>We now recommend that you use the automated
+installer provided for UNIX or Linux platforms. </span></p>
+
+<h4><a name="_Toc151732200"><span lang=AF>Mac-OsX</span></a></h4>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-tab-count:1'>&nbsp;&nbsp; </span>Click on tge .dmg file</p>
+
+</div>
+
+<h4><a name="_Toc151732201"><span lang=AF>Unix</span></a></h4>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-tab-count:1'>&nbsp;&nbsp; </span>rpm &#8211;i &lt;rmp&gt;</p>
+
+</div>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<h3><a name="_Toc151732202"><span style='mso-hansi-font-family:"Arial Black"'>Unix</span></a></h3>
+
+<p class=MyNormaBoldl><span lang=AF>You need to have: gcc, g77, CPAN and an
+internet connection and your root password. You will also need the two
+following perl modules: LWP and XML::Simple. These are needed if you want to
+use the web services provided by the EBI via REST (http://www.ebi.ac.uk/Tools/webservices/tutorials/02_rest)</span></p>
+
+<p class=MsoNormal style='margin-left:72.0pt'><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
+margin-left:72.0pt;text-indent:-18.0pt;mso-list:l24 level2 lfo39;tab-stops:
+list 72.0pt'><![if !supportLists]><span style='font-family:Arial;mso-fareast-font-family:
+Arial;mso-bidi-font-family:Arial'><span style='mso-list:Ignore'>1.<span
+style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><code><span
+style='font-size:10.0pt'>gunzip t_coffee.tar.gz</span></code><span
+style='font-family:Arial;mso-bidi-font-family:Arial'><o:p></o:p></span></p>
+
+<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
+margin-left:72.0pt;text-indent:-18.0pt;mso-list:l24 level2 lfo39;tab-stops:
+list 72.0pt'><![if !supportLists]><span style='font-family:Arial;mso-fareast-font-family:
+Arial;mso-bidi-font-family:Arial'><span style='mso-list:Ignore'>2.<span
+style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><code><span
+style='font-size:10.0pt'>tar -xvf t_coffee.tar</span></code><span
+style='font-family:Arial;mso-bidi-font-family:Arial'><o:p></o:p></span></p>
+
+<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
+margin-left:72.0pt;text-indent:-18.0pt;mso-list:l24 level2 lfo39;tab-stops:
+list 72.0pt'><![if !supportLists]><span style='font-family:Arial;mso-fareast-font-family:
+Arial;mso-bidi-font-family:Arial'><span style='mso-list:Ignore'>3.<span
+style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><code><span
+style='font-size:10.0pt'>cd t_coffee</span></code><span style='font-family:
+Arial;mso-bidi-font-family:Arial'><o:p></o:p></span></p>
+
+<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
+margin-left:72.0pt;text-indent:-18.0pt;mso-list:l24 level2 lfo39;tab-stops:
+list 72.0pt'><![if !supportLists]><span style='font-family:Arial;mso-fareast-font-family:
+Arial;mso-bidi-font-family:Arial'><span style='mso-list:Ignore'>4.<span
+style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><code><span
+style='font-size:10.0pt'>./install t_coffee</span></code><span
+style='font-family:Arial;mso-bidi-font-family:Arial'><o:p></o:p></span></p>
+
+<p class=MyNormal><span lang=AF>This installation will only install the stand
+alone T-Coffee. If you want to install a specific mode of T-Coffee, you may try
+the following commands that will try to gather all the necessary third party
+packages. Note that a package already found on your system will not be
+re-installed.</span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-tab-count:1'>&nbsp;&nbsp; </span>./install t_coffee</p>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-tab-count:1'>&nbsp;&nbsp; </span>./install mcoffee</p>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-tab-count:1'>&nbsp;&nbsp; </span>./install 3dcoffee</p>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-tab-count:1'>&nbsp;&nbsp; </span>./install rcoffee</p>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-tab-count:1'>&nbsp;&nbsp; </span>./install psicoffee</p>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><o:p>&nbsp;</o:p></p>
+
+</div>
+
+<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
+
+<p class=MyNormal><span lang=AF>Or even</span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-tab-count:1'>&nbsp;&nbsp; </span>./install all</p>
+
+</div>
+
+<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
+
+<p class=MyNormal><span lang=AF>-All the corresponding executables will be
+downloaded automatically and installed in</span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-tab-count:1'>&nbsp;&nbsp; </span>$HOME/.t_coffee/plugins</p>
+
+</div>
+
+<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
+
+<p class=MyNormal><span lang=AF>-if you executables are in a different location,
+give it to T-Coffee using the -plugins flag.</span></p>
+
+<p class=MyNormal><span lang=AF>-If the installation of any of the companion
+package fails, you should install it yourself using the provided link (see
+below) and following the authors instructions.<span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></p>
+
+<p class=MyNormal><span lang=AF>-If you have not managed to install SOAP::Lite,
+you can re-install it later (from anywhere) following steps 1-2.</span></p>
+
+<p class=MsoNormal style='margin-left:72.0pt'><o:p>&nbsp;</o:p></p>
+
+<p class=MyNormaBoldl><span lang=AF>-This procedure attempts 3 things:
+installing and Compiling T-Coffee (C program), Installing and compiling <a
+href="http://zhang.bioinformatics.ku.edu/TM-align/"><span lang=EN-US
+style='mso-ansi-language:EN-US'>TMalign</span></a> (Fortran), Installing and
+compiling XML::Simple</span></p>
+
+<p class=MyNormaBoldl><span lang=AF><o:p>&nbsp;</o:p></span></p>
+
+<p class=MyNormaBoldl><span lang=AF>-If you have never installed a perl module
+before, CPAN will ask you many questions: say Yes to all </span></p>
+
+<p class=MyNormaBoldl><span lang=AF>-If everything went well, the procedure has
+created in the <b>bin</b> directory two executables: t_coffee and TMalign (<b>Make
+sure these executables are on your $PATH!</b>)</span></p>
+
+<p class=MyNormaBoldl><span lang=AF><o:p>&nbsp;</o:p></span></p>
+
+<h3><a name="_Toc151732203">Microsoft Windows/Cygwin</a></h3>
+
+<p class=MyNormaBoldl><span lang=AF>Install <a href="http://www.cygwin.com"><span
+lang=EN-US style='color:windowtext;mso-ansi-language:EN-US;text-decoration:
+none;text-underline:none'>Cygwin</span></a></span></p>
+
+<p class=MyNormaBoldl><span lang=AF>Download The Installer (NOT Cygwin/X)</span></p>
+
+<p class=MyNormaBoldl><span lang=AF>Click on view to list ALL the packages</span></p>
+
+<p class=MyNormaBoldl><span lang=AF>Select: gcc-core, make, wget</span></p>
+
+<p class=MyNormaBoldl><span lang=AF>Optional: ssh, xemacs, nano</span></p>
+
+<p class=MyNormaBoldl><span lang=AF>Run mkpasswd in Cywin (as requested when
+you start cygwin)</span></p>
+
+<p class=MyNormaBoldl><span lang=AF>Install T-Coffee within Cygwin using the
+Unix procedure</span></p>
+
+<h3><a name="_Toc151732204">MAC osX, Linux</a></h3>
+
+<p class=MyNormaBoldl><span lang=AF>Make sure you have the Developer's kit installed
+(compilers and makefile)</span></p>
+
+<p class=MyNormaBoldl><span lang=AF>Follow the Unix Procedure</span></p>
+
+<p class=Mylist><span lang=AF><o:p>&nbsp;</o:p></span></p>
+
+<h3><a name="_Toc151732205">CLUSTER Installation</a></h3>
+
+<p class=MyNormal><span lang=AF>In order to run, T-Coffee must have a value for
+the http_proxy and for the E-mail. In order to do so you can either:</span></p>
+
+<p class=MyNormaBoldl><span lang=AF>export the following values:</span></p>
+
+<p class=MyNormaBoldl><span lang=AF>export
+http_proxy_4_TCOFFEE=&quot;proxy&quot; or &quot;&quot; if no proxy</span></p>
+
+<p class=MyNormaBoldl><span lang=AF>export EMAIL_4_TCOFFEE=&quot;your
+email&quot;</span></p>
+
+<p class=MyNormaBoldl><span lang=AF>OR </span></p>
+
+<p class=MyNormaBoldl><span lang=AF>modify the file ~/.t_coffee/t_coffee_env</span></p>
+
+<p class=MyNormaBoldl><span lang=AF>OR</span></p>
+
+<p class=MyNormaBoldl><span lang=AF>add to your command line: t_coffee \85.
+-proxy=&lt;proxy&gt; -email=&lt;email</span></p>
+
+<p class=MyNormaBoldl><span lang=AF>if you have no proxy: t_coffee \85 -proxy
+-email=&lt;email&gt;</span></p>
+
+<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<h3><a name="_Toc151732206">If you have PDB installed:</a></h3>
+
+<p class=MyNormal><span lang=AF>Assuming you have a standard PDB installation
+in your file system</span></p>
+
+<p class=example2CxSpFirst>setenv (or export)<span style="mso-spacerun:
+yes">&nbsp; </span>PDB_DIR &lt;abs path&gt;/data/structures/all/pdb/</p>
+
+<p class=example2CxSpMiddle>OR</p>
+
+<p class=example2CxSpLast>setenv (or export)<span style="mso-spacerun:
+yes">&nbsp; </span>PDB_DIR &lt;abs path&gt;/structures/divided/pdb/</p>
+
+<p class=MyNormal><span lang=AF>If you do not have PDB installed, don't worry,
+t_coffee will go and fetch any structure it needs directly from the PDB
+repository. It will simply be a bit slower than if you had PDB locally. </span></p>
+
+<h2><a name="_Toc101065206"></a><a name="_Toc102494295"></a><a
+name="_Toc102494675"></a><a name="_Toc151732207"><span style='mso-bookmark:
+_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:
+_Toc101065206'>Installing BLAST for T-Coffee</span></span></span></a><span
+style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'></span></span></span></h2>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>BLAST is a program that search sequence databases for homologues of a
+query sequence. It works for proteins and Nucleic Acids. In theory BLAST is
+just a package like any, but in practice things are a bit more complex. To run
+well, BLST requires up to date databases (that can be fairly large, like NR or
+UNIPROT) and a powerful computer.</span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>Fortunately, an increasing number of institutes or companies are now
+providing BLAST clients that run over the net. It means that all you need is a
+small program that send your query to the big server and gets the results back.
+This prevents you from the hassle of installing and maintaining BLAST, but of
+course it is less private and you rely on the network and the current load of
+these busy servers.</span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>Thanks to its interaction with BLAST, T-Coffee can gather structures
+and protein profiles and deliver an alignment significantly more accurate than
+the default you would get with T-Coffee or any similar method.</span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>Let us go through the various modes available for T-Coffee</span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
+
+<h3><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'><a name="_Toc151732208">Why Do I need BLAST
+with T-Coffee?</a></span></span></span></h3>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>The most accurate modes of T-Coffe scan the databases for templates
+that they use to align the sequences. There are currently two types of templates
+for proteins:</span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>structures (PDB) that can be found by a blastp against the PDB database
+and profiles that can be constructed with eiether a blastp or a psiblast
+against nr or uniprot.</span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>These templates are automatically built if you use:</span></span></span></span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'>&nbsp;&nbsp; </span>t_coffee
+&lt;yourseq&gt; -mode expresso</span></span></span></p>
+
+</div>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>that
+fetches aand uses pdb templates, or</span></span></span></span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'>&nbsp;&nbsp; </span><span
+style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>t_coffee
+&lt;your seq&gt; -mode psicoffee</span></span></span></p>
+
+</div>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>that
+fetches and uses profile templates, or</span></span></span></span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'>&nbsp;&nbsp; </span><span
+style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>t_coffee
+&lt;your seq&gt; -mode accurate</span></span></span></p>
+
+</div>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>that
+does everything and tries to use the best template. Now that you see why it is
+useful let's see how to get BLAST up and running, from the easy solution to
+tailor made ones.</span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
+
+<h3><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'><a name="_Toc151732209">Using the EBI BLAST
+Client</a></span></span></span></h3>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>This is by far the easiest (and the default mode). The perl clients are
+already incorporated in T-Coffee and all you need is are the proper perl
+library. In theory, T-Coffee should have already installed these libraries during
+the standard installation. Yet, this requires having toot access. It really is
+worth the effort, since the EBI is providing one of the best webservice available
+around, and most notably, the only public psiblast via a web service.</span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>Whenever you use a T-Coffee mode requiring Blast access, it will ask
+you for an authentification E-mail. <b>Be Careful! </b>If you provide a fake
+E-mail, the EBI may suspend the service for all machines associated with your
+IP address (that could mean your entire lab, or entire institute, or even the
+entire country or, but I doubt it, the whole universe).</span></span></span></span></p>
+
+<h3><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'><a name="_Toc151732210">Using the NCBI BLAST
+Client</a></span></span></span></h3>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>The NCBI is the next best alternative. In my hand it was always a bit
+slower and most of all, it does not incorporate PSI-BLAST (as a web sevice). A
+big miss. The NCBI web blast client is a small executable that you should
+install on your system following the instructions given on this link</span></span></span></span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'>ftp://ftp.ncbi.nih.gov/blast/executables/LATEST</span></span></span></p>
+
+</div>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>Simply go for <b>netbl,</b> download the executable that corresponds to
+your architecture (cygwin users should go for the win executable). Despite all
+the files that come along the executable blastcl3 is a stand alone executable
+that you can safely move to your $BIN.</span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>All you will then need to do is to make sure that T-Coffee uses the
+right client, when you run it.</span></span></span></span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'>-blast_server=NCBI</span></span></span></p>
+
+</div>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>No need for any E-mail here, but you don't get psiblast, and whenever
+T-Coffee wants to use it, blastp will be used instead.</span></span></span></span></p>
+
+<h3><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'><a name="_Toc151732211">Using another Client</a></span></span></span></h3>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>You may have your own client (lucky you). If that is so, all you need
+is to make sure that this client is complient with the blast command line. If
+your client is named foo.pl, all you need to to is run T-Coffee with</span></span></span></span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'>-blast_server=CLIENT_foo.pl</span></span></span></p>
+
+</div>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>Foo will be called as if it were blastpgp, and it is your
+responsability to make sure it can handle the following command line:</span></span></span></span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'>foo.pl -p &lt;method&gt; -d &lt;db&gt; -i &lt;infile&gt;
+-o &lt;outfile&gt; -m 7</span></span></span></p>
+
+</div>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>method can either be blastp or psiblast.</span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>infile is a FASTA file</span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>-m7 triggers the XML output. T-Coffee is able to parse both the EBI XML
+output and the NCBI XML output.</span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>If foo.pl behaves differently, the easiest will probably be to write a
+wrapper around it so that wrapped_foo.pl behaves like blastpgp</span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
+
+<h3><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'><a name="_Toc151732212">Using a BLAST local
+version on UNIX</a></span></span></span></h3>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>If you have blastpgp installed, you can run it instead of the remote
+clients by using:</span></span></span></span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'>-blast_server=LOCAL</span></span></span></p>
+
+</div>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF><span style="mso-spacerun: yes">&nbsp;</span>The documentation for
+blastpgp can be found on:</span></span></span></span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'>www.ncbi.nlm.nih.gov/staff/tao/URLAPI/blastpgp.html</span></span></span></p>
+
+</div>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>and the package is part of the standard BLAST distribution</span></span></span></span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'>ftp://ftp.ncbi.nih.gov/blast/executables/LATEST</span></span></span></p>
+
+</div>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>Depending on your system, your own skills, your requirements and on
+more parameters than I have fingers to count, installing a BLAST server suited
+for your needs can range from a 10 minutes job to an achivement spread over
+several generations. So at this point, you should roam the NCBI website for
+suitable information.</span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>If you want to have your own BLAST server to run your own databases,
+you should know that it is possible to control both the database and the
+program used by BLAST:</span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
+
+<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
+mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
+background:#E6E6E6'>
+
+<p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>-protein_db:
+will specify the database used by all the psi-blast modes</span></span></span></p>
+
+<p class=examplefileCxSpLast><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>-pdb_db:
+will specify the database used by the pdb modes</span></span></span></p>
+
+</div>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><b
+style='mso-bidi-font-weight:normal'><span lang=AF><o:p>&nbsp;</o:p></span></b></span></span></span></p>
+
+<div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
+padding:0cm 0cm 0cm 0cm;background:#F7CBB7'>
+
+<p class=Warning><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>Note
+that T-Coffee is compliant with BLAST+, the latest NCBI Blast.</span></span></span></p>
+
+</div>
+
+<h3><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'><a name="_Toc151732213">Using a BLAST local
+version on Windows/cygwin</a></span></span></span></h3>
+
+<h4><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'><a name="_Toc151732214"><span lang=AF>BLAST+</span></a></span></span></span></h4>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>Blast+ is tghe latest NCBI Blast. IT is easier to install. A default
+installation should be compliant with a default T-Coffee installation. </span></span></span></span></p>
+
+<p class=MsoNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><o:p>&nbsp;</o:p></span></span></span></p>
+
+<h4><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'><a name="_Toc151732215"><span lang=AF>ORIGINAL
+NCBI BLAST</span></a></span></span></span></h4>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>For those of you using cygwin, be careful. While cygwin behaves like a
+UNIX system, the BLAST executable required for cygwin (win32) is expecting
+WINDOWS path and not UNIX path. This has three important consequences:</span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>1- the ncbi file declaring the Data directory must be:</span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>C:WINDOWS//ncbi.init<span
+style="mso-spacerun: yes">&nbsp; </span>[at the root of your WINDOWS]</span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>2- the address mentionned with this file must be WINDOWS formated, for
+instance, on my system:</span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>Data=C:\cygwin\home\notredame\blast\data</span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>3- When you pass database addresses to BLAST, these must be in Windows format:</span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>-protein_db=&quot;c:/somewhere/somewhereelse/database&quot;</span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>(using the slash (/) or the andtislash (\) does not matter on new
+systems but I would reommand against incorporating white spaces.</span></span></span></span></p>
+
+<h2><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'><a name="_Toc151732216">Installing Other
+Companion Packages</a></span></span></span></h2>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>T-Coffee is meant to interact with as many packages as possible, either
+for aligning or using predictions. If you type </span></span></span></span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'>&nbsp;&nbsp; </span>t_coffee</span></span></span></p>
+
+</div>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>You will receive a list of supported packages that looks like the next
+table. In theory, most of these packages can be installed by T-Coffee <b
+style='mso-bidi-font-weight:normal'>and we welcome any reasonnable request.<o:p></o:p></b></span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
+
+<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
+mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
+background:#E6E6E6'>
+
+<p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>******
+Pairwise Sequence Alignment Methods:</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>--------------------------------------------</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>fast_pair<span
+style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>built_in</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>exon3_pair<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>built_in</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>exon2_pair<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>built_in</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>exon_pair<span
+style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>built_in</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>slow_pair<span
+style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>built_in</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>proba_pair<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>built_in</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>lalign_id_pair<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp; </span>built_in</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>seq_pair<span
+style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>built_in</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>externprofile_pair
+built_in</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>hh_pair<span
+style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>built_in</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>profile_pair<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>built_in</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>cdna_fast_pair<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp; </span>built_in</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>cdna_cfast_pair<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp; </span>built_in</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>clustalw_pair<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>ftp://www.ebi.ac.uk/pub/clustalw</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>mafft_pair<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>mafftjtt_pair<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>mafftgins_pair<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;
+</span>http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>dialigntx_pair<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;
+</span>http://dialign-tx.gobics.de/</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>dialignt_pair<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>http://dialign-t.gobics.de/</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>poa_pair<span
+style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>http://www.bioinformatics.ucla.edu/poa/</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>probcons_pair<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>http://probcons.stanford.edu/</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>muscle_pair<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>http://www.drive5.com/muscle/</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>t_coffee_pair<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>http://www.tcoffee.org</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>pcma_pair<span
+style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>ftp://iole.swmed.edu/pub/PCMA/</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>kalign_pair<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>http://msa.cgb.ki.se</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>amap_pair<span
+style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>http://bio.math.berkeley.edu/amap/</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>proda_pair<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>http://bio.math.berkeley.edu/proda/</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>prank_pair<span
+style="mso-spacerun: yes">&nbsp;&nbsp; </span><span style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span>http://www.ebi.ac.uk/goldman-srv/prank/</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>consan_pair<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>http://selab.janelia.org/software/consan/</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><o:p>&nbsp;</o:p></span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>******
+Pairwise Structural Alignment Methods:</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>--------------------------------------------</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>align_pdbpair<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>built_in</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>lalign_pdbpair<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp; </span>built_in</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>extern_pdbpair<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp; </span>built_in</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>thread_pair<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>built_in</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>fugue_pair<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>http://www-cryst.bioc.cam.ac.uk/fugue/download.html</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>pdb_pair<span
+style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>built_in</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>sap_pair<span
+style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>http://www-cryst.bioc.cam.ac.uk/fugue/download.html</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>mustang_pair<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>http://www.cs.mu.oz.au/~arun/mustang/</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>tmalign_pair<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>http://zhang.bioinformatics.ku.edu/TM-align/</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><o:p>&nbsp;</o:p></span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>******
+Multiple Sequence Alignment Methods:</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>--------------------------------------------</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>clustalw_msa<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>ftp://www.ebi.ac.uk/pub/clustalw</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>mafft_msa<span
+style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>mafftjtt_msa<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>mafftgins_msa<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>dialigntx_msa<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>http://dialign-tx.gobics.de/</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>dialignt_msa<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>http://dialign-t.gobics.de/</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>poa_msa<span
+style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>http://www.bioinformatics.ucla.edu/poa/</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>probcons_msa<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>http://probcons.stanford.edu/</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>muscle_msa<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>http://www.drive5.com/muscle/</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>t_coffee_msa<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>http://www.tcoffee.org</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>pcma_msa<span
+style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>ftp://iole.swmed.edu/pub/PCMA/</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>kalign_msa<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>http://msa.cgb.ki.se</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>amap_msa<span
+style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>http://bio.math.berkeley.edu/amap/</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>proda_msa<span
+style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>http://bio.math.berkeley.edu/proda/</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>prank_msa<span
+style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>http://www.ebi.ac.uk/goldman-srv/prank/</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><o:p>&nbsp;</o:p></span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>#######<span
+style="mso-spacerun: yes">&nbsp;&nbsp; </span>Prediction Methods available to
+generate Templates</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>-------------------------------------------------------------</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>RNAplfold<span
+style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>http://www.tbi.univie.ac.at/~ivo/RNA/</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>HMMtop<span
+style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>www.enzim.hu/hmmtop/</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>GOR4<span
+style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>http://mig.jouy.inra.fr/logiciels/gorIV/</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>wublast_client<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;
+</span>http://www.ebi.ac.uk/Tools/webservices/services/wublast</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>blastpgp_client<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;
+</span>http://www.ebi.ac.uk/Tools/webservices/services/blastpgp<span
+style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span></span></p>
+
+<p class=examplefileCxSpLast><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>==========================================================</span></span></span></p>
+
+</div>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
+
+<h2><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'><a name="_Toc151732217">Installation of
+PSI-Coffee and Expresso</a></span></span></span></h2>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>PSI-Coffee is a mode of T-Coffee that runs a a Psi-BLAST on each of
+your sequences and makes a multiple profile alignment. If you do not have any
+structural information, it is by far the most accurate mode of T-Coffee. To use
+it, you must have SOAP installed so that the EBI BLAST client can run on your
+system.</span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>It is a bit slow, but really worth it if your sequences are hard to
+align and if the accuracy of your alignment is important.<span
+style="mso-spacerun: yes">&nbsp; </span></span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>To use this mode, try:</span></span></span></span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'>&nbsp;&nbsp; </span>t_coffee
+&lt;yoursequence&gt; -mode psicoffee</span></span></span></p>
+
+</div>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>Note that because PSI-BLAST is time consuming, T-Coffee stores the runs
+in its cache (./tcoffee/cache) so that it does not need to be re-run. It means
+that if you re-align your sequences (or add a few extra sequences), things will
+be considerably faster.</span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>If your installation procedure has managed to compile TMalign, and if
+T-Coffee has access to the EBI BLAST server (or any other server) you can also
+do the following:</span></span></span></span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'>&nbsp;&nbsp; </span>t_coffee
+&lt;yoursequence&gt; -mode expresso</span></span></span></p>
+
+</div>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>That will look for structural templates. And if both these modes are
+running fine, then you are ready for the best, the &quot;crème de la
+crème&quot;:</span></span></span></span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'>&nbsp;&nbsp; </span>t_coffee
+&lt;yoursequence&gt; -mode accurate</span></span></span></p>
+
+</div>
+
+<h2><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'><a name="_Toc151732218">Installation of
+M-Coffee</a></span></span></span></h2>
+
+<p class=MsoNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><o:p>&nbsp;</o:p></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>M-Coffee is a special mode of T-Coffee that makes it possible to combine
+the output of many multiple sequence alignment packages. </span></span></span></span><span
+style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'><span style='mso-ansi-language:EN-US'><o:p></o:p></span></span></span></span></p>
+
+<h3><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'><a name="_Toc151732219">Automated
+Installation</a></span></span></span></h3>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>In the T-Coffee distribution, type:</span></span></span></span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'>./install mcoffee</span></span></span></p>
+
+</div>
+
+<p class=MsoNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><o:p>&nbsp;</o:p></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>In theory, this command should download and install every required
+package. If, however, it fails, you should switch to the manual installation
+(see next).</span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>By default these packages will be in </span></span></span></span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'>$HOME/.t_coffee/plugins</span></span></span></p>
+
+</div>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>If you want to have these companion packages in a different directory,
+you can either set the environement variable </span></span></span></span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'>setenv PLUGINS_4_TCOFFEE=&lt;plugins dir&gt;</span></span></span></p>
+
+</div>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>Or use the command line flag -plugin (over-rides every other setting)</span></span></span></span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'>t_coffee ... -plugins=&lt;plugins dir&gt;</span></span></span></p>
+
+</div>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
+
+<h3><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'><a name="_Toc151732220">Manual Installation</a></span></span></span></h3>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>M-Coffee requires a standard T-Coffee installation (c.f. previous
+section) and the following packages to be installed on your system:</span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span></span></span></p>
+
+<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
+mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
+background:#E6E6E6'>
+
+<p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>Package<span
+style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Where
+From</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>==========================================================</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>ClustalW<span
+style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>can
+interact with t_coffee</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>----------------------------------------------------------</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>Poa<span
+style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>http://www.bioinformatics.ucla.edu/poa/</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>----------------------------------------------------------</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>Muscle<span
+style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>http://www.drive5.com</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+style="mso-spacerun:
+yes">&nbsp;</span>----------------------------------------------------------</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>ProbCons<span
+style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>http://probcons.stanford.edu/</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>ProbConsRNA<span
+style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>http://probcons.stanford.edu/</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>----------------------------------------------------------</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>MAFFT<span
+style='mso-tab-count:1'> </span></span></span></span><a
+href="http://www.biophys.kyoto-/"><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>http://www.biophys.kyoto-</span></span></span><span
+style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'></span></span></span></a><span
+style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'>u.ac.jp/~katoh/programs/align/mafft/</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>----------------------------------------------------------</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>Dialign-T<span
+style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span></span><a
+href="http://dialign-t.gobics.de/"><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>http://dialign-t.gobics.de/</span></span></span><span
+style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'></span></span></span></a><span
+style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'></span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>Dialign-TX<span
+style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span></span><a
+href="http://dialign-t.gobics.de/"><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>http://dialign-tx.gobics.de/</span></span></span><span
+style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'></span></span></span></a><span
+style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'></span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>----------------------------------------------------------</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>PCMA<span
+style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span></span><a
+href="file://localhost/pub/PCMA"><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>ftp://iole.swmed.edu/pub/PCMA/</span></span></span><span
+style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'></span></span></span></a><span
+style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'></span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>----------------------------------------------------------</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>kalign<span
+style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>http://msa.cgb.ki.se</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>----------------------------------------------------------</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>amap<span
+style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>http://bio.math.berkeley.edu/amap/</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>-----------------------------------------------------------</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>proda_msa<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>http://bio.math.berkeley.edu/proda/</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>-----------------------------------------------------------</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>prank_msa<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>http://www.ebi.ac.uk/goldman-srv/prank/</span></span></span></p>
+
+<p class=examplefileCxSpLast><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><o:p>&nbsp;</o:p></span></span></span></p>
+
+</div>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>In our hands all these packages where very straightforward to compile
+and install on a standard cygwin or Linux configuration. Just make sure you
+have gcc, the C compiler, properly installed.</span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>Once the package is compiled and ready to use, make sure that the
+executable is on your path, so that t_coffee can find it automatically. Our
+favorite procedure is to create a bin directory in the home. If you do so, make
+sure this bin is in your path and fill it with all your executables (this is a
+standard Unix practice).</span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>If for some reason, you do not want this directory to be on your path,
+or you want to specify a precise directory containing the executables, you can
+use:</span></span></span></span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'>&nbsp;&nbsp; </span>export
+PLUGINS_4_TCOFFEE=&lt;dir&gt;</span></span></span></p>
+
+</div>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>By default this directory is set to $HOME/.t_coffee/plugins/$OS, but
+you can over-ride it with the environement variable or using the flag:</span></span></span></span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'>&nbsp;&nbsp; </span>t_coffee
+...-plugins=&lt;dir&gt;</span></span></span></p>
+
+</div>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>If you cannot, or do not want to use a single bin directory, you can
+set the following environment variables to the absolute path values of the
+executable you want to use. Whenever they are set, these variables will
+supersede any other declaration. This is a convenient way to experiment with
+multiple package versions.</span></span></span></span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:70.2pt;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'>POA_4_TCOOFFEE<br>
+CLUSTALW_4_TCOFFEE<br>
+POA_4_TCOFFEE<br>
+TCOFFEE_4_TCOFFEE<br>
+MAFFT_4_TCOFFEE<br>
+MUSCLE_4_TCOFFEE<br>
+DIALIGNT_4_TCOFFEE<br>
+PRANK_4_TCOFFEE<br>
+DIALIGNTX_4_TCOFFEE<br>
+<span style="mso-spacerun: yes">&nbsp;</span></span></span></span></p>
+
+</div>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>For three of these packages, you will need to copy some of the files in
+a special T-Coffee directory.</span></span></span></span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'>&nbsp;&nbsp; </span>cp
+POA_DIR/* ~/.t_coffee/mcoffee/</span></span></span></p>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'>&nbsp;&nbsp; </span>cp
+DIALIGN-T/conf/*<span style="mso-spacerun: yes">&nbsp;
+</span>~/.t_coffee/mcoffee</span></span></span></p>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'>&nbsp;&nbsp; </span>cp
+DIALIGN-TX/conf/*<span style="mso-spacerun: yes">&nbsp;
+</span>~/.t_coffee/mcoffee</span></span></span></p>
+
+</div>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>Note that the following files are enough for default usage:</span></span></span></span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'>BLOSUM.diag_prob_t10<span
+style="mso-spacerun: yes">&nbsp;&nbsp; </span>BLOSUM75.scr<span
+style="mso-spacerun: yes">&nbsp; </span>blosum80_trunc.mat<span
+style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span></span></p>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'>dna_diag_prob_100_exp_330000<span
+style="mso-spacerun: yes">&nbsp; </span>dna_diag_prob_200_exp_110000</span></span></span></p>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'>BLOSUM.scr<span style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>BLOSUM90.scr<span style="mso-spacerun: yes">&nbsp;
+</span>dna_diag_prob_100_exp_110000</span></span></span></p>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'>dna_diag_prob_100_exp_550000<span
+style="mso-spacerun: yes">&nbsp; </span>dna_diag_prob_250_exp_110000</span></span></span></p>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'>BLOSUM75.diag_prob_t2<span
+style="mso-spacerun: yes">&nbsp; </span>blosum80.mat<span style="mso-spacerun:
+yes">&nbsp; </span>dna_diag_prob_100_exp_220000<span style="mso-spacerun:
+yes">&nbsp; </span></span></span></span></p>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'>dna_diag_prob_150_exp_110000<span
+style="mso-spacerun: yes">&nbsp; </span>dna_matrix.scr</span></span></span></p>
+
+</div>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF>If you would rather have the mcoffee directory in some other location,
+set the MCOFFEE_4_TCOFFEE environement variable to the propoer directory:</span></span></span></span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'>&nbsp;&nbsp; </span>setenv
+MCOFFEE_4_TCOFFEE &lt;directory containing mcoffee files&gt;</span></span></span></p>
+
+</div>
+
+<h2><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'><a name="_Toc151732221">Installation of APDB
+and iRMSD</a></span></span></span></h2>
+
+<p class=MsoBodyText><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>APDB
+and iRMSD are incorporated in T-Coffee. Once t_coffee is installed, you can
+invoque these programs by typing:</span></span></span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'>&nbsp;&nbsp; </span>t_coffee
+&#8211;other_pg apdb<br>
+<span style='mso-tab-count:1'>&nbsp;&nbsp; </span>t_coffee &#8211;other_pg
+irmsd</span></span></span></p>
+
+</div>
+
+<h2><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'><a name="_Toc151732222">Installation of tRMSD</a></span></span></span></h2>
+
+<p class=MsoBodyText><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>tRMSD
+comes along with t_coffee but it also requires the package phylip in order to
+be functional. Phylip can be obtained from:</span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+lang=AF><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span></span></span></p>
+
+<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
+mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
+background:#E6E6E6'>
+
+<p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>Package<span
+style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Function</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>===================================================</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>---------------------------------------------------</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>Phylip<span
+style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Phylogenetic
+tree computation</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
+style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>evolution.genetics.washington.edu/phylip.html</span></span></span></p>
+
+<p class=examplefileCxSpLast><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>---------------------------------------------------</span></span></span></p>
+
+</div>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;text-indent:14.1pt;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'>t_coffee &#8211;other_pg trmsd</span></span></span></p>
+
+</div>
+
+<h2><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'><o:p>&nbsp;</o:p></span></span></span></h2>
+
+<h2><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'><a name="_Toc151732223">Installation of
+seq_reformat</a></span></span></span></h2>
+
+<p class=MsoBodyText><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>Seq_reformat
+is a reformatting package that is part of t_coffee. To use it (and see the
+available options), type:</span></span></span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'>&nbsp;&nbsp; </span>t_coffee
+&#8211;other_pg seq_reformat</span></span></span></p>
+
+</div>
+
+<h2><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'><a name="_Toc151732224">Installation of
+extract_from_pdb</a></span></span></span></h2>
+
+<p class=MsoBodyText><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>Extract_from_pdb
+is a PDB reformatting package that is part of t_coffee. To use it (and see the
+available options), type.</span></span></span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
+style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'>&nbsp;&nbsp; </span>t_coffee
+&#8211;other_pg extract_from_pdb &#8211;h</span></span></span></p>
+
+</div>
+
+<p class=MsoBodyText><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>Extract_from_pdb
+requires wget in order to automatically fetch PDB structures.</span></span></span></p>
+
+<p class=MsoBodyText><span style='mso-bookmark:_Toc102494675'><span
+style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><o:p>&nbsp;</o:p></span></span></span></p>
+
+<span style='mso-bookmark:_Toc101065206'></span><span style='mso-bookmark:_Toc102494295'></span><span
+style='mso-bookmark:_Toc102494675'></span>
+
+<h2><a name="_Toc151732225">Installation of 3D-Coffee/Expresso</a></h2>
+
+<p class=MyNormal><span lang=AF>3D-Coffee/Expresso is a special mode of
+T-Coffee that makes it possible to combine sequences and structures. The main
+difference between Expresso and 3D-Coffee is that Expresso fetches the
+structures itself. </span><span style='mso-ansi-language:EN-US'><o:p></o:p></span></p>
+
+<h3><a name="_Toc151732226">Automated Installation</a></h3>
+
+<p class=MyNormal><span lang=AF>In the T-Coffee distribution, type:</span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>./install
+expresso</p>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>OR</p>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>./install
+3dcoffee</p>
+
+</div>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MyNormal><span lang=AF>In theory, this command should download and
+install every required package (<b>except fugue</b>). If, however, it fails,
+you should switch to the manual installation (see next).</span></p>
+
+<h3><a name="_Toc151732227">Manual Installation</a></h3>
+
+<p class=MyNormal><span lang=AF>In order to make the most out of T-Coffee, you
+will need to install the following packages (make sure the executable is named
+as indicated below):</span></p>
+
+<p class=MyNormal><span lang=AF><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></p>
+
+<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
+mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
+background:#E6E6E6'>
+
+<p class=examplefileCxSpFirst>Package<span style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Function</p>
+
+<p class=examplefileCxSpMiddle>===================================================</p>
+
+<p class=examplefileCxSpMiddle>---------------------------------------------------</p>
+
+<p class=examplefileCxSpMiddle>wget<span style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>3DCoffee
+</p>
+
+<p class=examplefileCxSpMiddle><span style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Automatic
+Downloading of Structures</p>
+
+<p class=examplefileCxSpMiddle>---------------------------------------------------</p>
+
+<p class=examplefileCxSpMiddle>sap<span style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>structure/structure
+comparisons </p>
+
+<p class=examplefileCxSpMiddle>(obtain it from W. Taylor, NIMR-MRC).</p>
+
+<p class=examplefileCxSpMiddle>---------------------------------------------------</p>
+
+<p class=examplefileCxSpMiddle>TMalign<span style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>zhang.bioinformatics.ku.edu/TM-align/</p>
+
+<p class=examplefileCxSpMiddle>---------------------------------------------------</p>
+
+<p class=examplefileCxSpMiddle>mustang<span style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>www.cs.mu.oz.au/~arun/mustang/</p>
+
+<p class=examplefileCxSpMiddle>---------------------------------------------------</p>
+
+<p class=examplefileCxSpMiddle>wublastclient<span style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;
+</span>www.ebi.ac.uk/Tools/webservices/clients/wublast</p>
+
+<p class=examplefileCxSpMiddle>---------------------------------------------------</p>
+
+<p class=examplefileCxSpMiddle>Blast<span style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><a
+href="http://www.ncbi.nih.nlm.gov/">www.ncbi.nih.nlm.gov</a></p>
+
+<p class=examplefileCxSpMiddle>---------------------------------------------------</p>
+
+<p class=examplefileCxSpMiddle>Fugue*<span style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>protein
+to structure alignment program</p>
+
+<p class=examplefileCxSpMiddle><span style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>http://www-cryst.bioc.cam.ac.uk/fugue/download.html</p>
+
+<p class=examplefileCxSpLast><span style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>***NOT
+COMPULSORY***</p>
+
+</div>
+
+<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
+
+<p class=MyNormal><span lang=AF>Once the package is installed, make sure make
+sure that the executable is on your path, so that t_coffee can find it
+automatically.</span></p>
+
+<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
+
+<p class=MyNormal><span lang=AF>The wublast client makes it possible to run
+BLAST at the EBI without having to install any database locally. It is an ideal
+solution if you are only using expresso occasionally.</span></p>
+
+<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
+
+<h3><a name="_Toc151732228">Installing Fugue for T-Coffee</a></h3>
+
+<p class=MyNormal><span lang=AF>Uses a standard fugue installation. You only
+need to install the following packages:</span></p>
+
+<p class=MyNormal><span lang=AF><span style="mso-spacerun:
+yes">&nbsp;</span>joy, melody, fugueali, sstruc, hbond</span></p>
+
+<p class=MyNormal><span lang=AF>If you have root privileges, you can install
+the common data in: </span></p>
+
+<p class=MyNormal><span lang=AF>cp fugue/classdef.dat<span style='mso-tab-count:
+1'> </span>/data/fugue/SUBST/classdef.dat</span></p>
+
+<p class=MyNormal><span lang=AF>otherwise</span></p>
+
+<p class=MyNormal><span lang=AF>Setenv MELODY_CLASSDEF=&lt;location&gt;</span></p>
+
+<p class=MyNormal><span lang=AF>Setenv MELODY_SUBST=fugue/allmat.dat</span></p>
+
+<p class=MyNormal><span lang=AF><span style="mso-spacerun: yes">&nbsp;</span></span></p>
+
+<p class=MyNormal><span lang=AF>All the other configuration files must be in
+the right location. </span></p>
+
+<h2><a name="_Toc151732229">Installation of R-Coffee</a></h2>
+
+<p class=MyNormal><span lang=AF>R-Coffee is a special mode able to align RNA
+sequences while taking into account their secondary structure.</span><span
+style='mso-ansi-language:EN-US'><o:p></o:p></span></p>
+
+<h3><a name="_Toc151732230">Automated Installation</a></h3>
+
+<p class=MyNormal><span lang=AF>In the T-Coffee distribution, type:</span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>./install rcoffee</p>
+
+</div>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MyNormal><span lang=AF>In theory, this command should download and
+install every required package (except <b>consan</b>). If, however, it fails,
+you should switch to the manual installation (see next).</span></p>
+
+<h3><a name="_Toc151732231">Manual Installation</a></h3>
+
+<p class=MyNormal><span lang=AF>R-Coffee only requires the package Vienna to be
+installed, in order to compute multiple sequence alignments. To make the best
+out of it, you should also have all the packages required by M-Coffee</span></p>
+
+<p class=MyNormal><span lang=AF><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></p>
+
+<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
+mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
+background:#E6E6E6'>
+
+<p class=examplefileCxSpFirst>Package<span style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Function</p>
+
+<p class=examplefileCxSpMiddle>===================================================</p>
+
+<p class=examplefileCxSpMiddle>---------------------------------------------------</p>
+
+<p class=examplefileCxSpMiddle>consan<span style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>R-Coffee
+</p>
+
+<p class=examplefileCxSpMiddle><span style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Computes
+highly accurate pairwise Alignments</p>
+
+<p class=examplefileCxSpMiddle><span style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>***NOT
+COMPULSORY***</p>
+
+<p class=examplefileCxSpMiddle><span style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>selab.janelia.org/software/consan/</p>
+
+<p class=examplefileCxSpMiddle>---------------------------------------------------</p>
+
+<p class=examplefileCxSpMiddle>RNAplfold<span style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Computes
+RNA secondary Structures </p>
+
+<p class=examplefileCxSpMiddle><span style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>www.tbi.univie.ac.at/~ivo/RNA/</p>
+
+<p class=examplefileCxSpMiddle>---------------------------------------------------</p>
+
+<p class=examplefileCxSpMiddle>probconsRNA<span style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>probcons.stanford.edu/</p>
+
+<p class=examplefileCxSpMiddle><span style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></p>
+
+<p class=examplefileCxSpMiddle>---------------------------------------------------</p>
+
+<p class=examplefileCxSpMiddle>M-Coffee<span style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>T-Coffee
+and the most common MSA Packages</p>
+
+<p class=examplefileCxSpLast><span style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>(cf
+M-Coffee in this installation guide)</p>
+
+</div>
+
+<h3><a name="_Toc151732232">Installing ProbbonsRNA for R-Coffee</a></h3>
+
+<p class=MyNormal><span lang=AF>Follow the installation procedure, but make
+sure you rename the probcons executable into probconsRNA.</span></p>
+
+<h3><a name="_Toc151732233">Installing Consan for R-Coffee</a></h3>
+
+<p class=MyNormal><span lang=AF>In order to insure a proper interface beween
+consan and R-Coffee, you must make sure that the file mix80.mod is in the
+directory ~/.t_coffee/mcoffee or in the mcoffee directory otherwise declared.</span></p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
+padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0cm;margin-right:
+4.25pt'>
+
+<p class=ChapterTitle><a name="_Toc101065207"></a><a name="_Toc102494676"><span
+style='mso-bookmark:_Toc101065207'>Q</span></a>uick Start</p>
+
+</div>
+
+<p class=MsoBodyText>We only give you the very basics here. Please use the
+Tutorial for more detailed information on how to use our tools.</p>
+
+<div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
+padding:0cm 0cm 0cm 0cm;background:#F7CBB7'>
+
+<p class=Warning><a name="_Toc101065208"></a><a name="_Toc102494296"></a><a
+name="_Toc102494677"><span style='mso-bookmark:_Toc102494296'><span
+style='mso-bookmark:_Toc101065208'>IMPORTANT: All the files mentionned here
+(sampe_seq...) can be found in the example directory of the distribution.</span></span></a></p>
+
+</div>
+
+<h2><span style='mso-bookmark:_Toc102494677'><span style='mso-bookmark:_Toc102494296'><span
+style='mso-bookmark:_Toc101065208'><a name="_Toc151732234">T-COFFEE</a></span></span></span></h2>
+
+<p class=MyNormal><span lang=AF>Write your sequences in the same file
+(Swiss-prot, Fasta or Pir) and type. </span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+sample_seq1.fasta<span style="mso-spacerun: yes">&nbsp; </span></p>
+
+</div>
+
+<p class=MyNormal><span lang=AF>This will output two files:</span></p>
+
+<p class=example2CxSpFirst>sample_seq1.aln: your Multiple Sequence Alignment</p>
+
+<p class=example2CxSpLast>sample_seq1.dnd: The Guide tree (newick Format)</p>
+
+<div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
+padding:0cm 0cm 0cm 0cm;background:#F7CBB7'>
+
+<p class=Warning>IMPORTANT: </p>
+
+<p class=Warning>In theory nucleic acids should be automatically detected and
+the default methods should be adapted appropriately. However, sometimes this
+may fail, either because the sequences are too short or contain too many
+ambiguity codes. </p>
+
+<p class=Warning>When this happens, you are advised to explicitly set the type
+of your sequences</p>
+
+<p class=Warning>NOTE: the &#8211;mode=dna is not needed or supported anymore</p>
+
+</div>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+sample_dnaseq1.fasta &#8211;type=dna</p>
+
+</div>
+
+<h2><a name="_Toc101065209"></a><a name="_Toc102494297"></a><a
+name="_Toc102494678"></a><a name="_Toc151732235"><span style='mso-bookmark:
+_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:
+_Toc101065209'>M-Coffee</span></span></span></a><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'></span></span></span></h2>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
+lang=AF>M-Coffee is a Meta version of T-Coffee that makes it possible to
+combine the output of at least eight packages (Muscle, probcons, poa, dialignT,
+mafft, clustalw, PCMA and T-Coffee).</span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
+lang=AF>If all these packages are already installed on your machine. You must:</span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
+lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
+lang=AF>1-set the following environment variables</span></span></span></span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span
+style='mso-bookmark:_Toc101065209'><span style='mso-tab-count:1'>&nbsp;&nbsp; </span>export
+POA_DIR=[absolute path of the POA installation dir]</span></span></span></p>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span
+style='mso-bookmark:_Toc101065209'><span style='mso-tab-count:1'>&nbsp;&nbsp; </span>export
+DIALIGNT_DIR=[Absolute path of the DIALIGN-T/conf</span></span></span></p>
+
+</div>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
+lang=AF>Once this is done, write your sequences in a file and run: same file
+(Swiss-prot, Fasta or Pir) and type. </span></span></span></span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span
+style='mso-bookmark:_Toc101065209'>PROMPT: t_coffee sample_seq1.fasta &#8211;mode
+mcoffee </span></span></span></p>
+
+</div>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
+lang=AF>If the program starts complaining one package or the other is missing,
+this means you will have to go the hard way and install all these packages
+yourself... Proceed to the M-Coffee section for more detailed instructions.</span></span></span></span></p>
+
+<h2><span style='mso-bookmark:_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span
+style='mso-bookmark:_Toc101065209'><a name="_Toc151732236">Expresso</a></span></span></span></h2>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
+lang=AF>If you have installed the EBI wublast.pl client, Expresso will BLAST
+your sequences against PDB, identify the best targets and use these to align
+your proteins.</span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
+lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span
+style='mso-bookmark:_Toc101065209'>PROMPT: t_coffee sample_seq1.fasta &#8211;mode
+expresso</span></span></span></p>
+
+</div>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
+lang=AF>If you did not manage to install all the required structural packages
+for Expresso, like Fugue or Sap, you can still run expresso by selecting
+yourself the structural packages you want to use. For instance, if you'd rather
+use TM-Align than sap, try: </span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
+lang=AF><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span></span></span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span
+style='mso-bookmark:_Toc101065209'>PROMPT: t_coffee sample_seq1.fasta
+&#8211;template_file EXPRESSO -method TMalign_pair</span></span></span></p>
+
+</div>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
+lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
+
+<h2><span style='mso-bookmark:_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span
+style='mso-bookmark:_Toc101065209'><a name="_Toc151732237">R-Coffee</a></span></span></span></h2>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
+lang=AF>R-Coffee can be used to align RNA sequences, using their RNApfold
+predicted secondary structures. The best results are obtained by using the
+consan pairwise method. If you have consan installed:</span></span></span></span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span
+style='mso-bookmark:_Toc101065209'>t_coffee sample_rnaseq1.fasta
+&#8211;special_mode rcoffee_consan </span></span></span></p>
+
+</div>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
+lang=AF>This will only work if your sequences are short enough (less than 200
+nucleotides). A good alternative is the rmcoffee mode that will run Muscle,
+Probcons4RNA and MAfft and then use the secondary structures predicted by
+RNApfold. </span></span></span></span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span
+style='mso-bookmark:_Toc101065209'>PROMPT: t_coffee sample_rnaseq1.fasta
+&#8211;mode mrcoffee </span></span></span></p>
+
+</div>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
+lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
+lang=AF>If you want to decide yourself which methods should be combined by
+R-Coffee, run:</span></span></span></span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span
+style='mso-bookmark:_Toc101065209'>PROMPT: t_coffee sample_rnaseq1.fasta
+&#8211;mode rcoffee -method lalign_id_pair slow_pair </span></span></span></p>
+
+</div>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
+lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
+lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
+
+<h2><span style='mso-bookmark:_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span
+style='mso-bookmark:_Toc101065209'><br>
+<a name="_Toc151732238">iRMSD and APDB</a></span></span></span></h2>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
+lang=AF>All you need is a file containing the alignment of sequences with a
+known structure. These sequences must be named according to their PDB ID,
+followed by the chain index ( 1aabA for instance). All the sequences do not
+need to have a known structure, but at least two need to have it.</span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
+lang=AF>Given the alignment:</span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
+lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:42.55pt;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span
+style='mso-bookmark:_Toc101065209'>PROMPT: t_coffee &#8211;other_pg irmsd -aln
+3d_sample4.aln </span></span></span></p>
+
+</div>
+
+<h2><span style='mso-bookmark:_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span
+style='mso-bookmark:_Toc101065209'><a name="_Toc151732239">tRMSD</a></span></span></span></h2>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
+lang=AF>tRMSD is a structure based clustering method using the iRMSD to drive
+the clustering. The T-RMSD supports all the parameters supported by iRMSD or
+APDB.</span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
+lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:42.55pt;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span
+style='mso-bookmark:_Toc101065209'>PROMPT: t_coffee &#8211;other_pg trmsd -aln
+3d_sample5.aln -template_file 3d_sample5.template_list </span></span></span></p>
+
+</div>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
+style='mso-ansi-language:EN-US'>3d_sample5.aln is a multiple alignment in which
+each sequence has a known structure. The file </span><span lang=AF>3d_sample5.template_list
+is a fasta like file declaring the structure associated with each sequence, in
+the form: </span></span></span></span></p>
+
+<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
+mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
+background:#E6E6E6;margin-left:0cm;margin-right:1.0cm'>
+
+<p class=examplefilesmall><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'>&gt;
+&lt;seq_name&gt; _P_ &lt;PDB structure file or name&gt; </span></span></span></p>
+
+</div>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
+lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
+
+<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
+mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
+background:#E6E6E6'>
+
+<p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'>*******
+3d_sample5.template_list ********<span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'>&gt;2UWI-3A
+_P_ 2UWI-3.pdb</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'>&gt;2UWI-2A
+_P_ 2UWI-2.pdb</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'>&gt;2UWI-1A
+_P_ 2UWI-1.pdb</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'>&gt;2HEY-4R
+_P_ 2HEY-4.pdb</span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'>...</span></span></span></p>
+
+<p class=examplefileCxSpLast><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'>**************************************</span></span></span></p>
+
+</div>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
+lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
+lang=AF>The program then outputs a series of files</span></span></span></span></p>
+
+<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
+mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
+background:#E6E6E6'>
+
+<p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
+style='font-size:8.0pt'>Template Type: [3d_sample5.template_list] Mode Or File:
+[3d_sample5.template_list] [Start]<o:p></o:p></span></span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
+style='font-size:8.0pt'><span style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>[Sample
+Columns][TOT=<span style="mso-spacerun: yes">&nbsp;&nbsp; </span>51][100
+%][ELAPSED TIME:<span style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp; </span>0
+sec.]<o:p></o:p></span></span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
+style='font-size:8.0pt'><span style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>[Tree
+Cmp][TOT=<span style="mso-spacerun: yes">&nbsp;&nbsp; </span>13][ 92 %][ELAPSED
+TIME:<span style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp; </span>0 sec.]<o:p></o:p></span></span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
+style='font-size:8.0pt'><span style="mso-spacerun: yes">&nbsp;</span>#### File
+Type=<span style="mso-spacerun: yes">&nbsp;&nbsp; </span>TreeList Format=<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp; </span>newick Name=
+3d_sample5.tot_pos_list<o:p></o:p></span></span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
+style='font-size:8.0pt'><span style="mso-spacerun: yes">&nbsp;</span>#### File
+Type=<span style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>Tree Format=<span style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;
+</span>newick Name= 3d_sample5.struc_tree10<o:p></o:p></span></span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
+style='font-size:8.0pt'><span style="mso-spacerun: yes">&nbsp;</span>#### File
+Type=<span style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>Tree Format=<span style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;
+</span>newick Name= 3d_sample5.struc_tree50<o:p></o:p></span></span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
+style='font-size:8.0pt'><span style="mso-spacerun: yes">&nbsp;</span>#### File
+Type=<span style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>Tree Format=<span style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;
+</span>newick Name= 3d_sample5.struc_tree100<o:p></o:p></span></span></span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
+style='font-size:8.0pt'><span style="mso-spacerun: yes">&nbsp;</span>#### File
+Type= Colored MSA Format= score_html Name= 3d_sample5.struc_tree.html<o:p></o:p></span></span></span></span></p>
+
+<p class=examplefileCxSpLast><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><o:p>&nbsp;</o:p></span></span></span></p>
+
+</div>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
+lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
+lang=AF>3d_sample5.tot_pos_list <span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp; </span>is
+a list of the tRMSD tree associated with every position. </span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
+lang=AF>3d_sample5.struc_tree100<span style='mso-tab-count:1'>&nbsp;&nbsp; </span>is
+a consensus tree (phylip/consense) of the trees contained in the previous file.
+<b>This file is the default output<o:p></o:p></b></span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
+lang=AF>3d_sample5.struc_tree10<span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp; </span>is
+a consensus tree (phylip/consense) of the 10% trees having the higest average
+agreement with the rest</span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
+lang=AF>3d_sample5.struc_tree10<span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp; </span>is
+a consensus tree (phylip/consense) of the 50% trees having the higest average
+agreement with the rest</span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
+lang=AF>3d_sample5.html<span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>is
+a colored version of the output showing in red the positions that give the
+highest support to 3d_sample5.struc_tree100</span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
+lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
+lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
+style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
+lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
+
+<h2><span style='mso-bookmark:_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span
+style='mso-bookmark:_Toc101065209'><a name="_Toc151732240">MOCCA</a></span></span></span></h2>
+
+<p class=MyNormal><span lang=AF>Write your sequences in the same file
+(Swiss-prot, Fasta or Pir) and type. </span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+&#8211;other_pg mocca sample_seq1.fasta </p>
+
+</div>
+
+<p class=MyNormal><span lang=AF>This command output one files (&lt;your
+sequences&gt;.mocca_lib) and starts an interactive menu. </span></p>
+
+<div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
+padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0cm;margin-right:
+4.25pt'>
+
+<p class=ChapterTitle><a name="_Toc101065210"></a><a name="_Toc102494679"><span
+style='mso-bookmark:_Toc101065210'>Recent M</span></a>odifications</p>
+
+</div>
+
+<p class=MyNormal><span lang=AF>Warning: This log of recent modifications is
+not as thorough and accurate as it should be.</span></p>
+
+<p class=MyNormal><span lang=AF>-9.86 New data structure for the primary
+library that results in highly improved running times for mcoffee and
+significantly decreased memory usage.</span></p>
+
+<p class=MyNormal><span lang=AF>-5.80 Novel assembly algorithm
+(linked_pair_wise) and the primary library is now made of probcons style
+pairwise alignments (proba_pair)</span></p>
+
+<p class=MyNormal><span lang=AF>-4.30 and upward: the FAQ has moved into a new
+tutorial document</span></p>
+
+<p class=MyNormal><span lang=AF>-4.30 and upward: -in has will be deprecated
+and replaced by the flags: -profile,-method,-aln,-seq,-pdb</span></p>
+
+<p class=MyNormal><span lang=AF>-4.02: -mode=dna is still available but not any
+more needed or supported. Use type=protein or dna if you need to force things</span></p>
+
+<p class=MyNormal><b style='mso-bidi-font-weight:normal'><span lang=AF>-</span></b><span
+lang=AF>3.28: corrected a bug that prevents short sequences from being
+correctly aligned</span></p>
+
+<p class=MyNormal><span lang=AF>-Use of @ as a separator when specifying
+methods parameters</span></p>
+
+<p class=MyNormal><span lang=AF>-The most notable modifications have to do with
+the structure of the input. From version 2.20, all files must be tagged to
+indicate their nature (A: alignment, S: Sequence, L: Library\85). We are becoming
+stricter, but that\92s for your own good\85 </span></p>
+
+<p class=MyNormal><span lang=AF>Another important modification has to do with
+the flag -matrix: it now controls the matrix being used for the computation </span></p>
+
+<span lang=AF style='font-size:11.0pt;font-family:"Times New Roman";mso-fareast-font-family:
+"Times New Roman";mso-bidi-font-family:"Courier New";mso-ansi-language:AF;
+mso-fareast-language:EN-US'><br clear=ALL style='page-break-before:always'>
+</span>
+
+<div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
+padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0cm;margin-right:
+4.25pt'>
+
+<p class=ChapterTitle>Reference Manual</p>
+
+</div>
+
+<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
+
+<p class=MyNormal><span lang=AF>This reference manual gives a list of all the
+flags that can be used to modify the behavior of T-Coffee. For your
+convenience, we have grouped them according to their nature. To display a list
+of all the flags used in the version of T-Coffee you are using (along with
+their default value), type:</span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee </p>
+
+</div>
+
+<p class=MyNormal><span lang=AF>Or</span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+&#8211;help </p>
+
+</div>
+
+<p class=MyNormal><span lang=AF>Or</span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+&#8211;help &#8211;in<span class=MyNormalChar><span style='font-size:11.0pt;
+mso-ansi-language:EN-US'><o:p></o:p></span></span></p>
+
+</div>
+
+<p class=MyNormal><span lang=AF>Or any other parameter</span></p>
+
+<h2><a name="_Toc101065212"></a><a name="_Toc102494358"></a><a
+name="_Toc102494743"><span style='mso-bookmark:_Toc102494358'><span
+style='mso-bookmark:_Toc101065212'><o:p>&nbsp;</o:p></span></span></a></h2>
+
+<h2><span style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
+style='mso-bookmark:_Toc101065212'><a name="_Toc151732241">Environment
+Variables</a></span></span></span></h2>
+
+<p class=MsoBodyText><span style='mso-bookmark:_Toc102494743'><span
+style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'>It
+is possible to modify T-Coffee\92s behavior by setting any of the following
+environment variables. On the bash shell, use export VAR=\94value\94. On the
+cshell, use set $VAR=\94xxx\94</span></span></span></p>
+
+<h3><span style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
+style='mso-bookmark:_Toc101065212'><o:p>&nbsp;</o:p></span></span></span></h3>
+
+<h3><span style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
+style='mso-bookmark:_Toc101065212'><a name="_Toc151732242">http_proxy_4_TCOFFEE</a></span></span></span></h3>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
+style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
+lang=AF>Sets the http_proxy and HTTP_proxy values used by T-Coffee. </span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
+style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
+lang=AF>These values get supersede http_proxy and HTTP_proxy.
+http_proxy_4_TCOFFEE gets superseded by the command line values (-proxy and
+-email)</span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
+style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
+lang=AF>If you have no proxy, just set this value to an empty string.</span></span></span></span></p>
+
+<h3><span style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
+style='mso-bookmark:_Toc101065212'><a name="_Toc151732243">email_4_TCOFFEE</a></span></span></span></h3>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
+style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
+lang=AF>Set the E-mail values provided to web services called upon by T-Coffee.
+Can be over-riden by the flag <i>-email.<o:p></o:p></i></span></span></span></span></p>
+
+<h3><span style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
+style='mso-bookmark:_Toc101065212'><a name="_Toc151732244">DIR_4_TCOFFEE</a></span></span></span></h3>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
+style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
+lang=AF>By default this variable is set to $HOME/.t_coffee. This is where
+T-Coffee expects to find its cache, tmp dir and possibly any temporary data
+stored by the program.</span></span></span></span></p>
+
+<h3><span style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
+style='mso-bookmark:_Toc101065212'><a name="_Toc151732245">TMP_4_TCOFFEE</a></span></span></span></h3>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
+style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
+lang=AF>By default this variable is set to $HOME/.t_coffee/tmp. This is where
+T-Coffee stores temporary files.</span></span></span></span></p>
+
+<h3><span style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
+style='mso-bookmark:_Toc101065212'><a name="_Toc151732246">CACHE_4_TCOFFEE</a></span></span></span></h3>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
+style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
+lang=AF>By default this variable is set to $HOME/.t_coffee/cache. This is where
+T-Coffee stores any data expensive to obtain: pdb files, sap alignments....</span></span></span></span></p>
+
+<h3><span style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
+style='mso-bookmark:_Toc101065212'><a name="_Toc151732247">PLUGINS_4_TCOFFEE</a></span></span></span></h3>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
+style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
+lang=AF>By default all the companion packages are searched in the directory
+DIR_4_TCOFFEE/plugins/&lt;OS&gt;. This variable overrides the default. This
+variable can also be overriden by the <i>-plugins</i> T-Coffee flag</span></span></span></span></p>
+
+<h3><span style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
+style='mso-bookmark:_Toc101065212'><a name="_Toc151732248">NO_ERROR_REPORT_4_TCOFFEE</a></span></span></span></h3>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
+style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
+lang=AF>By default this variable is no set. Set it if you do not want the
+program to generate a verbose error output file (useful for running a server).</span></span></span></span></p>
+
+<h3><span style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
+style='mso-bookmark:_Toc101065212'><a name="_Toc151732249">PDB_DIR</a></span></span></span></h3>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
+style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
+lang=AF>Indicate the location of your local PDB installation.</span></span></span></span></p>
+
+<h3><span style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
+style='mso-bookmark:_Toc101065212'><a name="_Toc151732250">NO_WARNING_4_TCOFFEE</a></span></span></span></h3>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
+style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
+lang=AF>Suppresses all the warnings.</span></span></span></span></p>
+
+<h3><span style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
+style='mso-bookmark:_Toc101065212'><a name="_Toc151732251">UNIQUE_DIR_4_TCOFFEE</a></span></span></span></h3>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
+style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
+lang=AF>Sets:</span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
+style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
+lang=AF><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>DIR_4_TCOFFEE</span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
+style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
+lang=AF><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>CACHE_4_TCOFFEE</span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
+style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
+lang=AF><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>TMP_4_TCOFFEE</span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
+style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
+lang=AF><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>PLUGINS_4_TCOFFEE</span></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
+style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
+lang=AF>To the same unique value. The string MUST be a valid directory<span
+style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp; </span></span></span></span></span></p>
+
+<h2><span style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
+style='mso-bookmark:_Toc101065212'><a name="_Toc151732252">Setting up the
+T-Coffee environment variables</a></span></span></span></h2>
+
+<p class=MsoBodyText><span style='mso-bookmark:_Toc102494743'><span
+style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'>T-Coffee
+can have its own environment file. This environment is kept in a file named
+$HOME/.t_coffee/t_coffee_env and can be edited. The value of any legal variable
+can be modified through that file. For instance, here is an example of a
+configuration file when not requiring a proxy.</span></span></span></p>
+
+<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
+mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
+background:#E6E6E6'>
+
+<p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc102494743'><span
+style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'>http_proxy_4_TCOFFEE=</span></span></span></p>
+
+<p class=examplefileCxSpLast><span style='mso-bookmark:_Toc102494743'><span
+style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'>EMAIL_4_TCOFFEE=cedric.notredame@europe.com</span></span></span></p>
+
+</div>
+
+<p class=MsoBodyText><span style='mso-bookmark:_Toc102494743'><span
+style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'>If
+you want to use a specific configuration file:</span></span></span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
+style='mso-bookmark:_Toc101065212'>t_coffee \85 -setenv
+ENV_4_TCOFFEE=&lt;location&gt;</span></span></span></p>
+
+</div>
+
+<p class=MsoBodyText><span style='mso-bookmark:_Toc102494743'><span
+style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'>In
+general, you can set any environment variable using the &#8211;setenv flag. You
+can also simply do an export:</span></span></span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
+style='mso-bookmark:_Toc101065212'>export ENV_4_TCOFFEE=&lt;location&gt;</span></span></span></p>
+
+</div>
+
+<div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
+padding:0cm 0cm 0cm 0cm;background:#F7CBB7'>
+
+<p class=Warning><span style='mso-bookmark:_Toc102494743'><span
+style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'>IMPORTANT:
+</span></span></span></p>
+
+<p class=Warning style='text-align:justify;text-indent:35.4pt;background:#F7CBB7'><span
+style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
+style='mso-bookmark:_Toc101065212'>export &gt; &#8211;setenv &gt; -proxy,
+-email &gt; t_coffee_env &gt; default<span style="mso-spacerun: yes">&nbsp;
+</span>environment</span></span></span></p>
+
+<p class=Warning style='text-align:justify;background:#F7CBB7'><span
+style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
+style='mso-bookmark:_Toc101065212'><o:p>&nbsp;</o:p></span></span></span></p>
+
+</div>
+
+<p class=MsoBodyText><span style='mso-bookmark:_Toc102494743'><span
+style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'>Note
+that when you use &#8211;setenv for <b style='mso-bidi-font-weight:normal'>PATH,</b>
+the value you provide is concatenated <b style='mso-bidi-font-weight:normal'>TO
+THE BEGINNING </b>of the current PATH value. This way you can force T-Coffee to
+use a specific version of an aligner.</span></span></span></p>
+
+<p class=MsoBodyText><span style='mso-bookmark:_Toc102494743'><span
+style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><o:p>&nbsp;</o:p></span></span></span></p>
+
+<h2><span style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
+style='mso-bookmark:_Toc101065212'><a name="_Toc151732253">Well Behaved
+Parameters</a></span></span></span></h2>
+
+<h3><a name="_Toc101065213"></a><a name="_Toc102494359"></a><a
+name="_Toc102494744"></a><a name="_Toc151732254"><span style='mso-bookmark:
+_Toc102494744'><span style='mso-bookmark:_Toc102494359'><span style='mso-bookmark:
+_Toc101065213'>Separation</span></span></span></a></h3>
+
+<p class=MyNormal><span lang=AF>You can use any kind of separator you want
+(i.e. ,; &lt;space&gt;=). The syntax used in this document is meant to be
+consistent with that of ClustalW. However, in order to take advantage of the
+automatic filename compleation provided by many shells, you can replace \93=\94 and
+\93,\94 with a space.</span></p>
+
+<h3><a name="_Toc101065214"></a><a name="_Toc102494360"></a><a
+name="_Toc102494745"></a><a name="_Toc151732255"><span style='mso-bookmark:
+_Toc102494745'><span style='mso-bookmark:_Toc102494360'><span style='mso-bookmark:
+_Toc101065214'>Posix</span></span></span></a></h3>
+
+<p class=MyNormal><span lang=AF>T-Coffee is not POSIX compliant (sorry </span><span
+lang=AF style='font-family:Wingdings;mso-ascii-font-family:"Times New Roman";
+mso-hansi-font-family:"Times New Roman";mso-char-type:symbol;mso-symbol-font-family:
+Wingdings'><span style='mso-char-type:symbol;mso-symbol-font-family:Wingdings'>L</span></span><span
+lang=AF>).</span></p>
+
+<h3><a name="_Toc101065215"></a><a name="_Toc102494361"></a><a
+name="_Toc102494746"></a><a name="_Toc151732256"><span style='mso-bookmark:
+_Toc102494746'><span style='mso-bookmark:_Toc102494361'><span style='mso-bookmark:
+_Toc101065215'>Entering the right parameters</span></span></span></a></h3>
+
+<p class=MyNormal><span lang=AF>There are many ways to enter parameters in T-Coffee,
+see the -parameter flag in </span></p>
+
+<p class=Noteboxtitle><o:p>&nbsp;</o:p></p>
+
+<div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
+padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#FFFF89'>
+
+<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut align=center
+style='text-align:center;background:#FFFF89'><span style='font-size:20.0pt;
+mso-bidi-font-size:10.0pt'>Parameters Priority<o:p></o:p></span></p>
+
+<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><o:p>&nbsp;</o:p></p>
+
+<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut>In general you will
+not need to use these complicated parameters. Yet, if you find yourself typing
+long command lines on a regular basis, it may be worth reading this section.</p>
+
+<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><o:p>&nbsp;</o:p></p>
+
+<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut>One may easily feel
+confused with the various manners in which the parameters can be passed to
+t_coffee. The reason for these many mechanisms is that they allow several
+levels of intervention. For instance, you may install t_coffee for all the
+users and decide that the defaults we provide are not the proper ones\85 In this
+case, you will need to make your own t_coffee_default file.</p>
+
+<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><o:p>&nbsp;</o:p></p>
+
+<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut>Later on, a user
+may find that he/she needs to keep re-using a specific set of parameters,
+different from those in t_coffee_default, hence the possibility to write an
+extra parameter file: parameters. In summary:</p>
+
+<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><o:p>&nbsp;</o:p></p>
+
+<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut>-parameters &gt;
+prompt parameters &gt; -t_coffee_defaults &gt; -mode</p>
+
+<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><o:p>&nbsp;</o:p></p>
+
+<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut>This means that -<i>parameters</i>
+supersede all the others, while parameters provided via -<i>special mode</i>
+are the weakest.</p>
+
+</div>
+
+<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
+
+<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
+
+<h2><a name="_Toc101065216"></a><a name="_Toc102494362"></a><a
+name="_Toc102494747"></a><a name="_Toc151732257"><span style='mso-bookmark:
+_Toc102494747'><span style='mso-bookmark:_Toc102494362'><span style='mso-bookmark:
+_Toc101065216'>Parameters Syntax</span></span></span></a></h2>
+
+<p class=flag><a name="_Toc101065218"></a><a name="_Toc102494748"></a><a
+name="_Toc151732258"><span style='mso-bookmark:_Toc102494748'><span
+style='mso-bookmark:_Toc101065218'><span lang=AF>No Flag</span></span></span></a></p>
+
+<p class=flagdescription>If no flag is used<b style='mso-bidi-font-weight:normal'>
+</b><i style='mso-bidi-font-style:normal'>&lt;your sequence&gt; </i>must be the
+first argument. See format for further information.</p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+sample_seq1.fasta </p>
+
+</div>
+
+<p class=flagdescription>Which is equivalent to</p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+Ssample_seq1.fasta </p>
+
+</div>
+
+<p class=flagdescription>When you do so, <b style='mso-bidi-font-weight:normal'>sample_seq1</b>
+is used as a name prefix for every file the program outputs.</p>
+
+<p class=flag><a name="_Toc101065219"></a><a name="_Toc102494749"></a><a
+name="_Toc151732259"><span style='mso-bookmark:_Toc102494749'><span
+style='mso-bookmark:_Toc101065219'><span lang=AF>-parameters</span></span></span></a><span
+lang=AF style='background:gray;mso-highlight:gray'><o:p></o:p></span></p>
+
+<p class=flagusage><span lang=FR>Usage: -parameters=parameters_file</span></p>
+
+<p class=instruction>Default: no parameters file</p>
+
+<p class=flagdescription>Indicates a file containing extra parameters.
+Parameters read this way behave as if they had been added on the right end of
+the command line that they either supersede(one value parameter) or complete
+(list of values). For instance, the following file (parameter.file) could be
+used </p>
+
+<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
+mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
+background:#E6E6E6'>
+
+<p class=examplefileCxSpFirst>*******sample_param_file.param********<span
+style='mso-tab-count:1'>&nbsp;&nbsp; </span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>-in=Ssample_seq1.fasta,Mfast_pair</p>
+
+<p class=examplefileCxSpMiddle><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>-output=msf_aln</p>
+
+<p class=examplefileCxSpLast>**************************************</p>
+
+</div>
+
+<p class=Note><span style='mso-ansi-language:EN-US'>Note: This is one of the
+exceptions (with &#8211;infile) where the identifier tag (S,A,L,M\85) can be
+omitted. Any dataset provided this way will be assumed to be a sequence (S).
+These exceptions have been designed to keep the program compatible with
+ClustalW.<o:p></o:p></span></p>
+
+<p class=Note><span style='mso-ansi-language:EN-US'>Note: This parameter file
+can ONLY contain valid parameters. Comments are not allowed. Parameters passed
+this way will be checked like normal parameters.<o:p></o:p></span></p>
+
+<p class=flagdescription>Used with:</p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+-parameters=sample_param_file.param</p>
+
+</div>
+
+<p class=flagdescription>Will cause t_coffee to apply the fast_pair method onto
+to the sequences contained in sample_seq.fasta. If you wish, you can also pipe
+these arguments into t_coffee, by naming the parameter file &quot;stdin&quot;
+(as a rule, any file named stdin is expected to receive its content via the
+stdin)</p>
+
+<p class=example2>cat sample_param_file.param<span style="mso-spacerun:
+yes">&nbsp; </span>| t_coffee -parameters=stdin <a name="_Toc101065220"></a></p>
+
+<p class=flag><span style='mso-bookmark:_Toc101065220'><a name="_Toc102494750"></a><a
+name="_Toc151732260"><span style='mso-bookmark:_Toc102494750'><span lang=AF>-t_coffee_defaults</span></span></a></span></p>
+
+<p class=flagusage><span lang=FR>Usage: -t_coffee_defaults=&lt;file_name&gt;</span></p>
+
+<p class=instruction>Default: not used.</p>
+
+<p class=flagdescription>This flag tells the program to use some default
+parameter file for t_coffee. The format of that file is the same as the one
+used with -parameters. The file used is either:</p>
+
+<p class=flagdescription><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>1.
+&lt;file name&gt; if a name has been specified</p>
+
+<p class=flagdescription><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>2.<span
+style="mso-spacerun: yes">&nbsp; </span><b>~/.t_coffee_defaults </b>if no file
+was specified</p>
+
+<p class=flagdescription><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>3.
+The file indicated by the environment variable <b>TCOFFEE_DEFAULTS</b></p>
+
+<p class=flag><a name="_Toc151732261"><span lang=AF>-mode</span></a></p>
+
+<p class=flagusage><span lang=FR>Usage: -mode= hard coded mode</span></p>
+
+<p class=instruction>Default: not used.</p>
+
+<p class=flagdescription>It indicates that t_coffee will use some hard coded
+parameters. These include:</p>
+
+<p class=flagdescription><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><b
+style='mso-bidi-font-weight:normal'>quickaln</b>: very fast approximate
+alignment</p>
+
+<p class=flagdescription><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><b
+style='mso-bidi-font-weight:normal'>dali</b>: a mode used to combine dali
+pairwise alignments</p>
+
+<p class=flagdescription><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><b
+style='mso-bidi-font-weight:normal'>evaluate</b>: defaults for evaluating an
+alignment</p>
+
+<p class=flagdescription><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><b
+style='mso-bidi-font-weight:normal'>3dcoffee</b>: runs t_coffee with the
+3dcoffee parameterization</p>
+
+<p class=flagdescription><o:p>&nbsp;</o:p></p>
+
+<p class=flagdescription>Other modes exist that are not yet fully supported<span
+style='mso-tab-count:1'> </span></p>
+
+<p class=flag><a name="_Toc101065222"></a><a name="_Toc102494752"></a><a
+name="_Toc151732262"><span style='mso-bookmark:_Toc102494752'><span
+style='mso-bookmark:_Toc101065222'><span lang=AF>-score</span></span><span
+lang=AF> [Deprecated]</span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage: -score</span></p>
+
+<p class=instruction>Default: not used</p>
+
+<p class=flagdescription>Toggles on the evaluate mode and causes t_coffee to
+evaluates a precomputed alignment provided via <b>-infile=&lt;alignment&gt;</b>.
+The flag <b>-output</b> must be set to an appropriate format (i.e.
+-output=score_ascii, score_html or score_pdf). A better default
+parameterization is obtained when using the flag <b>-mode=evaluate.</b></p>
+
+<p class=flag><a name="_Toc102494753"></a><a name="_Toc151732263"><span
+style='mso-bookmark:_Toc102494753'><span lang=AF>-evaluate</span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage: -evaluate</span></p>
+
+<p class=instruction>Default: not used</p>
+
+<p class=flagdescription>Replaces &#8211;score. This flag toggles on the
+evaluate mode and causes t_coffee to evaluates a pre-computed alignment
+provided via <b>-infile=&lt;alignment&gt;</b>. The flag <b>-output</b> must be
+set to an appropriate format (i.e. -output=score_ascii, score_html or
+score_pdf). </p>
+
+<p class=flagdescription><o:p>&nbsp;</o:p></p>
+
+<p class=flagdescription>The main purpose of &#8211;evaluate is to let you
+control every aspect of the evaluation. Yet it is advisable to use pre-defined
+parameterization: <b>mode=evaluate.</b></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+&#8211;infile=sample_aln1.aln -mode=evaluate </p>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+&#8211;infile=sample_seq1.aln &#8211;in<span style="mso-spacerun: yes">&nbsp;
+</span>Lsample_lib1.tc_lib &#8211;mode=evaluate </p>
+
+</div>
+
+<p class=flag><a name="_Toc101065223"></a><a name="_Toc102494754"></a><a
+name="_Toc151732264"><span style='mso-bookmark:_Toc102494754'><span
+style='mso-bookmark:_Toc101065223'><span lang=AF>-convert [cw]</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage: -convert</span></p>
+
+<p class=instruction>Default: turned off</p>
+
+<p class=flagdescription>Toggles on the conversion mode and causes T-Coffee to
+convert the sequences, alignments, libraries or structures provided via the <b>-infile</b>
+and <b>-in</b> flags. The output format must be set via the <b>-output</b>
+flag. This flag can also be used if you simply want to compute a library (i.e.
+you have an alignment and you want to turn it into a library).</p>
+
+<p class=flagdescription>This flag is ClustalW compliant.</p>
+
+<p class=flag><a name="_Toc101065224"></a><a name="_Toc102494755"></a><a
+name="_Toc151732265"><span style='mso-bookmark:_Toc102494755'><span
+style='mso-bookmark:_Toc101065224'><span lang=AF>-do_align [cw]</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
+</span>-do_align</span></p>
+
+<p class=instruction>Default: turned on</p>
+
+<h2><a name="_Toc101065225"></a><a name="_Toc102494363"></a><a
+name="_Toc102494756"></a><a name="_Toc151732266"><span style='mso-bookmark:
+_Toc102494756'><span style='mso-bookmark:_Toc102494363'><span style='mso-bookmark:
+_Toc101065225'>Special Parameters</span></span></span></a></h2>
+
+<p class=flag><a name="_Toc101065226"></a><a name="_Toc102494757"></a><a
+name="_Toc151732267"><span style='mso-bookmark:_Toc102494757'><span
+style='mso-bookmark:_Toc101065226'><span lang=AF>-version</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage: -version</span></p>
+
+<p class=instruction>Default: not used</p>
+
+<p class=flagdescription>Returns the current version number</p>
+
+<p class=flag><a name="_Toc101065227"></a><a name="_Toc102494758"></a><a
+name="_Toc151732268"><span style='mso-bookmark:_Toc102494758'><span
+style='mso-bookmark:_Toc101065227'><span lang=AF>-proxy</span></span></span></a><span
+style='mso-bookmark:_Toc102494758'><span style='mso-bookmark:_Toc101065227'></span></span></p>
+
+<p class=flagusage><span style='mso-bookmark:_Toc102494758'><span
+style='mso-bookmark:_Toc101065227'><span lang=FR>Usage: -proxy=&lt;proxy&gt;</span></span></span></p>
+
+<p class=instruction><span style='mso-bookmark:_Toc102494758'><span
+style='mso-bookmark:_Toc101065227'>Default: not used</span></span></p>
+
+<p class=flagdescription><span style='mso-bookmark:_Toc102494758'><span
+style='mso-bookmark:_Toc101065227'>Sets the proxy used by HTTP_proxy AND
+http_proxy. Setting with the propmpt supersedes ANY other setting.</span></span></p>
+
+<p class=flagdescription><span style='mso-bookmark:_Toc102494758'><span
+style='mso-bookmark:_Toc101065227'>Note that if you use no proxy, you should
+set</span></span></p>
+
+<p class=flagdescription><span style='mso-bookmark:_Toc102494758'><span
+style='mso-bookmark:_Toc101065227'><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>-proxy</span></span></p>
+
+<p class=flag><span style='mso-bookmark:_Toc102494758'><span style='mso-bookmark:
+_Toc101065227'><a name="_Toc151732269"><span lang=AF>-email</span></a></span></span></p>
+
+<p class=flagusage><span style='mso-bookmark:_Toc102494758'><span
+style='mso-bookmark:_Toc101065227'><span lang=FR>Usage: -email=&lt;email&gt;</span></span></span></p>
+
+<p class=instruction><span style='mso-bookmark:_Toc102494758'><span
+style='mso-bookmark:_Toc101065227'>Default: not used</span></span></p>
+
+<p class=flagdescription><span style='mso-bookmark:_Toc102494758'><span
+style='mso-bookmark:_Toc101065227'>Sets your email value as provided to web
+services</span></span></p>
+
+<p class=flag><span style='mso-bookmark:_Toc102494758'><span style='mso-bookmark:
+_Toc101065227'><a name="_Toc151732270"><span lang=AF>-check_configuration</span></a></span></span></p>
+
+<p class=flagusage><span lang=FR>Usage: -check_configuration</span></p>
+
+<p class=instruction>Default: not used</p>
+
+<p class=flagdescription>Checks your system to determine whether all the
+programs T-Coffee can interact with are installed.</p>
+
+<p class=flag><a name="_Toc101065228"></a><a name="_Toc102494759"></a><a
+name="_Toc151732271"><span style='mso-bookmark:_Toc102494759'><span
+style='mso-bookmark:_Toc101065228'><span lang=AF>-cache</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage: -cache=&lt;use, update, ignore,
+&lt;filename&gt;&gt;</span></p>
+
+<p class=instruction>Default: -cache=use</p>
+
+<p class=flagdescription>By default, t_coffee stores in a cache directory, the
+results of computationally expensive (structural alignment) or network
+intensive (BLAST search) operations.<a name="_Toc101065229"></a></p>
+
+<p class=flag><span style='mso-bookmark:_Toc101065229'><a name="_Toc102494760"></a><a
+name="_Toc151732272"><span style='mso-bookmark:_Toc102494760'><span lang=AF>-update</span></span></a></span></p>
+
+<p class=flagusage><span lang=FR>Usage: -update</span></p>
+
+<p class=instruction>Default: turned off</p>
+
+<p class=flagdescription>Causes a <span
+class=StyleflagdescriptionBoldItalicChar>wget</span> access that checks whether
+the t_coffee version you are using needs updating.<a name="_Toc101065230"></a></p>
+
+<p class=flag><span style='mso-bookmark:_Toc101065230'><a name="_Toc102494761"></a><a
+name="_Toc151732273"><span style='mso-bookmark:_Toc102494761'><span lang=AF>-full_log</span></span></a></span></p>
+
+<p class=flagusage><span lang=FR>Usage: -full_log=&lt;filename&gt;</span></p>
+
+<p class=instruction>Default: turned off</p>
+
+<p class=flagdescription>Causes t_coffee to output a full log file that
+contains all the input/output files.<a name="_Toc101065231"></a></p>
+
+<p class=flag><span style='mso-bookmark:_Toc101065231'><a name="_Toc102494762"></a><a
+name="_Toc151732274"><span style='mso-bookmark:_Toc102494762'><span lang=AF>-plugins</span></span></a><span
+style='mso-bookmark:_Toc102494762'></span></span></p>
+
+<p class=flagusage><span style='mso-bookmark:_Toc101065231'><span
+style='mso-bookmark:_Toc102494762'><span lang=FR>Usage: -plugins=&lt;dir&gt;</span></span></span></p>
+
+<p class=instruction><span style='mso-bookmark:_Toc101065231'><span
+style='mso-bookmark:_Toc102494762'>Default: default</span></span></p>
+
+<p class=flagdescription><span style='mso-bookmark:_Toc101065231'><span
+style='mso-bookmark:_Toc102494762'>Specifies the directory in which the
+companion packages (other multiple aligners used by M-Coffee, structural
+aligners, etc\85) are kept as an alternative, you can also set the environment
+variable PLUGINS_4_TCOFFEE</span></span></p>
+
+<p class=flagdescription><span style='mso-bookmark:_Toc101065231'><span
+style='mso-bookmark:_Toc102494762'>The default is ~/.t_coffee/plugins/</span></span></p>
+
+<p class=flag><span style='mso-bookmark:_Toc101065231'><span style='mso-bookmark:
+_Toc102494762'><a name="_Toc151732275"><span lang=AF>-other_pg</span></a></span></span></p>
+
+<p class=flagusage><span lang=FR>Usage: -other_pg=&lt;filename&gt;</span></p>
+
+<p class=instruction>Default: turned off</p>
+
+<p class=flagdescription>Some rumours claim that Tetris is embedded within
+T-Coffee and could be ran using some special set of commands. We wish to deny
+these rumours, although we may admit that several interesting reformatting
+programs are now embedded in t_coffee and can be ran through the
+&#8211;other_pg flag.</p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+&#8211;other_pg=seq_reformat </p>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+&#8211;other_pg=unpack_all </p>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+&#8211;other_pg=unpack_extract_from_pdb </p>
+
+</div>
+
+<h2><a name="_Toc101065232"></a><a name="_Toc102494364"></a><a
+name="_Toc102494763"></a><a name="_Toc151732276"><span style='mso-bookmark:
+_Toc102494763'><span style='mso-bookmark:_Toc102494364'><span style='mso-bookmark:
+_Toc101065232'>Input</span></span></span></a> </h2>
+
+<h3><a name="_Toc101065233"></a><a name="_Toc102494365"></a><a
+name="_Toc102494764"></a><a name="_Toc151732277"><span style='mso-bookmark:
+_Toc102494764'><span style='mso-bookmark:_Toc102494365'><span style='mso-bookmark:
+_Toc101065233'>Sequence Input</span></span></span></a></h3>
+
+<p class=flag><a name="_Toc101065234"></a><a name="_Toc102494765"></a><a
+name="_Toc151732278"><span style='mso-bookmark:_Toc102494765'><span
+style='mso-bookmark:_Toc101065234'><span lang=AF>-infile [cw]</span></span></span></a></p>
+
+<p class=flagdescription>To remain compatible with ClustalW, it is possible to
+indicate the sequences with this flag</p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+-infile=sample_seq1.fasta </p>
+
+</div>
+
+<p class=Note><span style='mso-ansi-language:EN-US'>Note: Common multiple sequence
+alignments format constitute a valid input format.<o:p></o:p></span></p>
+
+<p class=Note><span style='mso-ansi-language:EN-US'>Note: T-Coffee
+automatically removes the gaps </span><i><span style='mso-ansi-language:EN-US;
+mso-bidi-font-weight:bold'>before</span></i><span style='mso-ansi-language:
+EN-US'> doing the alignment. This behaviour is different from that of ClustalW
+where the gaps are kept.<o:p></o:p></span></p>
+
+<p class=flag><a name="_Toc101065235"></a><a name="_Toc102494766"></a><a
+name="_Toc151732279"><span style='mso-bookmark:_Toc102494766'><span
+style='mso-bookmark:_Toc101065235'><span lang=AF>-in</span></span><span
+lang=AF> (Cf &#8211;in from the Method and Library Input section)</span></span></a></p>
+
+<p class=flag><a name="_Toc101065236"></a><a name="_Toc102494767"></a><a
+name="_Toc151732280"><span style='mso-bookmark:_Toc102494767'><span
+style='mso-bookmark:_Toc101065236'><span lang=AF>-get_type</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage: -get_type</span></p>
+
+<p class=instruction>Default: turned off</p>
+
+<p class=flagdescription>Forces t_coffee to identify the sequences type
+(PROTEIN, DNA).</p>
+
+<p class=flag><a name="_Toc101065237"></a><a name="_Toc102494768"></a><a
+name="_Toc151732281"><span style='mso-bookmark:_Toc102494768'><span
+style='mso-bookmark:_Toc101065237'><span lang=AF>-type [cw]</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage: -type=DNA ¦ PROTEIN¦ DNA_PROTEIN</span></p>
+
+<p class=instruction>Default: -type=&lt;automatically set&gt;</p>
+
+<p class=flagdescription>This flag sets the type of the sequences. If omitted,
+the type is guessed automatically. This flag is compatible with ClustalW.</p>
+
+<div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
+padding:0cm 0cm 0cm 0cm;background:#F7CBB7'>
+
+<p class=Warning>Warning:<span style="mso-spacerun: yes">&nbsp; </span>In case
+of low complexity or short sequences, it is recommended to set the type
+manually.<a name="_Toc101065238"></a></p>
+
+</div>
+
+<p class=flag><span style='mso-bookmark:_Toc101065238'><a name="_Toc102494769"></a><a
+name="_Toc151732282"><span style='mso-bookmark:_Toc102494769'><span lang=AF>-seq</span></span></a></span></p>
+
+<p class=flagusage><span lang=FR>Usage: -seq=[&lt;P,S&gt;&lt;name&gt;,]</span></p>
+
+<p class=instruction>Default: none</p>
+
+<p class=MyNormal><span lang=AF>-seq is now the recommended flag to provide
+your sequences. It behaves mostly like the -in flag.</span></p>
+
+<p class=flag><a name="_Toc101065239"></a><a name="_Toc102494770"></a><a
+name="_Toc151732283"><span style='mso-bookmark:_Toc102494770'><span
+style='mso-bookmark:_Toc101065239'><span lang=AF>-seq_source</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage: -seq_source=&lt;ANY or<span
+style="mso-spacerun: yes">&nbsp; </span>_LS or LS &gt;</span></p>
+
+<p class=instruction>Default: ANY.</p>
+
+<p class=flagdescription>You may not want to combine all the provided sequences
+into a single sequence list. You can do by specifying that you do not want to
+treat all the &#8211;in files as potential sequence sources.</p>
+
+<p class=flagdescription>-seq_source=_LA indicates that neither sequences
+provided via the A (Alignment) flag or via the L (Library flag) should be added
+to the sequence list.</p>
+
+<p class=flagdescription>-seq_source=S means that only sequences provided via
+the S tag will be considered. All the other sequences will be ignored.</p>
+
+<p class=Note><span style='mso-ansi-language:EN-US'>Note:<span
+style="mso-spacerun: yes">&nbsp; </span>This flag is mostly designed for
+interactions between T-Coffee and T-CoffeeDPA (the large scale version of
+T-Coffee).</span><span style='mso-ansi-language:EN-US;mso-bidi-font-weight:
+bold'><o:p></o:p></span></p>
+
+<h3><a name="_Toc101065241"></a><a name="_Toc102494366"></a><a
+name="_Toc102494771"></a><a name="_Toc151732284"><span style='mso-bookmark:
+_Toc102494771'><span style='mso-bookmark:_Toc102494366'><span style='mso-bookmark:
+_Toc101065241'>Structure Input</span></span></span></a></h3>
+
+<p class=flag><a name="_Toc101065242"></a><a name="_Toc102494772"></a><a
+name="_Toc151732285"><span style='mso-bookmark:_Toc102494772'><span
+style='mso-bookmark:_Toc101065242'><span lang=AF>-pdb</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
+</span>-pdb=&lt;pdbid1&gt;,&lt;pdbid2&gt;\85[Max 200]</span></p>
+
+<p class=instruction>Default: None</p>
+
+<p class=flagdescription>Reads or fetch a pdb file. It is possible to specify a
+chain or even a sub-chain:</p>
+
+<p class=example2>PDBID(PDB_CHAIN)[opt] (FIRST,LAST)[opt]<a name="_Toc101065243"></a></p>
+
+<p class=flagdescription><span style='mso-bookmark:_Toc101065243'>It is also
+possible to input structures via the &#8211;in flag. In that case, you will
+need to use the TAG identifier:</span></p>
+
+<p class=example2><span style='mso-bookmark:_Toc101065243'>-in Ppdb1 Ppdb2\85 </span></p>
+
+<h3><span style='mso-bookmark:_Toc101065243'><a name="_Toc102494367"></a><a
+name="_Toc102494773"></a><a name="_Toc151732286"><span style='mso-bookmark:
+_Toc102494773'><span style='mso-bookmark:_Toc102494367'>Tree Input</span></span></a></span></h3>
+
+<p class=flag><a name="_Toc101065244"></a><a name="_Toc102494774"></a><a
+name="_Toc151732287"><span style='mso-bookmark:_Toc102494774'><span
+style='mso-bookmark:_Toc101065244'><span lang=AF>-usetree</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage: -usetree=&lt;tree file&gt;</span></p>
+
+<p class=instruction>Default: No file specified</p>
+
+<p class=instruction>Format: newick tree format (ClustalW Style)</p>
+
+<p class=flagdescription>This flag indicates that rather than computing a new
+dendrogram, t_coffee must use a pre-computed one. The tree files are in phylips
+format and compatible with ClustalW. In most cases, using a pre-computed tree
+will halve the computation time required by t_coffee. It is also possible to
+use trees output by ClustalW, Phylips and any other program.</p>
+
+<h3><a name="_Toc101065245"></a><a name="_Toc102494368"></a><a
+name="_Toc102494775"></a><a name="_Toc151732288"><span style='mso-bookmark:
+_Toc102494775'><span style='mso-bookmark:_Toc102494368'><span style='mso-bookmark:
+_Toc101065245'>Structures, Sequences Methods and Library Input</span></span></span>
+via the </a><span style='mso-bookmark:_Toc151732288'><span style='font-family:
+Symbol;mso-ascii-font-family:"Arial Black"'>-</span>in Flag</span></h3>
+
+<div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
+padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#FFFF89'>
+
+<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut align=center
+style='text-align:center;background:#FFFF89'><a name="_Toc101065246"><span
+style='font-size:20.0pt;mso-bidi-font-size:10.0pt'>The -in Flag and its
+Identifier TAGS<o:p></o:p></span></a></p>
+
+<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span
+style='mso-bookmark:_Toc101065246'><o:p>&nbsp;</o:p></span></p>
+
+<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span
+style='mso-bookmark:_Toc101065246'>&lt;-in&gt; is the real grinder of T-Coffee.
+Sequences, methods and alignments all pass through so that T-Coffee can turn it
+all into a single list of constraints (the library). Everything is done
+automatically with T-Coffee going through each file to extract the sequences it
+contains. The methods are then applied to the sequences. Pre-compiled
+constraint list can also be provided. Each file provided via this flag must be
+preceded with a symbol (Identifier TAG) that indicates its nature to T-Coffee.
+The TAGs currently supported are the following:</span></p>
+
+<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span
+style='mso-bookmark:_Toc101065246'><o:p>&nbsp;</o:p></span></p>
+
+<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span
+style='mso-bookmark:_Toc101065246'>P<span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>PDB
+structure</span></p>
+
+<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span
+style='mso-bookmark:_Toc101065246'>S <span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>for
+sequences (use it as well to treat an MSA as unaligned sequences)</span></p>
+
+<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span
+style='mso-bookmark:_Toc101065246'><o:p>&nbsp;</o:p></span></p>
+
+<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span
+style='mso-bookmark:_Toc101065246'>M <span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Methods
+used to build the library</span></p>
+
+<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span
+style='mso-bookmark:_Toc101065246'>L <span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Pre-computed
+T-Coffee library</span></p>
+
+<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span
+style='mso-bookmark:_Toc101065246'>A <span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Multiple
+Alignments that must be turned into a Library</span></p>
+
+<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span
+style='mso-bookmark:_Toc101065246'><o:p>&nbsp;</o:p></span></p>
+
+<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span
+style='mso-bookmark:_Toc101065246'>X <span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Substitution
+matrices.</span></p>
+
+<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:
+35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:
+_Toc101065246'>R <span style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Profiles.
+This is a legal multiple alignments that will be treated as single sequences
+(the sequences it contains will not be realigned). </span></p>
+
+<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:
+35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:
+_Toc101065246'><o:p>&nbsp;</o:p></span></p>
+
+<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:
+35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:
+_Toc101065246'>If you do not want to use the TAGS, you will need to use the
+following flags in replacement of -in. Do not use the TAGS when using these
+flags:</span></p>
+
+<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:
+35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:
+_Toc101065246'><o:p>&nbsp;</o:p></span></p>
+
+<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:
+35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:
+_Toc101065246'>-aln <span style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Alignments
+<span style='mso-tab-count:1'>&nbsp; </span>(A)</span></p>
+
+<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:
+35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:
+_Toc101065246'>-profile<span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Profiles
+<span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>(R)</span></p>
+
+<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:
+35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:
+_Toc101065246'>-method<span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Method
+<span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>(M)</span></p>
+
+<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:
+35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:
+_Toc101065246'>-seq<span style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Sequences
+<span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp; </span>(S)</span></p>
+
+<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:
+35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:
+_Toc101065246'>-lib<span style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Libraries<span
+style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>(L)<a
+name="_Toc102494776"></a></span></p>
+
+</div>
+
+<p class=flag><span style='mso-bookmark:_Toc101065246'><span style='mso-bookmark:
+_Toc102494776'><a name="_Toc151732289"><span lang=AF>-in</span></a></span></span></p>
+
+<p class=flagusage><span lang=FR>Usage: -in=[&lt;P,S,A,L,M,X&gt;&lt;name&gt;,]</span></p>
+
+<p class=instruction>Default: -in=Mlalign_id_pair,Mclustalw_pair</p>
+
+<div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
+padding:0cm 0cm 0cm 0cm;background:#F7CBB7'>
+
+<p class=Warning>Note: -in can be replaced with the combined usage of -aln,
+iprofile, .pdb, .lib, -method.</p>
+
+</div>
+
+<p class=flagdescription>See the box for an explanation of the -in flag. The
+following argument passed via -in</p>
+
+<p class=flagdescription><o:p>&nbsp;</o:p></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+-in=Ssample_seq1.fasta,Asample_aln1.aln,Asample_aln2.msf,Mlalign_id_pair,Lsample_lib1.tc_lib
+&#8211;outfile=outaln</p>
+
+</div>
+
+<p class=flagdescription><o:p>&nbsp;</o:p></p>
+
+<p class=flagdescription>This command will trigger the following chain of
+events:</p>
+
+<p class=flagdescription><o:p>&nbsp;</o:p></p>
+
+<p class=flagdescription>1-Gather all the sequences</p>
+
+<p class=flagdescription>Sequences within all the provided files are pooled
+together. Format recognition is automatic. Duplicates are removed (if they have
+the same name). Duplicates in a single file are only tolerated in FASTA format
+file, although they will cause sequences to be renamed.</p>
+
+<p class=flagdescription>In the above case, the total set of sequences will be
+made of sequences contained in sequences1.seq, alignment1.aln, alignment2.msf
+and library.lib, plus the sequences initially gathered<span
+style="mso-spacerun: yes">&nbsp; </span>by -infile.</p>
+
+<p class=flagdescription>2-Turn alignments into libraries</p>
+
+<p class=flagdescription>alignment1.aln and alignment2.msf will be read and
+turned into libraries. Another library will be produced by applying the method
+lalign_id_pair to the set of sequences previously obtained (1). The final
+library used for the alignment will be the combination of all this information.
+</p>
+
+<p class=flagdescription>Note as well the following rules: </p>
+
+<p class=flagdescription><o:p>&nbsp;</o:p></p>
+
+<p class=flagdescription><b style='mso-bidi-font-weight:normal'>1-Order</b><span
+style='mso-bidi-font-weight:bold'>:</span> The order in which sequences,
+methods, alignments and libraries are fed in is irrelevant.</p>
+
+<p class=flagdescription><b style='mso-bidi-font-weight:normal'>2-Heterogeneity</b><span
+style='mso-bidi-font-weight:bold'>:</span> There is no need for each element
+(A, S, L) to contain the same sequences.</p>
+
+<p class=flagdescription><b style='mso-bidi-font-weight:normal'>3-No Duplicate</b><span
+style='mso-bidi-font-weight:bold'>:</span> Each file should contain only one
+copy of each sequence. Duplicates are only allowed in FASTA files but will
+cause the sequences to be renamed.</p>
+
+<p class=flagdescription><b style='mso-bidi-font-weight:normal'>4-Reconciliation</b><span
+style='mso-bidi-font-weight:bold'>:</span> If two files (for instance two
+alignments) contain different versions of the same sequence due to an indel, a
+new sequence will be reconstructed and used instead:</p>
+
+<p class=example2CxSpFirst>aln 1:hgab1 <span style='mso-tab-count:1'>&nbsp; </span>AAAAABAAAAA</p>
+
+<p class=example2CxSpLast>aln 2:hgab1<span style='mso-tab-count:1'>&nbsp;&nbsp; </span>AAAAAAAAAACCC</p>
+
+<p class=flagdescription>will cause the program to reconstruct and use the
+following sequence </p>
+
+<p class=example2>hgab1<span style='mso-tab-count:1'>&nbsp;&nbsp; </span>AAAAABAAAAACCC
+</p>
+
+<p class=flagdescription>This can be useful if you are trying to combine
+several runs of blast, or structural information where residues may have been
+deleted. However substitutions are forbidden. If two sequences with the same
+name cannot be merged, they will cause the program to exit with an information
+message.</p>
+
+<p class=flagdescription><b style='mso-bidi-font-weight:normal'>5-Methods</b><span
+style='mso-bidi-font-weight:bold'>:</span> The method describer can either be
+built in (See ### for a list of all the available methods) or be a file
+describing the method to be used. The exact syntax is provided in part 4 of
+this manual.</p>
+
+<p class=flagdescription><b style='mso-bidi-font-weight:normal'>6-Substitution
+Matrices</b><span style='mso-bidi-font-weight:bold'>: </span>If the method is a
+substitution matrix (X) then no other type of information should be provided.
+For instance:</p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+sample_seq1.fasta -in=Xpam250mt<span style="mso-spacerun: yes">&nbsp;
+</span>-gapopen=-10<span style="mso-spacerun: yes">&nbsp; </span>-gapext=-1 </p>
+
+</div>
+
+<p class=flagdescription>This command results in a progressive alignment
+carried out on the sequences in seqfile. The procedure does not use any more
+the T-Coffee concistency based algorithm, but switches to a standard
+progressive alignment algorithm (like ClustalW or Pileup) much less accurate.
+In this context, appropriate gap penalties should be provided. The matrices are
+in the file source/matrices.h. Add-Hoc matrices can also be provided by the
+user (see the matrices format section at the end of this manual).</p>
+
+<div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
+padding:0cm 0cm 0cm 0cm;background:#F7CBB7'>
+
+<p class=Warning>Warning: Xmatrix does not have the same effect as using the
+-matrix flag.<span style="mso-spacerun: yes">&nbsp; </span>The -matrix defines
+the matrix that will be used while compiling the library while the Xmatrix
+defines the matrix used when assembling the final alignment.</p>
+
+</div>
+
+<h3><a name="_Toc101065247"></a><a name="_Toc102494369"></a><a
+name="_Toc102494777"></a><a name="_Toc151732290"><span style='mso-bookmark:
+_Toc102494777'><span style='mso-bookmark:_Toc102494369'><span style='mso-bookmark:
+_Toc101065247'>Profile Input</span></span></span></a></h3>
+
+<p class=flag><a name="_Toc101065248"></a><a name="_Toc102494778"></a><a
+name="_Toc151732291"><span style='mso-bookmark:_Toc102494778'><span
+style='mso-bookmark:_Toc101065248'><span lang=AF>-profile</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage: -profile=[&lt;name&gt;,] maximum of 200
+profiles.</span></p>
+
+<p class=instruction>Default: no default</p>
+
+<p class=flagdescription>This flag causes T-Coffee to treat multiple alignments
+as a single sequences, thus making it possible to make multiple profile alignments.
+The profile-profile alignment is controlled by <span style='mso-bidi-font-weight:
+bold'>-profile_mode</span> and <span style='mso-bidi-font-weight:bold'>-profile_comparison</span>.
+When provided with the <b style='mso-bidi-font-weight:normal'>-in</b> flag,
+profiles must be preceded with the letter R.</p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+&#8211;profile sample_aln1.aln,sample_aln2.aln &#8211;outfile=profile_aln</p>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+&#8211;in Rsample_aln1.aln,Rsample_aln2.aln,Mslow_pair,Mlalign_id_pair
+&#8211;outfile=profile_aln</p>
+
+</div>
+
+<p class=flagdescription>Note that when using &#8211;template_file, the program
+will also look for the templates associated with the profiles, even if the
+profiles have been provided as templates themselves (however it will not look
+for the template of the profile templates of the profile templates\85)</p>
+
+<p class=flag><a name="_Toc101065249"></a><a name="_Toc102494779"></a><a
+name="_Toc151732292"><span style='mso-bookmark:_Toc102494779'><span
+style='mso-bookmark:_Toc101065249'><span lang=AF>-profile1 [cw]</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage: -profile1=[&lt;name&gt;], one name only</span></p>
+
+<p class=instruction>Default: no default</p>
+
+<p class=flagdescription>Similar to the previous one and was provided for
+compatibility with ClustalW.</p>
+
+<p class=flag><a name="_Toc101065250"></a><a name="_Toc102494780"></a><a
+name="_Toc151732293"><span style='mso-bookmark:_Toc102494780'><span
+style='mso-bookmark:_Toc101065250'><span lang=AF>-profile2 [cw]</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage: -profile1=[&lt;name&gt;], one name only</span></p>
+
+<p class=instruction>Default: no default</p>
+
+<p class=flagdescription>Similar to the previous one and was provided for
+compatibility with ClustalW.</p>
+
+<h2><a name="_Toc101065251"></a><a name="_Toc102494370"></a><a
+name="_Toc102494781"></a><a name="_Toc151732294"><span style='mso-bookmark:
+_Toc102494781'><span style='mso-bookmark:_Toc102494370'><span style='mso-bookmark:
+_Toc101065251'>Alignment Computation</span></span></span></a></h2>
+
+<h3><a name="_Toc101065252"></a><a name="_Toc102494371"></a><a
+name="_Toc102494782"></a><a name="_Toc151732295"><span style='mso-bookmark:
+_Toc102494782'><span style='mso-bookmark:_Toc102494371'><span style='mso-bookmark:
+_Toc101065252'>Library Computation: Methods</span></span></span></a></h3>
+
+<p class=flag><a name="_Toc102494783"></a><a name="_Toc151732296"><span
+style='mso-bookmark:_Toc102494783'><span lang=AF>-lalign_n_top</span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage: -lalign_n_top=&lt;Integer&gt;</span></p>
+
+<p class=instruction>Default: -lalign_n_top=10</p>
+
+<p class=flagdescription>Number of alignment reported by the local method
+(lalign).</p>
+
+<p class=flag><a name="_Toc102494784"></a><a name="_Toc151732297"><span
+style='mso-bookmark:_Toc102494784'><span lang=AF>-align_pdb_param_file</span></span></a></p>
+
+<p class=flagdescription>Unsuported</p>
+
+<p class=flag><a name="_Toc102494785"></a><a name="_Toc151732298"><span
+style='mso-bookmark:_Toc102494785'><span lang=AF>-align_pdb_hasch_mode</span></span></a></p>
+
+<p class=flagdescription>Unsuported<a name="_Toc101065253"></a></p>
+
+<h3><span style='mso-bookmark:_Toc101065253'><a name="_Toc102494372"></a><a
+name="_Toc102494786"></a><a name="_Toc151732299"><span style='mso-bookmark:
+_Toc102494786'><span style='mso-bookmark:_Toc102494372'>Library Computation:
+Extension</span></span></a></span></h3>
+
+<p class=flag><a name="_Toc101065255"></a><a name="_Toc101065254"></a><a
+name="_Toc102494787"></a><a name="_Toc151732300"><span style='mso-bookmark:
+_Toc102494787'><span style='mso-bookmark:_Toc101065254'><span style='mso-bookmark:
+_Toc101065255'><span lang=AF>-</span></span></span><span style='mso-bookmark:
+_Toc101065255'><span lang=AF>lib_list [Unsupported]</span></span></span></a><span
+style='mso-bookmark:_Toc101065255'></span></p>
+
+<p class=flagusage><span style='mso-bookmark:_Toc101065255'><span lang=FR>Usage:<span
+style="mso-spacerun: yes">&nbsp; </span>-lib_list=&lt;filename&gt; </span></span></p>
+
+<p class=instruction><span style='mso-bookmark:_Toc101065255'>Default:unset</span></p>
+
+<p class=flagdescription><span style='mso-bookmark:_Toc101065255'>Use this flag
+if you do not want the library computation to take into account all the
+possible pairs in your dataset. For instance</span></p>
+
+<p class=flagdescription><span style='mso-bookmark:_Toc101065255'>Format:</span></p>
+
+<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
+mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
+background:#E6E6E6'>
+
+<p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc101065255'><span
+style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>2 Name1 name2 </span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065255'><span
+style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>2 Name1 name4</span></p>
+
+<p class=examplefileCxSpLast><span style='mso-bookmark:_Toc101065255'><span
+style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>3 Name1 Name2
+Name3\85</span></p>
+
+</div>
+
+<p class=flagdescription><span style='mso-bookmark:_Toc101065255'><span
+style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>(the
+line 3 would be used by a multiple alignment method).</span></p>
+
+<p class=flag><span style='mso-bookmark:_Toc101065255'><a name="_Toc102494788"></a><a
+name="_Toc151732301"><span style='mso-bookmark:_Toc102494788'><span lang=AF>-do_normalise</span></span></a></span></p>
+
+<p class=flagusage><span style='mso-bookmark:_Toc101065255'><span lang=FR>Usage:<span
+style="mso-spacerun: yes">&nbsp; </span>-do_normalise=&lt;0 or a positive
+value&gt; </span></span></p>
+
+<p class=instruction><span style='mso-bookmark:_Toc101065255'>Default:-do_normalise=1000</span></p>
+
+<p class=instruction><span style='mso-bookmark:_Toc101065255'>Development Only</span></p>
+
+<p class=flagdescription><span style='mso-bookmark:_Toc101065255'>When using a
+value different from 0, this flag sets the score of the highest scoring pair to
+1000. </span></p>
+
+<p class=flag><span style='mso-bookmark:_Toc101065255'><a name="_Toc102494789"></a><a
+name="_Toc151732302"><span style='mso-bookmark:_Toc102494789'><span lang=AF>-extend</span></span></a></span></p>
+
+<p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
+</span>-extend=&lt;0,1 or a positive value&gt; </span></p>
+
+<p class=instruction>Default:-extend=1</p>
+
+<p class=instruction>Development Only</p>
+
+<p class=flagdescription>When turned on, this flag indicates that the library
+extension should be carried out when performing the multiple alignment. If <b>-extend
+=0</b>, the extension is not made, if it is set to 1, the extension is made on
+all the pairs in the library. If the extension is set to another positive
+value, the extension is only carried out on pairs having a weight value
+superior to the specified limit.<a name="_Toc101065256"></a></p>
+
+<p class=flag><span style='mso-bookmark:_Toc101065256'><a name="_Toc102494790"></a><a
+name="_Toc151732303"><span style='mso-bookmark:_Toc102494790'><span lang=AF>-extend_mode</span></span></a></span></p>
+
+<p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
+</span>-extend=&lt;string&gt;</span></p>
+
+<p class=instruction>Default:-extend=very_fast_triplet</p>
+
+<p class=instruction>Warning: Development Only</p>
+
+<p class=flagdescription>Controls the algorithm for matrix extension. Available
+modes include:</p>
+
+<p class=flagdescription>relative_triplet<span style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Unsupported</p>
+
+<p class=flagdescription>g_coffee<span style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Unsupported</p>
+
+<p class=flagdescription>g_coffee_quadruplets<span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp; </span>Unsupported</p>
+
+<p class=flagdescription>fast_triplet<span style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Fast
+triplet extension</p>
+
+<p class=flagdescription>very_fast_triplet<span style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>slow
+triplet extension, limited to the <b>-max_n_pair</b> best sequence pairs when
+aligning two profiles</p>
+
+<p class=flagdescription>slow_triplet<span style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Exhaustive
+use of all the triplets</p>
+
+<p class=flagdescription>mixt<span style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Unsupported</p>
+
+<p class=flagdescription>quadruplet<span style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Unsupported</p>
+
+<p class=flagdescription>test<span style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Unsupported</p>
+
+<p class=flagdescription>matrix<span style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Use
+of the matrix <b>-matrix<o:p></o:p></b></p>
+
+<p class=flagdescription>fast_matrix<span style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Use
+of the matrix <b>-matrix</b>. Profiles are turned into consensus</p>
+
+<p class=flag><a name="_Toc101065257"></a><a name="_Toc102494791"></a><a
+name="_Toc151732304"><span style='mso-bookmark:_Toc102494791'><span
+style='mso-bookmark:_Toc101065257'><span lang=AF>-max_n_pair</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
+</span>-max_n_pair=&lt;integer&gt;</span></p>
+
+<p class=instruction>Default:-extend=10</p>
+
+<p class=instruction>Development Only</p>
+
+<p class=flagdescription>Controls the number of pairs considered by the <b>-extend_mode</b>=very_fast_triplet.
+Setting it to 0 forces all the pairs to be considered (equivalent to <b>-extend_mode</b>=slow_triplet).</p>
+
+<p class=flag><a name="_Toc101065258"></a><a name="_Toc102494792"></a><a
+name="_Toc151732305"><span style='mso-bookmark:_Toc102494792'><span
+style='mso-bookmark:_Toc101065258'><span lang=AF>-seq_name_for_quadruplet</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
+</span>Unsupported</span></p>
+
+<p class=flag><a name="_Toc101065259"></a><a name="_Toc102494793"></a><a
+name="_Toc151732306"><span style='mso-bookmark:_Toc102494793'><span
+style='mso-bookmark:_Toc101065259'><span lang=AF>-compact</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
+</span>Unsupported</span></p>
+
+<p class=flag><a name="_Toc101065260"></a><a name="_Toc102494794"></a><a
+name="_Toc151732307"><span style='mso-bookmark:_Toc102494794'><span
+style='mso-bookmark:_Toc101065260'><span lang=AF>-clean</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
+</span>Unsupported</span></p>
+
+<p class=flag><a name="_Toc101065261"></a><a name="_Toc102494795"></a><a
+name="_Toc151732308"><span style='mso-bookmark:_Toc102494795'><span
+style='mso-bookmark:_Toc101065261'><span lang=AF>-maximise</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
+</span>Unsupported</span></p>
+
+<p class=flag><a name="_Toc101065262"></a><a name="_Toc102494796"></a><a
+name="_Toc151732309"><span style='mso-bookmark:_Toc102494796'><span
+style='mso-bookmark:_Toc101065262'><span lang=AF>-do_self</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
+</span>Flag -do_self</span></p>
+
+<p class=flagusage><span lang=FR>Default: No</span></p>
+
+<p class=flagdescription>This flag causes the extension to carried out within
+the sequences (as opposed to between sequences). This is necessary when looking
+for internal repeats with Mocca.</p>
+
+<p class=flag><a name="_Toc101065263"></a><a name="_Toc102494797"></a><a
+name="_Toc151732310"><span style='mso-bookmark:_Toc102494797'><span
+style='mso-bookmark:_Toc101065263'><span lang=AF>-seq_name_for_quadruplet</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
+</span>Unsupported</span></p>
+
+<p class=flag><a name="_Toc101065264"></a><a name="_Toc102494798"></a><a
+name="_Toc151732311"><span style='mso-bookmark:_Toc102494798'><span
+style='mso-bookmark:_Toc101065264'><span lang=AF>-weight</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
+</span>-weight=&lt;winsimN, sim or sim_&lt;matrix_name or matrix_file&gt; or
+&lt;integer value&gt;</span></p>
+
+<p class=instruction>Default: -weight=sim</p>
+
+<p class=flagdescription>Weight defines the way alignments are weighted when
+turned into a library.<span style="mso-spacerun: yes">&nbsp;
+</span>Overweighting can be obtained with the OW&lt;X&gt; weight mode.</p>
+
+<p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar><o:p>&nbsp;</o:p></span></p>
+
+<p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar>winsimN
+</span>indicates that the weight assigned to a given pair will be equal to the
+percent identity within a window of 2N+1 length centered on that pair. For
+instance winsim10 defines a window of 10 residues around the pair being
+considered. This gives its own weight to each residue in the output library. In
+our hands, this type of weighting scheme has not provided any significant
+improvement over the standard sim value.</p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+sample_seq1.fasta -weight=winsim10 &#8211;out_lib=test.tc_lib </p>
+
+</div>
+
+<p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar>sim</span>
+indicates that the weight equals the average identity within the sequences
+containing the matched residues.</p>
+
+<p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar>OW&lt;X&gt;</span><span
+class=StyleflagdescriptionBoldItalicChar><span style='font-style:normal;
+mso-bidi-font-style:italic'> </span></span><span
+class=StyleflagdescriptionBoldItalicChar><span style='font-weight:normal;
+mso-bidi-font-weight:bold;font-style:normal;mso-bidi-font-style:italic'>Will
+cause the sim weight to be multiplied by X<o:p></o:p></span></span></p>
+
+<p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar>sim_matrix_name</span>
+indicates the average identity with two residues regarded as identical when
+their substitution value is positive. The valid matrices names are in <i
+style='mso-bidi-font-style:normal'>matrices.h (pam250mt) .</i>Matrices not
+found in this header are considered to be filenames. See the format section for
+matrices. For instance, <i style='mso-bidi-font-style:normal'>-weight=sim_pam250mt</i>
+indicates that the grouping used for similarity will be the set of classes with
+positive substitutions. </p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+sample_seq1.fasta -weight=winsim10 &#8211;out_lib=test.tc_lib </p>
+
+</div>
+
+<p class=flagdescription>Other groups include </p>
+
+<p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar>sim_clustalw_col</span><i
+style='mso-bidi-font-style:normal'> </i>( categories of clustalw marked with :)</p>
+
+<p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar>sim_clustalw_dot</span>
+( categories of clustalw marked with .)</p>
+
+<p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar>Value</span><i
+style='mso-bidi-font-style:normal'> </i>indicates that all the pairs found in
+the alignments must be given the same weight equal to value. This is useful
+when the alignment one wishes to turn into a library must be given a
+pre-specified score (for instance if they come from a structure
+super-imposition program). Value is an integer:</p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+sample_seq1.fasta -weight=1000 &#8211;out_lib=test.tc_lib </p>
+
+</div>
+
+<h3><a name="_Toc101065265"></a><a name="_Toc102494373"></a><a
+name="_Toc102494799"></a><a name="_Toc151732312"><span style='mso-bookmark:
+_Toc102494799'><span style='mso-bookmark:_Toc102494373'><span style='mso-bookmark:
+_Toc101065265'>Tree Computation</span></span></span></a></h3>
+
+<p class=flag><a name="_Toc101065266"></a><a name="_Toc102494800"></a><a
+name="_Toc151732313"><span style='mso-bookmark:_Toc102494800'><span
+style='mso-bookmark:_Toc101065266'><span lang=AF>-</span></span></span><span
+lang=AF>distance_matrix_mode</span></a></p>
+
+<p class=flagusage><span lang=FR>Usage: -distance_matrix_mode=&lt;slow, fast,
+very_fast&gt;</span></p>
+
+<p class=instruction>Default: very_fast</p>
+
+<p class=flagdescription>This flag indicates the method used for computing the
+distance matrix (distance between every pair of sequences) required for the
+computation of the dendrogram. </p>
+
+<p class=flagdescription><b style='mso-bidi-font-weight:normal'>Slow</b> <span
+style='mso-tab-count:1'> </span>The chosen dp_mode using the extended library, </p>
+
+<p class=flagdescription><b style='mso-bidi-font-weight:normal'>fast</b>:<span
+style="mso-spacerun: yes">&nbsp;&nbsp; </span><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>The
+fasta dp_mode using the extended library.</p>
+
+<p class=flagdescription><b style='mso-bidi-font-weight:normal'>very_fast</b><span
+style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>The
+fasta dp_mode using blosum62mt.</p>
+
+<p class=flagdescription><b style='mso-bidi-font-weight:normal'>ktup<span
+style='mso-tab-count:1'>&nbsp; </span></b>Ktup matching (Muscle kind) </p>
+
+<p class=flagdescription><b style='mso-bidi-font-weight:normal'>aln<span
+style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></b>Read
+the distances on a precomputed MSA</p>
+
+<p class=flag><a name="_Toc101065267"></a><a name="_Toc102494801"></a><a
+name="_Toc151732314"><span style='mso-bookmark:_Toc102494801'><span
+style='mso-bookmark:_Toc101065267'><span lang=AF>-quicktree [CW]</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage: -quicktree</span></p>
+
+<p class=instruction>Description: Causes T-Coffee to compute a fast approximate
+guide tree</p>
+
+<p class=MyNormal><span lang=AF>This flag is kept for compatibility with
+ClustalW. It indicates that:</span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+sample_seq1.fasta &#8211;distance_matrix_mode=very_fast </p>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+sample_seq1.fasta &#8211;quicktree </p>
+
+</div>
+
+<h3><a name="_Toc101065268"></a><a name="_Toc102494374"></a><a
+name="_Toc102494802"></a><a name="_Toc151732315"><span style='mso-bookmark:
+_Toc102494802'><span style='mso-bookmark:_Toc102494374'><span style='mso-bookmark:
+_Toc101065268'>Pair-wise Alignment Computation</span></span></span></a></h3>
+
+<p class=Noteboxtitle><o:p>&nbsp;</o:p></p>
+
+<div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
+padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#FFFF89'>
+
+<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut align=center
+style='text-align:center;background:#FFFF89'><span style='font-size:20.0pt'>Controlling
+Alignment Computation<o:p></o:p></span></p>
+
+<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><o:p>&nbsp;</o:p></p>
+
+<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut>Most parameters in
+this section refer to the alignment mode fasta_pair_wise and cfatsa_pair_wise.
+When using these alignment modes, things proceed as follow:</p>
+
+<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut>1-Sequences are
+recoded using a degenerated alphabet provided with &lt;-sim_matrix&gt; </p>
+
+<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut>2-Recoded sequences
+are then hashed into ktuples of size <u>&lt;-ktup&gt;</u></p>
+
+<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut>3-Dynamic
+programming runs on the <u>&lt;-ndiag&gt;</u> best diagonals whose score is
+higher than <u>&lt;-diag_threshold&gt;</u>, the way diagonals are scored is
+controlled via <u>&lt;-diag_mode&gt;</u> .</p>
+
+<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut>4-The Dynamic
+computation is made to optimize either the library scoring scheme (as defined
+by the <u>-in</u> flag) or a substitution matrix as provided via the <u>-matrix</u>
+flag. The penalty scheme is defined by <u>-gapopen</u> and <u>-gapext</u>. If <u>-gapopen</u>
+is undefined, the value defined in <u>-cosmetic_penalty</u> is used instead.</p>
+
+<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut>5-Terminal gaps are
+scored according to <u>-tg_mode</u></p>
+
+</div>
+
+<p class=noteboxbody><o:p>&nbsp;</o:p></p>
+
+<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
+
+<p class=flag><a name="_Toc101065269"></a><a name="_Toc102494803"></a><a
+name="_Toc151732316"><span style='mso-bookmark:_Toc102494803'><span
+style='mso-bookmark:_Toc101065269'><span lang=AF>-dp_mode</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
+</span>-dp_mode=&lt;string&gt;</span></p>
+
+<p class=instruction>Default: -dp_mode=cfasta_fair_wise</p>
+
+<p class=flagdescription>This flag indicates the type of dynamic programming
+used by the program:</p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+sample_seq1.fasta &#8211;dp_mode myers_miller_pair_wise </p>
+
+</div>
+
+<p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar>gotoh_pair_wise</span>:
+implementation of the gotoh algorithm (quadratic in memory and time)</p>
+
+<p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar>myers_miller_pair_wise</span>:
+implementation of the Myers and Miller dynamic programming algorithm (
+quadratic in time and linear in space). This algorithm is recommended for very
+long sequences. It is about 2 times slower than gotoh and only accepts <i
+style='mso-bidi-font-style:normal'>tg_mode=1or 2 (i.e. gaps penalized for
+opening).<o:p></o:p></i></p>
+
+<p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar>fasta_pair_wise</span><i
+style='mso-bidi-font-style:normal'>: </i>implementation of the fasta algorithm.
+The sequence is hashed, looking for <i style='mso-bidi-font-style:normal'>ktuples</i>
+words. Dynamic programming is only carried out on the <i style='mso-bidi-font-style:
+normal'>ndiag</i> best scoring diagonals. This is much faster but less accurate
+than the two previous. This mode is controlled by the parameters <b>-ktuple,
+-diag_mode and -ndiag<o:p></o:p></b></p>
+
+<p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar>cfasta_pair_wise</span>:
+c stands for checked. It is the same algorithm. The dynamic programming is made
+on the <i style='mso-bidi-font-style:normal'>ndiag</i> best diagonals, and then
+on the 2*ndiags, and so on until the scores converge. Complexity will depend on
+the level of divergence of the sequences, but will usually be L*log(L), with an
+accuracy comparable to the two first mode ( this was checked on BaliBase). This
+mode is controlled by the parameters <b>-ktuple, -diag_mode and &#8211;ndiag<o:p></o:p></b></p>
+
+<p class=Note><span style='mso-ansi-language:EN-US'>Note: Users may find by
+looking into the code that other modes with fancy names exists
+(viterby_pair_wise\85) Unless mentioned in this documentation, these modes are
+not supported.<o:p></o:p></span></p>
+
+<p class=flag><a name="_Toc101065270"></a><a name="_Toc102494804"></a><a
+name="_Toc151732317"><span style='mso-bookmark:_Toc102494804'><span
+style='mso-bookmark:_Toc101065270'><span lang=AF>-ktuple</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
+</span>-ktuple=&lt;value&gt;</span></p>
+
+<p class=instruction>Default: -ktuple=1 or 2</p>
+
+<p class=flagdescription>Indicates the ktuple size for cfasta_pair_wise dp_mode
+and fasta_pair_wise. It is set to 1 for proteins, and 2 for DNA. The alphabet
+used for protein can be a degenerated version, set with <b><u>-sim_matrix.</u></b>.
+</p>
+
+<p class=flag><a name="_Toc101065271"></a><a name="_Toc102494805"></a><a
+name="_Toc151732318"><span style='mso-bookmark:_Toc102494805'><span
+style='mso-bookmark:_Toc101065271'><span lang=AF>-ndiag</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
+</span>-ndiag=&lt;value&gt;</span></p>
+
+<p class=instruction>Default: -ndiag=0</p>
+
+<p class=flagdescription>Indicates the number of diagonals used by the <i>fasta_pair_wise</i>
+algorithm (cf <b>-dp_mode</b>). When<span style="mso-spacerun: yes">&nbsp;
+</span><b>-ndiag=0</b>, n_diag=Log (length of the smallest sequence)+1. </p>
+
+<p class=Note><span style='mso-ansi-language:EN-US'>When &#8211;ndiag and
+&#8211;diag_threshold are set, diagonals are selected if and only if they
+fulfill both conditions.<o:p></o:p></span></p>
+
+<p class=flag><a name="_Toc101065272"></a><a name="_Toc102494806"></a><a
+name="_Toc151732319"><span style='mso-bookmark:_Toc102494806'><span
+style='mso-bookmark:_Toc101065272'><span lang=AF>-diag_mode</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
+</span>-diag_mode=&lt;value&gt;</span></p>
+
+<p class=instruction>Default: -diag_mode=0</p>
+
+<p class=flagdescription>Indicates the manner in which diagonals are scored
+during the fasta hashing. </p>
+
+<p class=flagdescription>0: indicates that the score of a diagonal is equal to
+the sum of the scores of the exact matches it contains. </p>
+
+<p class=flagdescription>1 indicates that this score is set equal to the score
+of the best uninterrupted segment (useful when dealing with fragments of
+sequences).</p>
+
+<p class=flag><a name="_Toc101065273"></a><a name="_Toc102494807"></a><a
+name="_Toc151732320"><span style='mso-bookmark:_Toc102494807'><span
+style='mso-bookmark:_Toc101065273'><span lang=AF>-diag_threshold</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
+</span>-diag_threshold=&lt;value&gt;</span></p>
+
+<p class=instruction>Default: -diag_threshold=0</p>
+
+<p class=flagdescription>Sets the value of the threshold when selecting
+diagonals. </p>
+
+<p class=flagdescription>0: indicates that &#8211;ndiag should be used to
+select the diagonals (cf &#8211;ndiag section).</p>
+
+<p class=flag><a name="_Toc101065274"></a><a name="_Toc102494808"></a><a
+name="_Toc151732321"><span style='mso-bookmark:_Toc102494808'><span
+style='mso-bookmark:_Toc101065274'><span lang=AF>-sim_matrix</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
+</span>-sim_matrix=&lt;string&gt;</span></p>
+
+<p class=instruction>Default: -sim_matrix=vasiliky</p>
+
+<p class=flagdescription>Indicates the manner in which the amino acid alphabet
+is degenerated when hashing in the fasta_pairwise dynamic programming. Standard
+ClustalW matrices are all valid. They are used to define groups of amino acids
+having positive substitution values. In T-Coffee, the default is a 13 letter
+grouping named Vasiliky, with residues grouped as follows:</p>
+
+<p class=example2>rk, de, qh, vilm, fy (other residues kept alone).</p>
+
+<p class=flagdescription>This alphabet is set with the flag <b>-sim_matrix=vasiliky</b>.
+In order to keep the alphabet non degenerated, <b>-sim_matrix=idmat </b>can be
+used to retain the standard alphabet.</p>
+
+<p class=flag><a name="_Toc101065275"></a><a name="_Toc102494809"></a><a
+name="_Toc151732322"><span style='mso-bookmark:_Toc102494809'><span
+style='mso-bookmark:_Toc101065275'><span lang=AF>-matrix [CW]</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
+</span>-matrix=&lt;blosum62mt&gt;</span></p>
+
+<p class=instruction>Default: -matrix=blosum62mt</p>
+
+<p class=flagdescription>The usage of this flag has been modified from previous
+versions, due to frequent mistakes in its usage. This flag sets the matrix that
+will be used by alignment methods within t_coffee (slow_pair, lalign_id_pair).
+It does not affect external methods (like clustal_pair, clustal_aln\85). </p>
+
+<p class=flagdescription>Users can also provide their own matrices, using the
+matrix format described in the appendix.</p>
+
+<p class=flag><a name="_Toc101065276"></a><a name="_Toc102494810"></a><a
+name="_Toc151732323"><span style='mso-bookmark:_Toc102494810'><span
+style='mso-bookmark:_Toc101065276'><span lang=AF>-nomatch</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
+</span>-nomatch=&lt;positive value&gt;</span></p>
+
+<p class=instruction>Default: -nomatch=0</p>
+
+<p class=flagdescription>Indicates the penalty to associate with a match. When
+using a library, all matches are positive or equal to 0. Matches equal to 0 are
+unsupported by the library but non-penalized. Setting nomatch to a non-negative
+value makes it possible to penalize these null matches and prevent unrelated
+sequences from being aligned (this can be useful when the alignments are meant
+to be used for structural modeling).</p>
+
+<p class=flag><a name="_Toc101065277"></a><a name="_Toc102494811"></a><a
+name="_Toc151732324"><span style='mso-bookmark:_Toc102494811'><span
+style='mso-bookmark:_Toc101065277'><span lang=AF>-gapopen</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
+</span>-gapopen=&lt;negative value&gt;</span></p>
+
+<p class=instruction>Default: -gapopen=0</p>
+
+<p class=flagdescription>Indicates the penalty applied for opening a gap. The
+penalty must be negative. If no value is provided when using a substitution
+matrix, a value will be automatically computed.</p>
+
+<p class=flagdescription>Here are some guidelines regarding the tuning of
+gapopen and gapext. In T-Coffee matches get a score between 0 (match) and 1000
+(match perfectly consistent with the library). The default cosmetic penalty is
+set to -50 (5% of a perfect match). If you want to tune -gapoen and see a
+strong effect, you should therefore consider values between 0 and -1000. </p>
+
+<p class=flag><a name="_Toc101065278"></a><a name="_Toc102494812"></a><a
+name="_Toc151732325"><span style='mso-bookmark:_Toc102494812'><span
+style='mso-bookmark:_Toc101065278'><span lang=AF>-gapext</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
+</span>-gapext=&lt;negative value&gt;</span></p>
+
+<p class=instruction>Default: -gapext=0</p>
+
+<p class=flagdescription>Indicates the penalty applied for extending a gap (cf <b><u>-gapopen</u></b>)</p>
+
+<p class=flag><a name="_Toc101065279"></a><a name="_Toc102494813"></a><a
+name="_Toc151732326"><span style='mso-bookmark:_Toc102494813'><span
+style='mso-bookmark:_Toc101065279'><span lang=AF>-fgapopen</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Unsupported</span></p>
+
+<p class=flag><a name="_Toc101065280"></a><a name="_Toc102494814"></a><a
+name="_Toc151732327"><span style='mso-bookmark:_Toc102494814'><span
+style='mso-bookmark:_Toc101065280'><span lang=AF>-fgapext</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Unsupported</span></p>
+
+<p class=flag><a name="_Toc101065281"></a><a name="_Toc102494815"></a><a
+name="_Toc151732328"><span style='mso-bookmark:_Toc102494815'><span
+style='mso-bookmark:_Toc101065281'><span lang=AF>-cosmetic_penalty</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
+</span>-cosmetic_penalty=&lt;negative value&gt;</span></p>
+
+<p class=instruction>Default: -cosmetic_penalty=-50</p>
+
+<p class=flagdescription>Indicates the penalty applied for opening a gap. This
+penalty is set to a very low value. It will only have an influence on the
+portions of the alignment that are unalignable. It will not make them more
+correct, but only more pleasing to the eye ( i.e. Avoid stretches of lonely
+residues).</p>
+
+<p class=flagdescription>The cosmetic penalty is automatically turned off if a
+substitution matrix is used rather than a library.</p>
+
+<p class=flag><a name="_Toc101065282"></a><a name="_Toc102494816"></a><a
+name="_Toc151732329"><span style='mso-bookmark:_Toc102494816'><span
+style='mso-bookmark:_Toc101065282'><span lang=AF>-tg_mode</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
+</span>-tg_mode=&lt;0, 1, or 2&gt;</span></p>
+
+<p class=instruction>Default: -tg_mode=1</p>
+
+<p class=flagdescription>0: terminal gaps penalized with <span
+class=StyleflagdescriptionBoldItalicChar>-gapopen + -gapext*len<o:p></o:p></span></p>
+
+<p class=flagdescription>1: terminal gaps penalized with a <span
+class=StyleflagdescriptionBoldItalicChar>-gapext*len<o:p></o:p></span></p>
+
+<p class=flagdescription>2: terminal gaps unpenalized.</p>
+
+<p class=flagdescription><o:p>&nbsp;</o:p></p>
+
+<h3><a name="_Toc101065283"></a><a name="_Toc102494375"></a><a
+name="_Toc102494817"></a><a name="_Toc151732330"><span style='mso-bookmark:
+_Toc102494817'><span style='mso-bookmark:_Toc102494375'><span style='mso-bookmark:
+_Toc101065283'>Weighting Schemes</span></span></span></a></h3>
+
+<p class=flag><a name="_Toc101065284"></a><a name="_Toc102494818"></a><a
+name="_Toc151732331"><span style='mso-bookmark:_Toc102494818'><span
+style='mso-bookmark:_Toc101065284'><span lang=AF>-seq_weight</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage: -seq_weight=&lt;t_coffee or
+&lt;file_name&gt;&gt;</span></p>
+
+<p class=instruction>Default: -seq_weight=t_coffee</p>
+
+<p class=flagdescription>These are the individual weights assigned to each
+sequence. The t_coffee weights try to compensate the bias in consistency caused
+by redundancy in the sequences.</p>
+
+<p class=Formula><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>sim(A,B)=%similarity
+between A and B, between 0 and 1. </p>
+
+<p class=Formula><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>weight(A)=1/sum(sim(A,X)^3)</p>
+
+<p class=flagdescription>Weights are normalized so that their sum equals the
+number of sequences. They are applied onto the primary library in the following
+manner:</p>
+
+<p class=Formula><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>res_score(Ax,By)=Min(weight(A),
+weight(B))*res_score(Ax, By)</p>
+
+<p class=flagdescription>These are very simple weights. Their main goal is to
+prevent a single sequence present in many copies to dominate the alignment.</p>
+
+<p class=Note><span style='mso-ansi-language:EN-US'>Note: The library output by
+-out_lib is the un-weighted<span style="mso-spacerun: yes">&nbsp;
+</span>library. <o:p></o:p></span></p>
+
+<p class=Note><span style='mso-ansi-language:EN-US'>Note: Weights can be output
+using the -outseqweight flag.<o:p></o:p></span></p>
+
+<p class=Note><span style='mso-ansi-language:EN-US'>Note: You can use your own
+weights (see the format section). <o:p></o:p></span></p>
+
+<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
+
+<h3><a name="_Toc101065285"></a><a name="_Toc102494376"></a><a
+name="_Toc102494819"></a><a name="_Toc151732332"><span style='mso-bookmark:
+_Toc102494819'><span style='mso-bookmark:_Toc102494376'><span style='mso-bookmark:
+_Toc101065285'>Multiple Alignment Computation</span></span></span></a></h3>
+
+<p class=flag><a name="_Toc101065286"></a><a name="_Toc102494820"></a><a
+name="_Toc151732333"><span style='mso-bookmark:_Toc102494820'><span
+style='mso-bookmark:_Toc101065286'><span lang=AF>-msa_mode</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage:
+-msa_mode=&lt;tree,graph,precomputed&gt;</span></p>
+
+<p class=instruction>Default: -evaluate_mode=tree</p>
+
+<p class=flagdescription>Unsupported</p>
+
+<p class=flag><a name="_Toc101065287"></a><a name="_Toc102494821"></a><a
+name="_Toc151732334"><span style='mso-bookmark:_Toc102494821'><span
+style='mso-bookmark:_Toc101065287'><span lang=AF>-one2all</span></span></span></a><span
+style='mso-bookmark:_Toc102494821'><span style='mso-bookmark:_Toc101065287'></span></span></p>
+
+<p class=flagusage><span style='mso-bookmark:_Toc102494821'><span
+style='mso-bookmark:_Toc101065287'><span lang=FR>Usage: -one2all=&lt;name&gt;</span></span></span></p>
+
+<p class=instruction><span style='mso-bookmark:_Toc102494821'><span
+style='mso-bookmark:_Toc101065287'>Default: not used</span></span></p>
+
+<p class=flagdescription><span style='mso-bookmark:_Toc102494821'><span
+style='mso-bookmark:_Toc101065287'>Will generate a one to all library with
+respect to the specified sequence and will then align all the sequences in turn
+to that sequence, in a sequence determined by the order in which the sequences
+were provided.<span style="mso-spacerun: yes">&nbsp; </span></span></span></p>
+
+<p class=flagdescription><span style='mso-bookmark:_Toc102494821'><span
+style='mso-bookmark:_Toc101065287'><b style='mso-bidi-font-weight:normal'>&#8211;profile_comparison
+=profile</b>, the MSAs provided via &#8211;profile are vectorized and the
+function specified by &#8211;profile_comparison is used to make profile profile
+alignments. In that case, the complexity is NL^2</span></span></p>
+
+<p class=flag><span style='mso-bookmark:_Toc102494821'><span style='mso-bookmark:
+_Toc101065287'><a name="_Toc151732335"><span lang=AF>-profile</span></a></span></span><span
+style='mso-bookmark:_Toc151732335'><span lang=AF>_comparison</span></span></p>
+
+<p class=flagusage><span lang=FR>Usage: -profile_mode=&lt;fullN,profile&gt;</span></p>
+
+<p class=instruction>Default: -profile_mode=full50</p>
+
+<p class=flagdescription>The profile mode flag controls the multiple profile
+alignments in T-Coffee. There are two instances where t_coffee can make
+multiple profile alignments:</p>
+
+<p class=flagdescription>1-When N, the number of sequences is higher than <b
+style='mso-bidi-font-weight:normal'>&#8211;maxnseq, </b>the program switches to
+its multiple profile alignment mode (t_coffee_dpa).</p>
+
+<p class=flagdescription>2-When MSAs are provided via the <b style='mso-bidi-font-weight:
+normal'>&#8211;profile</b> flag or via <b style='mso-bidi-font-weight:normal'>&#8211;profile1</b>
+and <b style='mso-bidi-font-weight:normal'>&#8211;profile2</b>. </p>
+
+<p class=flagdescription>In these situations, the &#8211;profile_mode value
+influences the alignment computation, these values are:</p>
+
+<p class=flagdescription><b style='mso-bidi-font-weight:normal'>&#8211;profile_comparison
+=profile</b>, the MSAs provided via &#8211;profile are vectorized and the
+function specified by &#8211;profile_comparison is used to make profile profile
+alignments. In that case, the complexity is NL^2</p>
+
+<p class=flagdescription><span class=ListChar><b style='mso-bidi-font-weight:
+normal'><span style='font-size:12.0pt;mso-bidi-font-size:10.0pt'>-profile_comparison=fullN</span></b></span>,
+N is an integer value that can omitted. <i style='mso-bidi-font-style:normal'>Full</i>
+indicates that given two profiles, the alignment will be based on a library
+that includes every possible pair of sequences between the two profiles. If N
+is set, then the library will be restricted to the N most similar pairs of
+sequences between the two profiles, as judged from a measure made on a pairwise
+alignment of these two profiles.</p>
+
+<p class=flag><a name="_Toc101065288"></a><a name="_Toc102494822"></a><a
+name="_Toc151732336"><span style='mso-bookmark:_Toc102494822'><span
+style='mso-bookmark:_Toc101065288'><span lang=AF>-profile_</span></span></span><span
+lang=AF>mode</span></a></p>
+
+<p class=flagusage><span lang=FR>Usage: -profile_mode=&lt;cw_profile_profile,
+muscle_profile_profile, multi_channel&gt;</span></p>
+
+<p class=instruction>Default: -profile_mode=cw_profile_profile</p>
+
+<p class=flagdescription>When <b style='mso-bidi-font-weight:normal'>&#8211;profile_comparison=profile</b>,
+this flag selects a profile scoring function.</p>
+
+<h3><a name="_Toc101065289"></a><a name="_Toc102494377"></a><a
+name="_Toc102494823"></a><a name="_Toc151732337"><span style='mso-bookmark:
+_Toc102494823'><span style='mso-bookmark:_Toc102494377'><span style='mso-bookmark:
+_Toc101065289'>Alignment Post-Processing</span></span></span></a></h3>
+
+<p class=flag><a name="_Toc101065290"></a><a name="_Toc102494824"></a><a
+name="_Toc151732338"><span style='mso-bookmark:_Toc102494824'><span
+style='mso-bookmark:_Toc101065290'><span lang=AF>-clean_aln</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
+</span>-clean_aln<span style="mso-spacerun: yes">&nbsp; </span></span></p>
+
+<p class=instruction>Default:-clean_aln</p>
+
+<p class=flagdescription>This flag causes T-Coffee to post-process the multiple
+alignment. Residues that have a reliability score smaller or equal to
+-clean_threshold (as given by an evaluation that uses
+-clean_evaluate_mode)<span style="mso-spacerun: yes">&nbsp; </span>are
+realigned to the rest of the alignment. Residues with a score higher than the
+threshold constitute a rigid framework that cannot be altered.</p>
+
+<p class=flagdescription>The cleaning algorithm is greedy. It starts from the
+top left segment of low constituency residues and works its way left to right,
+top to bottom along the alignment. You can require this operation to be carried
+out for several cycles using the -clean_iterations flag.</p>
+
+<p class=flagdescription>The rationale behind this operation is mostly
+cosmetic. In order to ensure a decent looking alignment, the gop is set to -20
+and the gep to -1. There is no penalty for terminal gaps, and the matrix is
+blosum62mt.</p>
+
+<p class=Note><span style='mso-ansi-language:EN-US'>Note: Gaps are always
+considered to have a reliability score of 0.<o:p></o:p></span></p>
+
+<p class=Note><span class=WarningChar>Note: The use of the cleaning option can
+result in memory overflow when aligning large</span><span style='mso-ansi-language:
+EN-US'> </span><span class=WarningChar>sequences,<o:p></o:p></span></p>
+
+<p class=flag><a name="_Toc101065291"></a><a name="_Toc102494825"></a><a
+name="_Toc151732339"><span style='mso-bookmark:_Toc102494825'><span
+style='mso-bookmark:_Toc101065291'><span lang=AF>-clean_threshold</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
+</span>-clean_threshold=&lt;0-9&gt;<span style="mso-spacerun: yes">&nbsp;
+</span></span></p>
+
+<p class=flagusage><span lang=FR>Default:-clean_aln=1</span></p>
+
+<p class=MyNormal><span lang=AF>See -clean_aln for details.</span></p>
+
+<p class=flag><a name="_Toc101065292"></a><a name="_Toc102494826"></a><a
+name="_Toc151732340"><span style='mso-bookmark:_Toc102494826'><span
+style='mso-bookmark:_Toc101065292'><span lang=AF>-clean_iteration</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
+</span>-clean_iteration=&lt;value between 1 and &gt;<span style="mso-spacerun:
+yes">&nbsp; </span></span></p>
+
+<p class=instruction>Default:-clean_iteration=1</p>
+
+<p class=MyNormal><span lang=AF>See -clean_aln for details.</span></p>
+
+<p class=flag><a name="_Toc101065293"></a><a name="_Toc102494827"></a><a
+name="_Toc151732341"><span style='mso-bookmark:_Toc102494827'><span
+style='mso-bookmark:_Toc101065293'><span lang=AF>-clean_evaluation_mode</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
+</span>-clean_iteration=&lt;evaluation_mode &gt;<span style="mso-spacerun:
+yes">&nbsp; </span></span></p>
+
+<p class=instruction>Default:-clean_iteration=t_coffee_non_extended</p>
+
+<p class=flagdescription>Indicates the mode used for the evaluation that will
+indicate the segments that should be realigned. See -evaluation_mode for the
+list of accepted modes.</p>
+
+<p class=flag><a name="_Toc101065294"></a><a name="_Toc102494828"></a><a
+name="_Toc151732342"><span style='mso-bookmark:_Toc102494828'><span
+style='mso-bookmark:_Toc101065294'><span lang=AF>-iterate</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage: -iterate=&lt;integer&gt;</span></p>
+
+<p class=instruction>Default: -iterate=0</p>
+
+<p class=flagdescription>Sequences are extracted in turn and realigned to the
+MSA. If iterate is set to -1, each sequence is realigned, otherwise the number
+of iterations is set by &#8211;iterate.</p>
+
+<h2><a name="_Toc101065295"></a><a name="_Toc102494378"></a><a
+name="_Toc102494829"></a><a name="_Toc151732343"><span style='mso-bookmark:
+_Toc102494829'><span style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:
+_Toc101065295'>BLAST Template Selection Parameters</span></span></span></a><span
+style='mso-bookmark:_Toc102494829'><span style='mso-bookmark:_Toc102494378'><span
+style='mso-bookmark:_Toc101065295'></span></span></span></h2>
+
+<p class=MsoBodyText><span style='mso-bookmark:_Toc102494829'><span
+style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'>These
+parameters are used by T-Coffee when running expresso, accurate and psicoffee</span></span></span></p>
+
+<p class=flag><span style='mso-bookmark:_Toc102494829'><span style='mso-bookmark:
+_Toc102494378'><span style='mso-bookmark:_Toc101065295'><a name="_Toc151732344"><span
+lang=AF>-blast_server</span></a><span lang=AF> </span></span></span></span></p>
+
+<p class=flagusage><span style='mso-bookmark:_Toc102494829'><span
+style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'><span
+style='mso-ansi-language:EN-US'>Usage:<span style="mso-spacerun: yes">&nbsp;
+</span>-blast_server=</span> <span lang=FR>EBI, NCBI or LOCAL_BLAST</span></span></span></span><span
+style='mso-bookmark:_Toc102494829'><span style='mso-bookmark:_Toc102494378'><span
+style='mso-bookmark:_Toc101065295'><span style='mso-ansi-language:EN-US'><o:p></o:p></span></span></span></span></p>
+
+<p class=instruction><span style='mso-bookmark:_Toc102494829'><span
+style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'>Default:
+EBI</span></span></span></p>
+
+<p class=instruction style='text-indent:28.25pt'><span style='mso-bookmark:
+_Toc102494829'><span style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:
+_Toc101065295'><span style='mso-bidi-font-weight:bold'>Defines whih way BLAST
+will be used<o:p></o:p></span></span></span></span></p>
+
+<p class=flag><span style='mso-bookmark:_Toc102494829'><span style='mso-bookmark:
+_Toc102494378'><span style='mso-bookmark:_Toc101065295'><a name="_Toc151732345"><span
+lang=AF>-prot_min_sim</span></a><span lang=AF> </span></span></span></span></p>
+
+<p class=flagusage><span style='mso-bookmark:_Toc102494829'><span
+style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'><span
+lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp; </span>-prot_min_sim= &lt;percent_id&gt;</span></span></span></span></p>
+
+<p class=instruction><span style='mso-bookmark:_Toc102494829'><span
+style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'>Default:
+40</span></span></span></p>
+
+<p class=instruction style='text-indent:28.25pt'><span style='mso-bookmark:
+_Toc102494829'><span style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:
+_Toc101065295'><span style='mso-bidi-font-weight:bold'>Minimum id for inclusion
+of a sequence in a psi-blast profile<o:p></o:p></span></span></span></span></p>
+
+<p class=flag><span style='mso-bookmark:_Toc102494829'><span style='mso-bookmark:
+_Toc102494378'><span style='mso-bookmark:_Toc101065295'><a name="_Toc151732346"><span
+lang=AF>-prot_max_sim</span></a><span lang=AF> </span></span></span></span></p>
+
+<p class=flagusage><span style='mso-bookmark:_Toc102494829'><span
+style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'><span
+lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp; </span>-prot_max_sim= &lt;percent_id&gt;</span></span></span></span></p>
+
+<p class=instruction><span style='mso-bookmark:_Toc102494829'><span
+style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'>Default:
+90</span></span></span></p>
+
+<p class=instruction style='text-indent:28.25pt'><span style='mso-bookmark:
+_Toc102494829'><span style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:
+_Toc101065295'><span style='mso-bidi-font-weight:bold'>Maximum id for inclusion
+of a sequence in a psi-blast profile.<o:p></o:p></span></span></span></span></p>
+
+<p class=flag><span style='mso-bookmark:_Toc102494829'><span style='mso-bookmark:
+_Toc102494378'><span style='mso-bookmark:_Toc101065295'><a name="_Toc151732347"><span
+lang=AF>-prot_min_cov</span></a><span lang=AF> </span></span></span></span></p>
+
+<p class=flagusage><span style='mso-bookmark:_Toc102494829'><span
+style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'><span
+lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp; </span>-prot_min_cov= &lt;percent&gt;</span></span></span></span></p>
+
+<p class=instruction><span style='mso-bookmark:_Toc102494829'><span
+style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'>Default:
+40</span></span></span></p>
+
+<p class=instruction style='text-indent:28.25pt'><span style='mso-bookmark:
+_Toc102494829'><span style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:
+_Toc101065295'><span style='mso-bidi-font-weight:bold'>Minimum coverage for
+inclusion of a sequence in a psi-blast profile<o:p></o:p></span></span></span></span></p>
+
+<p class=flag><span style='mso-bookmark:_Toc102494829'><span style='mso-bookmark:
+_Toc102494378'><span style='mso-bookmark:_Toc101065295'><a name="_Toc151732348"><span
+lang=AF>-protein_db</span></a><span lang=AF> </span></span></span></span></p>
+
+<p class=flagusage><span style='mso-bookmark:_Toc102494829'><span
+style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'><span
+lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp; </span>-protein_db= &lt;BLAST
+database&gt;</span></span></span></span></p>
+
+<p class=instruction><span style='mso-bookmark:_Toc102494829'><span
+style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'>Default:
+nr</span></span></span></p>
+
+<p class=instruction style='text-indent:28.25pt'><span style='mso-bookmark:
+_Toc102494829'><span style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:
+_Toc101065295'><span style='mso-bidi-font-weight:bold'>Database used for
+construction of psi-blast profiles</span></span></span></span></p>
+
+<p class=flag><span style='mso-bookmark:_Toc102494829'><span style='mso-bookmark:
+_Toc102494378'><span style='mso-bookmark:_Toc101065295'><a name="_Toc151732349"><span
+lang=AF>-pdb_min_sim</span></a><span lang=AF> </span></span></span></span></p>
+
+<p class=flagusage><span style='mso-bookmark:_Toc102494829'><span
+style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'><span
+lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp; </span>-pdb_min_sim= &lt;percent_id&gt;</span></span></span></span></p>
+
+<p class=instruction><span style='mso-bookmark:_Toc102494829'><span
+style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'>Default:
+35</span></span></span></p>
+
+<p class=instruction style='text-indent:28.25pt'><span style='mso-bookmark:
+_Toc102494829'><span style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:
+_Toc101065295'><span style='mso-bidi-font-weight:bold'>Minimum id for a PDB
+template to be selected by expresso<o:p></o:p></span></span></span></span></p>
+
+<p class=flag><span style='mso-bookmark:_Toc102494829'><span style='mso-bookmark:
+_Toc102494378'><span style='mso-bookmark:_Toc101065295'><a name="_Toc151732350"><span
+lang=AF>-pdb_max_sim</span></a><span lang=AF> </span></span></span></span></p>
+
+<p class=flagusage><span style='mso-bookmark:_Toc102494829'><span
+style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'><span
+lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp; </span>-pdb_max_sim= &lt;percent_id&gt;</span></span></span></span></p>
+
+<p class=instruction><span style='mso-bookmark:_Toc102494829'><span
+style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'>Default:
+100</span></span></span></p>
+
+<p class=instruction style='text-indent:28.25pt'><span style='mso-bookmark:
+_Toc102494829'><span style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:
+_Toc101065295'><span style='mso-bidi-font-weight:bold'>Maximum id for a PDB
+template to be selected by expresso <o:p></o:p></span></span></span></span></p>
+
+<p class=flag><span style='mso-bookmark:_Toc102494829'><span style='mso-bookmark:
+_Toc102494378'><span style='mso-bookmark:_Toc101065295'><a name="_Toc151732351"><span
+lang=AF>-pdb_min_cov</span></a><span lang=AF> </span></span></span></span></p>
+
+<p class=flagusage><span style='mso-bookmark:_Toc102494829'><span
+style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'><span
+lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp; </span>-pdb_min_cov= &lt;percent&gt;</span></span></span></span></p>
+
+<p class=instruction><span style='mso-bookmark:_Toc102494829'><span
+style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'>Default:
+50</span></span></span></p>
+
+<p class=instruction style='text-indent:28.25pt'><span style='mso-bookmark:
+_Toc102494829'><span style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:
+_Toc101065295'><span style='mso-bidi-font-weight:bold'>Minimum coverage for a
+PDB template to be selected by expresso. <o:p></o:p></span></span></span></span></p>
+
+<p class=flag><span style='mso-bookmark:_Toc102494829'><span style='mso-bookmark:
+_Toc102494378'><span style='mso-bookmark:_Toc101065295'><a name="_Toc151732352"><span
+lang=AF>-pdb_db</span></a><span lang=AF> </span></span></span></span></p>
+
+<p class=flagusage><span style='mso-bookmark:_Toc102494829'><span
+style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'><span
+lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp; </span>-protein_db= &lt;BLAST
+database&gt;</span></span></span></span></p>
+
+<p class=instruction><span style='mso-bookmark:_Toc102494829'><span
+style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'>Default:
+pdb</span></span></span></p>
+
+<p class=instruction style='text-indent:28.25pt'><span style='mso-bookmark:
+_Toc102494829'><span style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:
+_Toc101065295'><span style='mso-bidi-font-weight:bold'>Database for PDB
+template to be selected by expresso.</span></span></span></span></p>
+
+<p class=flag><span style='mso-bookmark:_Toc102494829'><span style='mso-bookmark:
+_Toc102494378'><span style='mso-bookmark:_Toc101065295'><a name="_Toc151732353"><span
+lang=AF>-pdb_type</span></a><span lang=AF> </span></span></span></span></p>
+
+<p class=flagusage><span style='mso-bookmark:_Toc102494829'><span
+style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'><span
+lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp; </span>-pdb_type= d,n,m,dnm,dn</span></span></span></span></p>
+
+<p class=instruction><span style='mso-bookmark:_Toc102494829'><span
+style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'>Default:
+d</span></span></span></p>
+
+<p class=instruction style='text-indent:28.25pt'><span style='mso-bookmark:
+_Toc102494829'><span style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:
+_Toc101065295'><span style='mso-bidi-font-weight:bold'>d: diffraction<o:p></o:p></span></span></span></span></p>
+
+<p class=instruction style='text-indent:28.25pt'><span style='mso-bookmark:
+_Toc102494829'><span style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:
+_Toc101065295'><span style='mso-bidi-font-weight:bold'>n: NMR<o:p></o:p></span></span></span></span></p>
+
+<p class=instruction style='text-indent:28.25pt'><span style='mso-bookmark:
+_Toc102494829'><span style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:
+_Toc101065295'><span style='mso-bidi-font-weight:bold'>m: model</span></span></span></span></p>
+
+<h2><span style='mso-bookmark:_Toc102494829'><span style='mso-bookmark:_Toc102494378'><span
+style='mso-bookmark:_Toc101065295'><a name="_Toc151732354">CPU Control</a></span></span></span></h2>
+
+<h3><a name="_Toc101065296"></a><a name="_Toc102494379"></a><a
+name="_Toc102494830"></a><a name="_Toc151732355"><span style='mso-bookmark:
+_Toc102494830'><span style='mso-bookmark:_Toc102494379'><span style='mso-bookmark:
+_Toc101065296'>Multithreading</span></span></span></a></h3>
+
+<p class=flag><a name="_Toc101065297"></a><a name="_Toc102494831"></a><a
+name="_Toc151732356"><span style='mso-bookmark:_Toc102494831'><span
+style='mso-bookmark:_Toc101065297'><span lang=AF>-multi_core</span></span></span></a><span
+style='mso-bookmark:_Toc102494831'><span style='mso-bookmark:_Toc101065297'><span
+lang=AF> </span></span></span></p>
+
+<p class=flagusage><span style='mso-ansi-language:EN-US'>Usage:<span
+style="mso-spacerun: yes">&nbsp; </span>-multi_core=</span><span lang=FR>
+templates_jobs_relax_msa</span><span style='mso-ansi-language:EN-US'><o:p></o:p></span></p>
+
+<p class=instruction>Default: 0</p>
+
+<p class=instruction style='text-indent:28.25pt'><span style='mso-bidi-font-weight:
+bold'>template: </span>fetch the templates in a parallel way</p>
+
+<p class=instruction style='text-indent:28.25pt'><span style='mso-bidi-font-weight:
+bold'>jobs:</span> compute the library</p>
+
+<p class=instruction style='text-indent:28.25pt'><span style='mso-bidi-font-weight:
+bold'>relax:</span> extend the library in a parallel way</p>
+
+<p class=instruction style='text-indent:28.25pt'><span style='mso-bidi-font-weight:
+bold'>msa:</span> compute the msa in a parallel way</p>
+
+<p class=instruction><o:p>&nbsp;</o:p></p>
+
+<p class=flagdescription>Specifies that the steps of T-Coffee that should be
+multi threaded. by default all relevant steps are parallelized.</p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+sample_seq2.fasta -multi_core jobs</p>
+
+</div>
+
+<p class=flagdescription><a name="_Toc101065298"></a><a name="_Toc102494380"></a><a
+name="_Toc102494832"><span style='mso-bookmark:_Toc102494380'><span
+style='mso-bookmark:_Toc101065298'>In order to prevent the use of the parallel
+mode it is possible to use:</span></span></a></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494832'><span style='mso-bookmark:_Toc102494380'><span
+style='mso-bookmark:_Toc101065298'>PROMPT: t_coffee sample_seq2.fasta
+-multi_core no</span></span></span></p>
+
+</div>
+
+<p class=flag><span style='mso-bookmark:_Toc102494832'><span style='mso-bookmark:
+_Toc102494380'><span style='mso-bookmark:_Toc101065298'><span lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
+
+<p class=flag><span style='mso-bookmark:_Toc102494832'><span style='mso-bookmark:
+_Toc102494380'><span style='mso-bookmark:_Toc101065298'><a name="_Toc151732357"><span
+lang=AF>-n_core</span></a><span lang=AF> </span></span></span></span></p>
+
+<p class=flagusage><span style='mso-bookmark:_Toc102494832'><span
+style='mso-bookmark:_Toc102494380'><span style='mso-bookmark:_Toc101065298'><span
+style='mso-ansi-language:EN-US'>Usage:<span style="mso-spacerun: yes">&nbsp;
+</span>-n_core=</span> <span lang=FR>&lt;number of cores&gt;</span></span></span></span><span
+style='mso-bookmark:_Toc102494832'><span style='mso-bookmark:_Toc102494380'><span
+style='mso-bookmark:_Toc101065298'><span style='mso-ansi-language:EN-US'><o:p></o:p></span></span></span></span></p>
+
+<p class=instruction><span style='mso-bookmark:_Toc102494832'><span
+style='mso-bookmark:_Toc102494380'><span style='mso-bookmark:_Toc101065298'>Default:
+0</span></span></span></p>
+
+<p class=flagdescription><span style='mso-bookmark:_Toc102494832'><span
+style='mso-bookmark:_Toc102494380'><span style='mso-bookmark:_Toc101065298'>Default
+indicates that all cores will be used, as indicated by the environment via:</span></span></span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-bookmark:_Toc102494832'><span style='mso-bookmark:_Toc102494380'><span
+style='mso-bookmark:_Toc101065298'>PROMPT: t_coffee sample_seq2.fasta -multi_core
+jobs</span></span></span></p>
+
+</div>
+
+<h3><span style='mso-bookmark:_Toc102494832'><span style='mso-bookmark:_Toc102494380'><span
+style='mso-bookmark:_Toc101065298'><o:p>&nbsp;</o:p></span></span></span></h3>
+
+<h3><span style='mso-bookmark:_Toc102494832'><span style='mso-bookmark:_Toc102494380'><span
+style='mso-bookmark:_Toc101065298'><a name="_Toc151732358">Limits</a></span></span></span></h3>
+
+<p class=flag><a name="_Toc101065299"></a><a name="_Toc102494833"></a><a
+name="_Toc151732359"><span style='mso-bookmark:_Toc102494833'><span
+style='mso-bookmark:_Toc101065299'><span lang=AF>-mem_mode</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
+</span>deprecated</span><span lang=FR style='mso-bidi-font-weight:bold'><o:p></o:p></span></p>
+
+<p class=flag><a name="_Toc101065300"></a><a name="_Toc102494834"></a><a
+name="_Toc151732360"><span style='mso-bookmark:_Toc102494834'><span
+style='mso-bookmark:_Toc101065300'><span lang=AF>-ulimit</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
+</span>-ulimit=&lt;value&gt;</span></p>
+
+<p class=instruction>Default: -ulimit=0</p>
+
+<p class=flagdescription>Specifies the upper limit of memory usage (in
+Megabytes). Processes exceeding this limit will automatically exit. A value 0
+indicates that no limit applies.</p>
+
+<p class=flag><a name="_Toc101065301"></a><a name="_Toc102494835"></a><a
+name="_Toc151732361"><span style='mso-bookmark:_Toc102494835'><span
+style='mso-bookmark:_Toc101065301'><span lang=AF>-maxlen</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
+</span>-maxlen=&lt;value, 0=nolimit&gt;</span></p>
+
+<p class=instruction>Default: -maxlen=1000<span style='mso-bidi-font-weight:
+bold'><o:p></o:p></span></p>
+
+<p class=flagdescription>Indicates the maximum length of the sequences. <a
+name="_Toc101065302"></a></p>
+
+<h3><span style='mso-bookmark:_Toc101065302'><a name="_Toc102494381"></a><a
+name="_Toc102494836"></a><a name="_Toc151732362"><span style='mso-bookmark:
+_Toc102494836'><span style='mso-bookmark:_Toc102494381'>Aligning more than 100
+sequences with DPA</span></span></a></span></h3>
+
+<p class=flag><a name="_Toc101065303"></a><a name="_Toc102494837"></a><a
+name="_Toc151732363"><span style='mso-bookmark:_Toc102494837'><span
+style='mso-bookmark:_Toc101065303'><span lang=AF>-maxnseq</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
+</span>-maxnseq=&lt;value, 0=nolimit&gt;</span></p>
+
+<p class=instruction>Default: -maxnseq=50</p>
+
+<p class=flagdescription>Indicates the maximum number of sequences before
+triggering the use of t_coffee_dpa.</p>
+
+<p class=flag><a name="_Toc101065304"></a><a name="_Toc102494838"></a><a
+name="_Toc151732364"><span style='mso-bookmark:_Toc102494838'><span
+style='mso-bookmark:_Toc101065304'><span lang=AF>-dpa_master_aln</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage: -dpa_master_aln=&lt;File, method&gt;</span></p>
+
+<p class=instruction>Default: -dpa_master_aln=NO</p>
+
+<p class=flagdescription>When using dpa, t_coffee needs a seed alignment that
+can be computed using any appropriate method. By default, t_coffee computes a
+fast approximate alignment.</p>
+
+<p class=flagdescription>A pre-alignment can be provided through this flag, as
+well as any program using the following syntax:</p>
+
+<p class=example2>your_script &#8211;in &lt;fasta_file&gt; -out
+&lt;file_name&gt;</p>
+
+<p class=flag><a name="_Toc101065305"></a><a name="_Toc102494839"></a><a
+name="_Toc151732365"><span style='mso-bookmark:_Toc102494839'><span
+style='mso-bookmark:_Toc101065305'><span lang=AF>-dpa_maxnseq</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage: -dpa_maxnseq=&lt;integer value&gt;</span></p>
+
+<p class=instruction>Default: -dpa_maxnseq=30</p>
+
+<p class=flagdescription>Maximum number of sequences aligned simultaneously
+when DPA is ran. Given the tree computed from the master alignment, a node is
+sent to computation if it controls more than <b style='mso-bidi-font-weight:
+normal'>&#8211;dpa_maxnseq</b> OR if it controls a pair of sequences having
+less than <b style='mso-bidi-font-weight:normal'>&#8211;dpa_min_score2</b>
+percent ID.<a name="_Toc101065306"></a></p>
+
+<p class=flag><span style='mso-bookmark:_Toc101065306'><a name="_Toc102494840"></a><a
+name="_Toc151732366"><span style='mso-bookmark:_Toc102494840'><span lang=AF>-dpa_min_score1</span></span></a></span></p>
+
+<p class=flagusage><span lang=FR>Usage: -dpa_min_score1=&lt;integer value&gt;</span></p>
+
+<p class=instruction>Default: -dpa_min_score1=95</p>
+
+<p class=flagdescription>Threshold for not realigning the sequences within the
+master alignment. Given this alignment and the associated tree, sequences below
+a node are not realigned if none of them has less than<b style='mso-bidi-font-weight:
+normal'> &#8211;dpa_min_score1</b> % identity.<a name="_Toc101065307"></a></p>
+
+<p class=flag><span style='mso-bookmark:_Toc101065307'><a name="_Toc102494841"></a><a
+name="_Toc151732367"><span style='mso-bookmark:_Toc102494841'><span lang=AF>-dpa_min_score2</span></span></a></span></p>
+
+<p class=flagusage><span lang=FR>Usage: -dpa_min_score2</span></p>
+
+<p class=instruction>Default: -dpa_min_score2</p>
+
+<p class=flagdescription>Maximum number of sequences aligned simultaneously
+when DPA is ran. Given the tree computed from the master alignment, a node is
+sent to computation if it controls more than <b style='mso-bidi-font-weight:
+normal'>&#8211;dpa_maxnseq</b> OR if it controls a pair of sequences having
+less than <b style='mso-bidi-font-weight:normal'>&#8211;dpa_min_score2</b>
+percent ID.<a name="_Toc101065308"></a></p>
+
+<p class=flag><span style='mso-bookmark:_Toc101065308'><a name="_Toc102494842"></a><a
+name="_Toc151732368"><span style='mso-bookmark:_Toc102494842'><span lang=AF>-dap_tree
+[NOT IMPLEMENTED]</span></span></a></span></p>
+
+<p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
+</span>-dpa_tree=&lt;filename&gt;</span></p>
+
+<p class=instruction>Default: -unset</p>
+
+<p class=flagdescription>Guide tree used in DPA. This is a newick tree where
+the distance associated with each node is set to the minimum pairwise distance
+among all considered sequences.</p>
+
+<h2><a name="_Toc101065309"></a><a name="_Toc102494382"></a><a
+name="_Toc102494843"></a><a name="_Toc151732369"><span style='mso-bookmark:
+_Toc102494843'><span style='mso-bookmark:_Toc102494382'><span style='mso-bookmark:
+_Toc101065309'>Using Structures</span></span></span></a><a name="_Toc101065310"></a></h2>
+
+<h3><span style='mso-bookmark:_Toc101065310'><a name="_Toc102494383"></a><a
+name="_Toc102494844"></a><a name="_Toc151732370"><span style='mso-bookmark:
+_Toc102494844'><span style='mso-bookmark:_Toc102494383'>Generic</span></span></a></span></h3>
+
+<p class=flag><a name="_Toc151732371"><span lang=AF>-mode</span></a></p>
+
+<p class=flagusage><span lang=FR>Usage: -mode=3dcoffee</span></p>
+
+<p class=instruction>Default: turned off</p>
+
+<p class=flagdescription>Runs t_coffee with the 3dcoffee mode (cf next
+section).</p>
+
+<p class=flag><a name="_Toc101065312"></a><a name="_Toc102494846"></a><a
+name="_Toc151732372"><span style='mso-bookmark:_Toc102494846'><span
+style='mso-bookmark:_Toc101065312'><span lang=AF>-check_pdb_status</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage: -check_pdb_status</span></p>
+
+<p class=instruction>Default: turned off</p>
+
+<p class=flagdescription>Forces t_coffee to run extract_from_pdb to check the
+pdb status of each sequence. This can considerably slow down the program.</p>
+
+<p class=flagdescription><o:p>&nbsp;</o:p></p>
+
+<h3><a name="_Toc101065313"></a><a name="_Toc102494384"></a><a
+name="_Toc102494847"></a><a name="_Toc151732373"><span style='mso-bookmark:
+_Toc102494847'><span style='mso-bookmark:_Toc102494384'><span style='mso-bookmark:
+_Toc101065313'>3D Coffee: Using SAP</span></span></span></a></h3>
+
+<p class=flagdescription>It is possible to use t_coffee to compute multiple structural
+alignments. To do so, ensure that you have the sap program installed.</p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+&#8211;pdb=struc1.pdb,struc2.pdb,struc3.pdb -method sap_pair</p>
+
+</div>
+
+<p class=flagdescription>Will combine the pairwise alignments produced by
+SAP.<span style="mso-spacerun: yes">&nbsp; </span>There are currently four
+methods that can be interfaced with t_coffee:</p>
+
+<p class=flagdescription>sap_pair: that uses the sap algorithm</p>
+
+<p class=flagdescription>align_pdb: uses a t_coffee implementation of sap, not
+as accurate.</p>
+
+<p class=flagdescription>tmaliagn_pair
+(http://zhang.bioinformatics.ku.edu/TM-align/)</p>
+
+<p class=flagdescription>mustang_pair (http://www.cs.mu.oz.au/~arun/mustang)</p>
+
+<p class=flagdescription>When providing a PDB file, the computation is only
+carried out on the first chain of this file. If your original file contains
+several chain, you should extract the chain you want to work on. You can use <b
+style='mso-bidi-font-weight:normal'>t_coffee &#8211;other_pg extract_from_pdb </b>or
+any pdb handling program.</p>
+
+<p class=flagdescription>If you are working with public PDB files, you can use
+the PDB identifier and specify the chain by adding its index to the identifier
+(i.e. 1pdbC). If your structure is an NMR structure, you are advised to provide
+the program with one structure only.</p>
+
+<p class=flagdescription>If you wish to align only a portion of the structure,
+you should extract it yourself from the pdb file, using <b style='mso-bidi-font-weight:
+normal'>t_coffee &#8211;other_pg extract_from_pdb </b>or any pdb handling
+program.</p>
+
+<p class=flagdescription>You can provide t_coffee with a mixture of sequences
+and structure. In this case, you should use the special mode:</p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+&#8211;mode 3dcoffee &#8211;seq 3d_sample3.fasta -template_file
+template_file.template</p>
+
+</div>
+
+<h3><a name="_Toc101065314"></a><a name="_Toc102494385"></a><a
+name="_Toc102494848"></a><a name="_Toc151732374"><span style='mso-bookmark:
+_Toc102494848'><span style='mso-bookmark:_Toc102494385'><span style='mso-bookmark:
+_Toc101065314'>Using/finding PDB templates for the Sequences</span></span></span></a></h3>
+
+<p class=flag><a name="_Toc101065315"></a><a name="_Toc102494849"></a><a
+name="_Toc151732375"><span style='mso-bookmark:_Toc102494849'><span
+style='mso-bookmark:_Toc101065315'><span lang=AF>-template_file</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR style='mso-bidi-font-weight:bold'>Usage</span><span
+lang=FR>: -template_file =</span></p>
+
+<p class=flagusage><span lang=FR>&lt;filename, </span></p>
+
+<p class=flagusage><span lang=FR>SCRIPT_scriptame, </span></p>
+
+<p class=flagusage><span lang=FR>SELF_TAG </span></p>
+
+<p class=flagusage><span lang=FR>SEQFILE_TAG_filename,</span></p>
+
+<p class=flagusage><span lang=FR>no&gt;</span></p>
+
+<p class=instruction>Default: no</p>
+
+<p class=flagdescription>This flag instructs t_coffee on the templates that
+will be used when combining several types of information. For instance, when
+using structural information, this file will indicate the structural template
+that corresponds to your sequences. The identifier T indicates that the file
+should be a FASTA like file, formatted as follows. There are several ways to
+pass the templates:</p>
+
+<p class=flagheading2>Predefined Modes</p>
+
+<p class=MyNormaBoldl><span lang=AF>EXPRESSO: will use the EBI server to find
+_P_ templates</span></p>
+
+<p class=MyNormaBoldl><span lang=AF>PSIBLAST: will use the EBI sever to find
+profiles </span></p>
+
+<p class=MyNormaBoldl><span lang=AF><o:p>&nbsp;</o:p></span></p>
+
+<p class=flagheading2>File name</p>
+
+<p class=flagdescription>This file contains the sequence/template association
+it uses a FASTA-like format, as follows:</p>
+
+<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
+mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
+background:#E6E6E6'>
+
+<p class=examplefileCxSpFirst>&gt;&lt;sequence name&gt; _P_ &lt;pdb
+template&gt;</p>
+
+<p class=examplefileCxSpMiddle>&gt;&lt;sequence name&gt; _G_ &lt;gene
+template&gt;</p>
+
+<p class=examplefileCxSpMiddle>&gt;&lt;sequence name&gt; _R_ &lt;MSA
+template&gt;</p>
+
+<p class=examplefileCxSpMiddle>&gt;&lt;sequence name&gt; _F_ &lt;RNA Secondary
+Structure&gt;</p>
+
+<p class=examplefileCxSpMiddle>&gt;&lt;sequence name&gt; _T_ &lt;Transmembrane
+Secondary Structure&gt;</p>
+
+<p class=examplefileCxSpMiddle>&gt;&lt;sequence name&gt; _E_ &lt;Protein
+Secondary Structure&gt;</p>
+
+<p class=examplefileCxSpLast><o:p>&nbsp;</o:p></p>
+
+</div>
+
+<p class=flagdescription>Each template will be used in place of the sequence
+with the appropriate method. For instance, structural templates will be aligned
+with sap_pair and the information thus generated will be transferred onto the
+alignment.</p>
+
+<p class=flagdescription>Note the following rule:</p>
+
+<p class=flagdescription><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>-Each
+sequence can have one template of each type (structural, genomics\85)</p>
+
+<p class=flagdescription><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>-Each
+sequence can only have one template of a given type</p>
+
+<p class=flagdescription><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>-Several
+sequences can share the same template</p>
+
+<p class=flagdescription><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>-All
+the sequences do not need to have a template</p>
+
+<p class=flagdescription>The type of template on which a method works is
+declared with the SEQ_TYPE parameter in the method configuration file:</p>
+
+<p class=flagdescription><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>SEQ_TYPE<span
+style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>S: a method
+that uses sequences </p>
+
+<p class=flagdescription><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>SEQ_TYPE<span
+style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>PS: a
+pairwise method that aligns sequences and structures</p>
+
+<p class=flagdescription><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>SEQ_TYPE<span
+style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>P: a method
+that aligns structures (sap for instance)</p>
+
+<p class=flagdescription>There are 4 tags identifying the template type:</p>
+
+<p class=flagdescription>_P_<span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp; </span>Structural
+templates: a pdb identifier OR a pdb file</p>
+
+<p class=flagdescription>_G_<span style='mso-tab-count:1'>&nbsp;&nbsp; </span>Genomic
+templates: a protein sequence where boundary amino-acid have been recoded with
+( o:0, i:1, j:2)</p>
+
+<p class=flagdescription>_R_<span style='mso-tab-count:1'>&nbsp;&nbsp; </span>Profile
+Templates: a file containing a multiple sequence alignment</p>
+
+<p class=flagdescription>_F_<span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp; </span>RNA
+secondary Structures</p>
+
+<p class=flagdescription><o:p>&nbsp;</o:p></p>
+
+<p class=flagdescription>More than one template file can be provided. There is
+no need to have one template for every sequence in the dataset. </p>
+
+<p class=flagdescription>_P_, _G_, and _R_ are known as <b style='mso-bidi-font-weight:
+normal'>template TAGS<o:p></o:p></b></p>
+
+<p class=flagheading2>2-SCRIPT_&lt;scriptname&gt;</p>
+
+<p class=flagdescription>Indicates that filename is a script that will be used
+to generate a valid template file. The script will run on a file containing all
+your sequences using the following syntax:</p>
+
+<p class=example2>scriptname &#8211;infile=&lt;your sequences&gt;
+-outfile=&lt;template_file&gt;</p>
+
+<p class=flagdescription>It is also possible to pass some parameters, use @ as
+a separator and # in place of the = sign. For instance, if you want to call the
+a script named blast.pl with the foloowing parameters;</p>
+
+<p class=example2>blast.pl -db=pdb -dir=/local/test</p>
+
+<p class=flagdescription>Use</p>
+
+<p class=example2>SCRIPT_blast.pl@db#pdb@dir#/local/test</p>
+
+<p class=flagdescription>Bear in mind that the input output flags will then be
+concatenated to this command line so that t_coffee ends up calling the program
+using the following system call:</p>
+
+<p class=example2>blast.pl -db=pdb -dir=/local/test -infile=&lt;some tmp
+file&gt; -outfile=&lt;another tmp file&gt;</p>
+
+<p class=flagdescription><o:p>&nbsp;</o:p></p>
+
+<p class=flagheading2>3-SELF_TAG</p>
+
+<p class=flagdescription>TAG can take the value of any of the known TAGS (_S_,
+_G_, _P_). SELF indicates that the original name of the sequence will be used to
+fetch the template: </p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+3d_sample2.fasta &#8211;template_file SELF_P_</p>
+
+</div>
+
+<p class=flagdescription>The previous command will work because the sequences
+in 3d_sample3 are named </p>
+
+<p class=flagheading2>4-SEQFILE_TAG_filename</p>
+
+<p class=flagdescription>Use this flag if your templates are in filename, and
+are named according to the sequences. For instance, if your protein sequences
+have been recoded with Exon/Intron information, you should have the recoded
+sequences names according to the original:</p>
+
+<p class=example2>SEQFILE_G_recodedprotein.fasta<span style='mso-tab-count:
+1'> </span></p>
+
+<p class=flag><a name="_Toc101065316"></a><a name="_Toc102494850"></a><a
+name="_Toc151732376"><span style='mso-bookmark:_Toc102494850'><span
+style='mso-bookmark:_Toc101065316'><span lang=AF>-struc_to_use</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage: -struc_to_use=&lt;struc1, struc2\85&gt;</span></p>
+
+<p class=instruction>Default: -struc_to_use=NULL</p>
+
+<p class=flagdescription>Restricts the 3Dcoffee to a set of pre-defined
+structures.</p>
+
+<h2><a name="_Toc101065317"></a><a name="_Toc102494386"></a><a
+name="_Toc102494851"></a><a name="_Toc151732377"><span style='mso-bookmark:
+_Toc102494851'><span style='mso-bookmark:_Toc102494386'><span style='mso-bookmark:
+_Toc101065317'>Multiple Local Alignments</span></span></span></a></h2>
+
+<p class=MyNormal><span lang=AF>It is possible to compute multiple local
+alignments, using the moca routine. MOCA is a routine that allows extracting
+all the local alignments that show some similarity with another predefined
+fragment.</span></p>
+
+<p class=MyNormal><span lang=AF>'mocca' is a perl script that calls t-coffee
+and provides it with the appropriate parameters.</span></p>
+
+<p class=flag><a name="_Toc101065318"></a><a name="_Toc102494852"></a><a
+name="_Toc151732378"><span style='mso-bookmark:_Toc102494852'><span
+style='mso-bookmark:_Toc101065318'><span lang=AF>-domain</span></span><span
+lang=AF>/-mocca</span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage: -domain</span></p>
+
+<p class=instruction>Default: not set</p>
+
+<p class=flagdescription>This flag indicates that t_coffee will run using the
+domain mode. All the sequences will be concatenated, and the resulting sequence
+will be compared to itself using lalign_rs_s_pair mode (lalign of the sequence
+against itself using keeping the lalign raw score). This step is the most
+computer intensive, and it is advisable to save the resulting file.</p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+-in Ssample_seq1.fasta,Mlalign_rs_s_pair -out_lib=sample_lib1.mocca_lib -domain
+-start=100 -len=50 </p>
+
+</div>
+
+<p class=flagdescription>This instruction will use the fragment 100-150 on the
+concatenated sequences, as a template for the extracted repeats. The extraction
+will only be made once. The library will be placed in the file &lt;lib
+name&gt;.</p>
+
+<p class=flagdescription><o:p>&nbsp;</o:p></p>
+
+<p class=flagdescription>If you want, you can test other coordinates for the
+repeat, such as </p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+-in sample_lib1.mocca_lib -domain -start=100 -len=60 </p>
+
+</div>
+
+<p class=flagdescription>This run will use the fragment 100-160, and will be
+much faster because it does not need to re-compute the lalign library. </p>
+
+<p class=flag><a name="_Toc101065319"></a><a name="_Toc102494853"></a><a
+name="_Toc151732379"><span style='mso-bookmark:_Toc102494853'><span
+style='mso-bookmark:_Toc101065319'><span lang=AF>-start</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage: -start=&lt;int value&gt;</span></p>
+
+<p class=instruction>Default: not set</p>
+
+<p class=flagdescription>This flag indicates the starting position of the
+portion of sequence that will be used as a template for the repeat extraction.
+The value assumes that all the sequences have been concatenated, and is given
+on the resulting sequence.</p>
+
+<p class=flag><a name="_Toc101065320"></a><a name="_Toc102494854"></a><a
+name="_Toc151732380"><span style='mso-bookmark:_Toc102494854'><span
+style='mso-bookmark:_Toc101065320'><span lang=AF>-len</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage: -len=&lt;int value&gt;</span></p>
+
+<p class=instruction>Default: not set</p>
+
+<p class=flagdescription>This flag indicates the length of the portion of
+sequence that will be used as a template.</p>
+
+<p class=flag><a name="_Toc101065321"></a><a name="_Toc102494855"></a><a
+name="_Toc151732381"><span style='mso-bookmark:_Toc102494855'><span
+style='mso-bookmark:_Toc101065321'><span lang=AF>-scale</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage: -scale=&lt;int value&gt;</span></p>
+
+<p class=instruction>Default: -scale=-100</p>
+
+<p class=flagdescription>This flag indicates the value of the threshold for
+extracting the repeats. The actual threshold is equal to:</p>
+
+<p class=flagdescription><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>motif_len*scale</p>
+
+<p class=flagdescription>Increase the scale <span style='font-family:Wingdings;
+mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman";
+mso-char-type:symbol;mso-symbol-font-family:Wingdings'><span style='mso-char-type:
+symbol;mso-symbol-font-family:Wingdings'>ó</span></span>Increase sensitivity <span
+style='font-family:Wingdings;mso-ascii-font-family:"Times New Roman";
+mso-hansi-font-family:"Times New Roman";mso-char-type:symbol;mso-symbol-font-family:
+Wingdings'><span style='mso-char-type:symbol;mso-symbol-font-family:Wingdings'>ó</span></span>
+More alignments( i.e. -50).</p>
+
+<p class=flag><a name="_Toc101065322"></a><a name="_Toc102494856"></a><a
+name="_Toc151732382"><span style='mso-bookmark:_Toc102494856'><span
+style='mso-bookmark:_Toc101065322'><span lang=AF>-domain_interactive [Examples]</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage: -domain_interactive</span></p>
+
+<p class=instruction>Default: unset</p>
+
+<p class=flagdescription>Launches an interactive mocca session.</p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+-in Lsample_lib3.tc_lib,Mlalign_rs_s_pair -domain -start=100 -len=60</p>
+
+</div>
+
+<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
+mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
+background:#E6E6E6;margin-left:0cm;margin-right:1.0cm'>
+
+<p class=examplefilesmallCxSpFirst>TOLB_ECOLI_212_26<span style='mso-tab-count:
+3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp; </span>211 SKLAYVTFESGR--SALVIQTLANGAVRQV-ASFPRHNGAPAFSPDGSKLAFA</p>
+
+<p class=examplefilesmallCxSpMiddle>TOLB_ECOLI_165_218<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp; </span>164
+TRIAYVVQTNGGQFPYELRVSDYDGYNQFVVHRSPQPLMSPAWSPDGSKLAYV</p>
+
+<p class=examplefilesmallCxSpMiddle>TOLB_ECOLI_256_306<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp; </span>255
+SKLAFALSKTGS--LNLYVMDLASGQIRQV-TDGRSNNTEPTWFPDSQNLAFT</p>
+
+<p class=examplefilesmallCxSpMiddle>TOLB_ECOLI_307_350<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp; </span>306 -------DQAGR--PQVYKVNINGGAPQRI-TWEGSQNQDADVSSDGKFMVMV</p>
+
+<p class=examplefilesmallCxSpMiddle>TOLB_ECOLI_351_393<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp; </span>350
+-------SNGGQ--QHIAKQDLATGGV-QV-LSSTFLDETPSLAPNGTMVIYS<span style="mso-spacerun:
+yes">&nbsp; </span></p>
+
+<p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>1<span style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>*<span
+style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>*<span style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp; </span>:<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>.<span style="mso-spacerun: yes">&nbsp;&nbsp; </span>.:.<span
+style="mso-spacerun: yes">&nbsp; </span>:<span style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp; </span></p>
+
+<p class=examplefilesmallCxSpMiddle><o:p>&nbsp;</o:p></p>
+
+<p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>MENU: Type Letter
+Flag[number] and Return: ex |10</p>
+
+<p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>|x<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>--&gt;Set<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp; </span>the START to x</p>
+
+<p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>&gt;x<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>--&gt;Set<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp; </span>the LEN<span
+style="mso-spacerun: yes">&nbsp;&nbsp; </span>to x</p>
+
+<p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Cx<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>--&gt;Set<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp; </span>the sCale to x</p>
+
+<p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Sname<span
+style="mso-spacerun: yes">&nbsp;&nbsp; </span>--&gt;Save<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp; </span>the<span
+style="mso-spacerun: yes">&nbsp; </span>Alignment </p>
+
+<p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Bx<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>--&gt;Save<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp; </span>Goes back x it </p>
+
+<p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>return<span
+style="mso-spacerun: yes">&nbsp; </span>--&gt;Compute the<span
+style="mso-spacerun: yes">&nbsp; </span>Alignment</p>
+
+<p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>X<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>--&gt;eXit</p>
+
+<p class=examplefilesmallCxSpMiddle><o:p>&nbsp;</o:p></p>
+
+<p class=examplefilesmallCxSpMiddle>[ITERATION<span style="mso-spacerun:
+yes">&nbsp;&nbsp; </span>1] [START=211] [LEN= 50] [SCALE=-100]<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>YOUR CHOICE:</p>
+
+<p class=examplefilesmallCxSpMiddle>For instance, to set the length of the
+domain to 40, type: </p>
+
+<p class=examplefilesmallCxSpMiddle><o:p>&nbsp;</o:p></p>
+
+<p class=examplefilesmallCxSpMiddle>[ITERATION<span style="mso-spacerun:
+yes">&nbsp;&nbsp; </span>1] [START=211] [LEN= 50] [SCALE=-100]<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>YOUR
+CHOICE:&gt;40[return]</p>
+
+<p class=examplefilesmallCxSpMiddle>[return]</p>
+
+<p class=examplefilesmallCxSpMiddle><o:p>&nbsp;</o:p></p>
+
+<p class=examplefilesmallCxSpMiddle>Which will generate:</p>
+
+<p class=examplefilesmallCxSpMiddle><o:p>&nbsp;</o:p></p>
+
+<p class=examplefilesmallCxSpMiddle>TOLB_ECOLI_212_252<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp; </span>211
+SKLAYVTFESGRSALVIQTLANGAVRQVASFPRHNGAPAF<span style="mso-spacerun: yes">&nbsp;
+</span>251</p>
+
+<p class=examplefilesmallCxSpMiddle>TOLB_ECOLI_256_296<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp; </span>255
+SKLAFALSKTGSLNLYVMDLASGQIRQVTDGRSNNTEPTW<span style="mso-spacerun: yes">&nbsp;
+</span>295</p>
+
+<p class=examplefilesmallCxSpMiddle>TOLB_ECOLI_300_340<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp; </span>299
+QNLAFTSDQAGRPQVYKVNINGGAPQRITWEGSQNQDADV<span style="mso-spacerun: yes">&nbsp;
+</span>339</p>
+
+<p class=examplefilesmallCxSpMiddle>TOLB_ECOLI_344_383<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp; </span>343 KFMVMVSSNGGQQHIAKQDLATGGV-QVLSSTFLDETPSL<span
+style="mso-spacerun: yes">&nbsp; </span>382</p>
+
+<p class=examplefilesmallCxSpMiddle>TOLB_ECOLI_387_427<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp; </span>386
+TMVIYSSSQGMGSVLNLVSTDGRFKARLPATDGQVKFPAW<span style="mso-spacerun: yes">&nbsp;
+</span>426</p>
+
+<p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>1<span style="mso-spacerun: yes">&nbsp;&nbsp; </span>:<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp; </span>:<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp; </span>:<span
+style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>::<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>.<span style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp; </span>40</p>
+
+<p class=examplefilesmallCxSpMiddle><o:p>&nbsp;</o:p></p>
+
+<p class=examplefilesmallCxSpMiddle><o:p>&nbsp;</o:p></p>
+
+<p class=examplefilesmallCxSpMiddle><o:p>&nbsp;</o:p></p>
+
+<p class=examplefilesmallCxSpMiddle><o:p>&nbsp;</o:p></p>
+
+<p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>MENU: Type Letter
+Flag[number] and Return: ex |10</p>
+
+<p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span style="mso-spacerun:
+yes">&nbsp;&nbsp;</span>|x<span style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>--&gt;Set<span style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp; </span>the START to x</p>
+
+<p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>&gt;x<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>--&gt;Set<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp; </span>the LEN<span
+style="mso-spacerun: yes">&nbsp;&nbsp; </span>to x</p>
+
+<p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Cx<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>--&gt;Set<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp; </span>the sCale to x</p>
+
+<p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Sname<span
+style="mso-spacerun: yes">&nbsp;&nbsp; </span>--&gt;Save<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp; </span>the<span
+style="mso-spacerun: yes">&nbsp; </span>Alignment </p>
+
+<p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Bx<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>--&gt;Save<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp; </span>Goes back x it </p>
+
+<p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>return<span
+style="mso-spacerun: yes">&nbsp; </span>--&gt;Compute the<span
+style="mso-spacerun: yes">&nbsp; </span>Alignment</p>
+
+<p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>X<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span>--&gt;eXit</p>
+
+<p class=examplefilesmallCxSpMiddle><o:p>&nbsp;</o:p></p>
+
+<p class=examplefilesmallCxSpLast>[ITERATION<span style="mso-spacerun:
+yes">&nbsp;&nbsp; </span>3] [START=211] [LEN= 40] [SCALE=-100]<span
+style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>YOUR CHOICE: </p>
+
+</div>
+
+<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
+
+<p class=flagdescription>If you want to indicate the coordinates, relative to a
+specific sequence, type:</p>
+
+<p class=example2><span style='mso-tab-count:1'>&nbsp; </span>|&lt;seq_name&gt;:start</p>
+
+<p class=flagdescription>Type S&lt;your name&gt; to save the current alignment,
+and extract a new motif. </p>
+
+<p class=flagdescription>Type X when you are done.</p>
+
+<h2><a name="_Toc101065323"></a><a name="_Toc102494387"></a><a
+name="_Toc102494857"></a><a name="_Toc151732383"><span style='mso-bookmark:
+_Toc102494857'><span style='mso-bookmark:_Toc102494387'><span style='mso-bookmark:
+_Toc101065323'>Output Control</span></span></span></a></h2>
+
+<h3><a name="_Toc101065324"></a><a name="_Toc102494388"></a><a
+name="_Toc102494858"></a><a name="_Toc151732384"><span style='mso-bookmark:
+_Toc102494858'><span style='mso-bookmark:_Toc102494388'><span style='mso-bookmark:
+_Toc101065324'>Generic</span></span></span></a></h3>
+
+<p class=flag><a name="_Toc102494859"></a><a name="_Toc151732385"><span
+style='mso-bookmark:_Toc102494859'><span lang=AF>Conventions Regarding
+Filenames</span></span></a></p>
+
+<p class=MyNormal><span lang=AF>stdout, stderr, stdin, no, /dev/null are valid
+filenames. They cause the corresponding file to be output in stderr or stdout,
+for an input file, stdin causes the program to requests the corresponding file
+through pipe. No causes a suppression of the output, as does /dev/null.</span></p>
+
+<p class=flag><a name="_Toc102494860"></a><a name="_Toc151732386"><span
+style='mso-bookmark:_Toc102494860'><span lang=AF>Identifying the Output files
+automatically</span></span></a></p>
+
+<p class=MyNormal><span lang=AF>In the t_coffee output, each output appears in
+a line:</span></p>
+
+<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
+mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
+background:#E6E6E6'>
+
+<p class=examplefile>##### FILENAME &lt;name&gt; TYPE &lt;Type&gt; FORMAT
+&lt;Format&gt;</p>
+
+</div>
+
+<p class=flag><a name="_Toc101065325"></a><a name="_Toc102494389"></a><a
+name="_Toc102494861"></a><a name="_Toc151732387"><span style='mso-bookmark:
+_Toc102494861'><span style='mso-bookmark:_Toc102494389'><span style='mso-bookmark:
+_Toc101065325'><span lang=AF>-no_warning</span></span></span></span></a><span
+style='mso-bookmark:_Toc102494861'><span style='mso-bookmark:_Toc102494389'><span
+style='mso-bookmark:_Toc101065325'></span></span></span></p>
+
+<p class=flagusage><span style='mso-bookmark:_Toc102494861'><span
+style='mso-bookmark:_Toc102494389'><span style='mso-bookmark:_Toc101065325'><span
+lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp; </span>-no_warning</span></span></span></span></p>
+
+<p class=instruction><span style='mso-bookmark:_Toc102494861'><span
+style='mso-bookmark:_Toc102494389'><span style='mso-bookmark:_Toc101065325'>Default:
+Switched off</span></span></span></p>
+
+<p class=flagdescription><span style='mso-bookmark:_Toc102494861'><span
+style='mso-bookmark:_Toc102494389'><span style='mso-bookmark:_Toc101065325'>Suppresseswarning
+output.<i style='mso-bidi-font-style:normal'><o:p></o:p></i></span></span></span></p>
+
+<h3><span style='mso-bookmark:_Toc102494861'><span style='mso-bookmark:_Toc102494389'><span
+style='mso-bookmark:_Toc101065325'><o:p>&nbsp;</o:p></span></span></span></h3>
+
+<h3><span style='mso-bookmark:_Toc102494861'><span style='mso-bookmark:_Toc102494389'><span
+style='mso-bookmark:_Toc101065325'><a name="_Toc151732388">Alignments</a></span></span></span></h3>
+
+<p class=flag><a name="_Toc101065326"></a><a name="_Toc102494862"></a><a
+name="_Toc151732389"><span style='mso-bookmark:_Toc102494862'><span
+style='mso-bookmark:_Toc101065326'><span lang=AF>-outfile</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
+</span>-outfile=&lt;out_aln file,default,no&gt;</span></p>
+
+<p class=MyNormal><span lang=AF>Defau</span><!--[if supportFields]><span
+lang=AF><span style='mso-element:field-begin'></span> TOC \o &quot;1-1&quot; <span
+style='mso-element:field-separator'></span></span><![endif]--><span lang=AF><b
+style='mso-bidi-font-weight:normal'><span style='mso-no-proof:yes'>Word did not
+find any entries for your table of contents.</span></b></span><!--[if supportFields]><span
+lang=AF><span style='mso-element:field-end'></span></span><![endif]--><span
+lang=AF>lt:-outfile=default</span></p>
+
+<p class=flagdescription>Indicates the name of the alignment output by
+t_coffee. If the default is used, the alignment is named <i style='mso-bidi-font-style:
+normal'>&lt;your sequences&gt;.aln<o:p></o:p></i></p>
+
+<p class=flag><a name="_Toc101065327"></a><a name="_Toc102494863"></a><a
+name="_Toc151732390"><span style='mso-bookmark:_Toc102494863'><span
+style='mso-bookmark:_Toc101065327'><span lang=AF>-output</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
+</span>-output=&lt;format1,format2,...&gt; </span></p>
+
+<p class=instruction>Default:-output=clustalw</p>
+
+<p class=flagdescription>Indicates the format used for outputting the -outfile.</p>
+
+<p class=flagdescription>Supported formats are:</p>
+
+<p class=flagdescription><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></p>
+
+<p class=flagdescriptionid1>clustalw_aln, clustalw<span style='mso-tab-count:
+1'>&nbsp;&nbsp;&nbsp;&nbsp; </span>: ClustalW format.</p>
+
+<p class=flagdescriptionid1>gcg, msf_aln<span style="mso-spacerun:
+yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>:
+MSF alignment.</p>
+
+<p class=flagdescriptionid1>pir_aln<span style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>:
+pir alignment.</p>
+
+<p class=flagdescriptionid1>fasta_aln<span style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>:
+fasta alignment.</p>
+
+<p class=flagdescriptionid1>phylip<span style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>:
+Phylip format.</p>
+
+<p class=flagdescriptionid1>pir_seq<span style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>:
+pir sequences (no gap).</p>
+
+<p class=flagdescriptionid1>fasta_seq<span style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>:
+fasta sequences (no gap).</p>
+
+<p class=flagdescription><span style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></p>
+
+<p class=flagdescription>As well as:</p>
+
+<p class=flagdescription><o:p>&nbsp;</o:p></p>
+
+<p class=flagdescriptionid1>score_ascii<span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>:
+causes the output of a reliability flag </p>
+
+<p class=flagdescriptionid1>score_html<span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>:
+causes the output to be a reliability plot in HTML</p>
+
+<p class=flagdescriptionid1>score_pdf<span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>:
+idem in PDF (if ps2pdf is installed on your system).</p>
+
+<p class=flagdescriptionid1>score_ps<span style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>:
+idem in postscript.</p>
+
+<p class=flagdescription><o:p>&nbsp;</o:p></p>
+
+<p class=flagdescription>More than one format can be indicated:</p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+sample_seq1.fasta -output=clustalw,gcg, score_html </p>
+
+</div>
+
+<p class=flagdescription>A publication describing the CORE index is available
+on:</p>
+
+<p class=MyNormal><span lang=AF><a
+href="http://www.tcoffee.org/Publications/Pdf/core.pp.pdf"><span lang=EN-US
+style='mso-ansi-language:EN-US'>http://www.tcoffee.org/Publications/Pdf/core.pp.pdf</span></a></span></p>
+
+<p class=flag><a name="_Toc101065328"></a><a name="_Toc102494864"></a><a
+name="_Toc151732391"><span style='mso-bookmark:_Toc102494864'><span
+style='mso-bookmark:_Toc101065328'><span lang=AF>-outseqweight</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
+</span>-outseqweight=&lt;filename&gt;</span></p>
+
+<p class=instruction>Default: not used</p>
+
+<p class=flagdescription>Indicates the name of the file in which the sequences
+weights should be saved..</p>
+
+<p class=flag><a name="_Toc101065329"></a><a name="_Toc102494865"></a><a
+name="_Toc151732392"><span style='mso-bookmark:_Toc102494865'><span
+style='mso-bookmark:_Toc101065329'><span lang=AF>-case</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
+</span>-case=&lt;keep,upper,lower&gt;</span></p>
+
+<p class=instruction>Default: -case=keep</p>
+
+<p class=MyNormal><span lang=AF>Instructs the program on the case to be used in
+the output file (Clustalw uses upper case). The default keeps the case and
+makes it possible to maintain a mixture of upper and lower case residues.</span></p>
+
+<p class=MyNormal><span lang=AF>If you need to change the case of your file,
+you can use seq_reformat:</span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+&#8211;other_pg seq_reformat &#8211;in sample_aln1.aln &#8211;action +lower
+&#8211;output clustalw </p>
+
+</div>
+
+<p class=flag><a name="_Toc101065330"></a><a name="_Toc102494866"></a><a
+name="_Toc151732393"><span style='mso-bookmark:_Toc102494866'><span
+style='mso-bookmark:_Toc101065330'><span lang=AF>-cpu</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
+</span>deprecated</span></p>
+
+<p class=flag><a name="_Toc102494867"></a><a name="_Toc151732394"><span
+style='mso-bookmark:_Toc102494867'><span lang=AF>-outseqweight</span></span></a></p>
+
+<p class=MyNormal><span lang=AF>Usage: -outseqweight=&lt;name of the file
+containing the weights applied&gt;</span></p>
+
+<p class=MyNormal><span lang=AF>Default: -outseqweight=no</span></p>
+
+<p class=MyNormal><span lang=AF>Will cause the program to output the weights
+associated with every sequence in the dataset.</span></p>
+
+<p class=flag><a name="_Toc101065331"></a><a name="_Toc102494868"></a><a
+name="_Toc151732395"><span style='mso-bookmark:_Toc102494868'><span
+style='mso-bookmark:_Toc101065331'><span lang=AF>-outorder [cw]</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
+</span>-outorder=&lt;input OR aligned OR filename&gt; </span></p>
+
+<p class=instruction>Default:-outorder=input</p>
+
+<p class=flagdescription>Sets the order of the sequences in the output
+alignment: <b>-outorder=input</b> means the sequences are kept in the original
+order. <b>-outorder=aligned</b> means the sequences come in the order indicated
+by the tree. This order can be seen as a one-dimensional projection of the tree
+distances. <b style='mso-bidi-font-weight:normal'>&#8211;outdorder=&lt;filename&gt;</b>Filename
+is a legal fasta file, whose order will be used in the final alignment.</p>
+
+<p class=flag><a name="_Toc151732396"><span lang=AF>-inorder [cw]</span></a></p>
+
+<p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
+</span>-inorder=&lt;input OR aligned&gt; </span></p>
+
+<p class=instruction>Default:-inorder=aligned</p>
+
+<p class=flagdescription>Multiple alignments based on dynamic programming
+depend slightly on the order in which the incoming sequences are provided. To
+prevent this effect sequences are arbitrarily sorted at the beginning of the
+program (-inorder=aligned). However, this affects the sequence order within the
+library. You can switch this off by ststing &#8211;inorder=input.</p>
+
+<p class=flag><a name="_Toc102494869"></a><a name="_Toc151732397"><span
+style='mso-bookmark:_Toc102494869'><span lang=AF>-seqnos</span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
+</span>-seqnos=&lt;on or off&gt; </span></p>
+
+<p class=instruction>Default:-seqnos=off</p>
+
+<p class=MyNormal><span lang=AF>Causes the output alignment to contain residue
+numbers at the end of each line:</span></p>
+
+<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
+mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
+background:#E6E6E6'>
+
+<p class=examplefileCxSpFirst>T-COFFEE</p>
+
+<p class=examplefileCxSpMiddle>seq1 aaa---aaaa--------aa 9</p>
+
+<p class=examplefileCxSpMiddle>seq2 a-----aa-----------a 4</p>
+
+<p class=examplefileCxSpMiddle><o:p>&nbsp;</o:p></p>
+
+<p class=examplefileCxSpMiddle>seq1 a-----------------a 11</p>
+
+<p class=examplefileCxSpLast>seq2 aaaaaaaaaaaaaaaaaaa 19</p>
+
+</div>
+
+<h3><a name="_Toc101065332"></a><a name="_Toc102494390"></a><a
+name="_Toc102494870"></a><a name="_Toc151732398"><span style='mso-bookmark:
+_Toc102494870'><span style='mso-bookmark:_Toc102494390'><span style='mso-bookmark:
+_Toc101065332'>Libraries</span></span></span></a></h3>
+
+<p class=MyNormal><span lang=AF>Although, it does not necessarily do so
+explicitly, T-Coffee always end up combining libraries. Libraries are
+collections of pairs of residues. Given a set of libraries, T-Coffee makes an
+attempt to assemble the alignment with the highest level of consistence. You
+can think of the alignment as a timetable. Each library pair would be a request
+from students or teachers, and the job of T-Coffee would be to assemble the
+time table that makes as many people as possible happy\85</span></p>
+
+<p class=flag><a name="_Toc102494871"></a><a name="_Toc151732399"><span
+style='mso-bookmark:_Toc102494871'><span lang=AF>-out_lib</span></span></a></p>
+
+<p class=MyNormal><span lang=AF>Usage:<span style="mso-spacerun: yes">&nbsp;
+</span>-out_lib=&lt;name of the library,default,no&gt; </span></p>
+
+<p class=MyNormal><span lang=AF>Default:-out_lib=default</span></p>
+
+<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
+
+<p class=flagdescription>Sets the name of the library output. Default implies
+&lt;run_name&gt;.tc_lib</p>
+
+<p class=flag><a name="_Toc101065333"></a><a name="_Toc102494872"></a><a
+name="_Toc151732400"><span style='mso-bookmark:_Toc102494872'><span
+style='mso-bookmark:_Toc101065333'><span lang=AF>-lib_only</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
+</span>-lib_only</span></p>
+
+<p class=instruction>Default: unset</p>
+
+<p class=flagdescription>Causes the program to stop once the library has been
+computed. Must be used in conjunction with the flag <b style='mso-bidi-font-weight:
+normal'>&#8211;out_lib</b></p>
+
+<h3><a name="_Toc101065334"></a><a name="_Toc102494391"></a><a
+name="_Toc102494873"></a><a name="_Toc151732401"><span style='mso-bookmark:
+_Toc102494873'><span style='mso-bookmark:_Toc102494391'><span style='mso-bookmark:
+_Toc101065334'>Trees</span></span></span></a></h3>
+
+<p class=flag><a name="_Toc101065335"></a><a name="_Toc102494874"></a><a
+name="_Toc151732402"><span style='mso-bookmark:_Toc102494874'><span
+style='mso-bookmark:_Toc101065335'><span lang=AF>-newtree</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage: -newtree=&lt;tree file&gt;</span></p>
+
+<p class=instruction>Default: No file specified</p>
+
+<p class=flagdescription>Indicates the name of the file into which the guide
+tree will be written. The default will be &lt;sequence_name&gt;.dnd, or
+&lt;run_name.dnd&gt;. The tree is written in the parenthesis format known as
+newick or New Hampshire and used by Phylips (see the format section).</p>
+
+<div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
+padding:0cm 0cm 0cm 0cm;background:#F7CBB7'>
+
+<p class=Warning>Do NOT confuse this guide tree with a phylogenetic tree.</p>
+
+</div>
+
+<h2><a name="_Toc101065336"></a><a name="_Toc102494392"></a><a
+name="_Toc102494875"></a><a name="_Toc151732403"><span style='mso-bookmark:
+_Toc102494875'><span style='mso-bookmark:_Toc102494392'><span style='mso-bookmark:
+_Toc101065336'>Reliability Estimation</span></span></span></a></h2>
+
+<h3><a name="_Toc101065337"></a><a name="_Toc102494393"></a><a
+name="_Toc102494876"></a><a name="_Toc151732404"><span style='mso-bookmark:
+_Toc102494876'><span style='mso-bookmark:_Toc102494393'><span style='mso-bookmark:
+_Toc101065337'>CORE Computation</span></span></span></a></h3>
+
+<p class=MyNormal><span lang=AF>The CORE is an index that indicates the
+consistency between the library of piarwise alignments and the final multiple
+alignment. Our experiment indicate that the higher this consistency, the more
+reliable the alignment. A publication describing the CORE index can be found
+on:</span></p>
+
+<p class=MyNormal><a name="_Toc101065338"></a><a name="_Toc102494877"><span
+style='mso-bookmark:_Toc101065338'></span></a><a
+href="http://www.tcoffee.org/Publications/Pdf/core.pp.pdf"><span
+style='mso-bookmark:_Toc102494877'><span style='mso-bookmark:_Toc101065338'><span
+style='mso-ansi-language:EN-US'>http://www.tcoffee.org/Publications/Pdf/core.pp.pdf</span></span></span><span
+style='mso-bookmark:_Toc102494877'><span style='mso-bookmark:_Toc101065338'></span></span></a><span
+style='mso-bookmark:_Toc102494877'><span style='mso-bookmark:_Toc101065338'></span></span></p>
+
+<p class=flag><span style='mso-bookmark:_Toc102494877'><span style='mso-bookmark:
+_Toc101065338'><a name="_Toc151732405"><span lang=AF>-evaluate_mode</span></a></span></span></p>
+
+<p class=flagusage><span lang=FR>Usage:
+-evaluate_mode=&lt;t_coffee_fast,t_coffee_slow,t_coffee_non_extended &gt;</span></p>
+
+<p class=instruction>Default: -evaluate_mode=t_coffee_fast</p>
+
+<p class=flagdescription>This flag indicates the mode used to normalize the
+t_coffee score when computing the reliability score. </p>
+
+<p class=flagdescription><i style='mso-bidi-font-style:normal'>t_coffee_fast</i>:
+Normalization is made using the highest score in the MSA. This evaluation mode
+was validated and in our hands, pairs of residues with a score of 5 or higher
+have 90 % chances to be correctly aligned to one another. </p>
+
+<p class=flagdescription><i style='mso-bidi-font-style:normal'>t_coffee_slow:</i>
+Normalization is made using the library. This usually results in lower score
+and a scoring scheme more sensitive to the number of sequences in the dataset.
+Note that this scoring scheme is not any more slower, thanks to the
+implementation of a faster heuristic algorithm. </p>
+
+<p class=flagdescription><i style='mso-bidi-font-style:normal'>t_coffee_non_extended:</i>
+the score of each residue is the ratio between the sum of its non extended
+scores with the column and the sum of all its possible non extended scores.</p>
+
+<p class=flagdescription>These modes will be useful when generating colored
+version of the output, with the <b style='mso-bidi-font-weight:normal'>&#8211;output</b>
+flag:</p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+sample_seq1.fasta &#8211;evaluate_mode t_coffee_slow &#8211;output score_ascii,
+score_html </p>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+sample_seq1.fasta &#8211;evaluate_mode t_coffee_fast &#8211;output score_ascii,
+score_html </p>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+sample_seq1.fasta &#8211;evaluate_mode t_coffee_non_extended &#8211;output
+score_ascii, score_html </p>
+
+</div>
+
+<h2><a name="_Toc101065339"></a><a name="_Toc102494394"></a><a
+name="_Toc102494878"></a><a name="_Toc151732406"><span style='mso-bookmark:
+_Toc102494878'><span style='mso-bookmark:_Toc102494394'><span style='mso-bookmark:
+_Toc101065339'>Generic Output</span></span></span></a></h2>
+
+<p class=flag><a name="_Toc102494879"></a><a name="_Toc151732407"><span
+style='mso-bookmark:_Toc102494879'><span lang=AF>-run_name</span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage: -run_name=&lt;your run name&gt;</span></p>
+
+<p class=instruction>Default: no default set</p>
+
+<p class=MyNormal><span lang=AF>This flag causes the prefix &lt;your
+sequences&gt; to be replaced by &lt;your run name&gt; when renaming the default
+output files.</span></p>
+
+<p class=flag><a name="_Toc101065340"></a><a name="_Toc102494880"></a><a
+name="_Toc151732408"><span style='mso-bookmark:_Toc102494880'><span
+style='mso-bookmark:_Toc101065340'><span lang=AF>-quiet</span></span></span></a></p>
+
+<p class=flagusage><span lang=FR>Usage: -quiet=&lt;stderr,stdout,file name OR
+nothing&gt;.</span></p>
+
+<p class=instruction>Default:-quiet=stderr</p>
+
+<p class=flagdescription>Redirects the standard output to either a file. <b>-quiet</b>
+on its own redirect the output to /dev/null.</p>
+
+<p class=flag><a name="_Toc102494881"></a><a name="_Toc151732409"><span
+style='mso-bookmark:_Toc102494881'><span lang=AF>-align [CW]</span></span></a></p>
+
+<p class=MyNormal><span lang=AF>This flag indicates that the program must
+produce the alignment. It is here for compatibility with ClustalW.</span></p>
+
+<h2><a name="_Toc151732410">APDB, iRMSD and tRMSD Parameters</a></h2>
+
+<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
+
+<div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
+padding:0cm 0cm 0cm 0cm;background:#F7CBB7'>
+
+<p class=Warning>Warning: These flags will only work within the APDB package
+that can be invoked via the &#8211;other_pg parameter of T-Coffee:</p>
+
+<p class=Warning><span style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span
+style="mso-spacerun: yes">&nbsp;</span>t_coffee &#8211;other_pg apdb &#8211;aln
+&lt;your aln&gt;</p>
+
+<p class=Warning><o:p>&nbsp;</o:p></p>
+
+</div>
+
+<p class=flag><a name="_Toc151732411"><span lang=AF>-quiet [Same as T-Coffee]</span></a></p>
+
+<p class=flag><a name="_Toc151732412"><span lang=AF>-run_name [Same as
+T-Coffee]</span></a></p>
+
+<p class=flag><a name="_Toc151732413"><span lang=AF>-aln</span></a></p>
+
+<p class=flagusage><span lang=FR>Usage: -aln=&lt;file_name&gt;.</span></p>
+
+<p class=instruction>Default:none</p>
+
+<p class=flagdescription>Indicates the name of the file containing the
+sequences that need to be evaluated. The sequences whose structure is meant to
+be used must be named according to their PDB identifier. </p>
+
+<p class=flagdescription>The format can be FASTA, CLUSTAL or any of the formats
+supported by T-Coffee. APDB only evaluates residues in capital and ignores
+those in lower case. If your sequences are in lower case, you can upper case
+them using seq_reformat:</p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+&#8211;other_pg seq_reformat &#8211;in 3d_sample4.aln &#8211;action +upper
+&#8211;output clustalw &gt; 3d_sample4.cw_aln</p>
+
+</div>
+
+<p class=flagdescription>The alignment can then be evaluated using the defaultr
+of APDB:</p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+&#8211;other_pg apdb &#8211;aln 3d_sample4.aln</p>
+
+</div>
+
+<p class=flagdescription>The alignment can contain as many structures as you
+wish.</p>
+
+<p class=flag><a name="_Toc151732414"><span lang=AF>-n_excluded_nb</span></a></p>
+
+<p class=flagusage><span lang=FR>Usage: -n_excluded_nb=&lt;integer&gt;.</span></p>
+
+<p class=instruction>Default:1</p>
+
+<p class=flagdescription>When evaluating the local score of a pair of aligned
+residues, the residues immediately next to that column should not contribute to
+the measure. By default the first to the left and first to the right are
+excluded.</p>
+
+<p class=flag><a name="_Toc151732415"><span lang=AF>-maximum_distance</span></a></p>
+
+<p class=flagusage><span lang=FR>Usage: -maximum_distance=&lt;float&gt;.</span></p>
+
+<p class=instruction>Default:10</p>
+
+<p class=flagdescription>Size of the neighborhood considered around every
+residue. If .-local_mode is set to sphere, -maximum_distance is the radius of a
+sphere centered around each residue. If &#8211;local_mode is set to window,
+then &#8211;maximum_distance is the size of the half window (i.e. window_size=-maximum_distance*2+1).</p>
+
+<p class=flag><a name="_Toc151732416"><span lang=AF>-similarity_threshold</span></a></p>
+
+<p class=flagusage><span lang=FR>Usage: -similarity_threshold=&lt;integer&gt;.</span></p>
+
+<p class=instruction>Default:70</p>
+
+<p class=flagdescription>Fraction of the neighborhood that must be supportive
+for a pair of residue to be considered correct in APDB. The neighborhood is a
+sphere defined by &#8211;maximum_distance, and the support is defined by
+&#8211;md_threshold.</p>
+
+<p class=flag><a name="_Toc151732417"><span lang=AF>-local_mode</span></a></p>
+
+<p class=flagusage><span lang=FR>Usage: -local_mode=&lt;sphere,window&gt;.</span></p>
+
+<p class=instruction>Default:sphere</p>
+
+<p class=flagdescription>Defines the shape of a neighborhood, either as a
+sphere or as a window.</p>
+
+<p class=flag><a name="_Toc151732418"><span lang=AF>-filter</span></a></p>
+
+<p class=flagusage><span lang=FR>Usage: -filter=&lt;0.00-1.00&gt;.</span></p>
+
+<p class=instruction>Default:1.00</p>
+
+<p class=flagdescription>Defines the centiles that should be kept when making
+the local measure. Foir instance, -filter=0.90 means that the the 10 last
+centiles will be removed from the evaluation. The filtration is carried out on
+the iRMSD values.</p>
+
+<p class=flag><a name="_Toc151732419"><span lang=AF>-print_rapdb [Unsupported]</span></a></p>
+
+<p class=flagusage><span lang=FR>Usage: -print_rapdb (FLAG)</span></p>
+
+<p class=instruction>Default:off</p>
+
+<p class=flagdescription>This causes the prints out of the exact neighborhood
+of every considered pair of residues.</p>
+
+<p class=flag><a name="_Toc151732420"><span lang=AF>-outfile [Same as T-Coffee]</span></a></p>
+
+<p class=MyNormal><span lang=AF>This flag is meant to control the output name
+of the colored APDB output. This file will either display the local APDB score
+or the local iRMD, depending on the value of &#8211;color_mode. The default
+format is defined by &#8211;ouptut and is score_html.</span></p>
+
+<p class=flag><a name="_Toc151732421"><span lang=AF>-color_mode</span></a></p>
+
+<p class=flagusage><span lang=FR>Usage: -color_mode=&lt;apdb, irmsd&gt;</span></p>
+
+<p class=instruction>Default:apdb</p>
+
+<p class=MyNormal><span lang=AF>This flag is meant to control the colored APDB
+output (local score). This file will either display the local APDB score or the
+local iRMD.</span></p>
+
+<div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
+padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0cm;margin-right:
+4.25pt'>
+
+<p class=ChapterTitle>Building a Server</p>
+
+</div>
+
+<p class=MyNormal><span lang=AF>We maintain a T-Coffee server
+(www.tcoffee.org). We will be pleased to provide anyone who wants to set up a
+similar service with the sources</span></p>
+
+<h3><a name="_Toc102494396"></a><a name="_Toc102494884"></a><a
+name="_Toc151732422"><span style='mso-bookmark:_Toc102494884'><span
+style='mso-bookmark:_Toc102494396'>Environment Variables</span></span></a><span
+style='mso-bookmark:_Toc102494884'><span style='mso-bookmark:_Toc102494396'></span></span></h3>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494884'><span
+style='mso-bookmark:_Toc102494396'><span lang=AF>T-Coffee stores a lots of
+information in locations that may be unsuitable when running a server. </span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494884'><span
+style='mso-bookmark:_Toc102494396'><span lang=AF>By default, T-Coffee will
+generate and rely on the follwing directory structure:</span></span></span></p>
+
+<p class=example><span style='mso-bookmark:_Toc102494884'><span
+style='mso-bookmark:_Toc102494396'>/home/youraccount/<span style='mso-tab-count:
+2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>#HOME_4_TCOFFEE</span></span></p>
+
+<p class=example><span style='mso-bookmark:_Toc102494884'><span
+style='mso-bookmark:_Toc102494396'>HOME_4_TCOFFEE/.t_coffee/ <span
+style='mso-tab-count:1'>&nbsp; </span>#DIR_4_TCOFFEE</span></span></p>
+
+<p class=example><span style='mso-bookmark:_Toc102494884'><span
+style='mso-bookmark:_Toc102494396'>DIR_4_TCOFFEE/cache<span style='mso-tab-count:
+2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>#CACHE_4_TCOFFEE</span></span></p>
+
+<p class=example><span style='mso-bookmark:_Toc102494884'><span
+style='mso-bookmark:_Toc102494396'>DIR_4_TCOFFEE/tmp<span style='mso-tab-count:
+2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>#TMP_4_TCOFFEE</span></span></p>
+
+<p class=example><span style='mso-bookmark:_Toc102494884'><span
+style='mso-bookmark:_Toc102494396'>DIR_4_TCOFFEE/methods<span style='mso-tab-count:
+2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>#METHOS_4_TCOFFEE</span></span></p>
+
+<p class=example><span style='mso-bookmark:_Toc102494884'><span
+style='mso-bookmark:_Toc102494396'>DIR_4_TCOFFEE/mcoffee<span style='mso-tab-count:
+2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>#MCOFFEE_4_TCOFFEE</span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494884'><span
+style='mso-bookmark:_Toc102494396'><span lang=AF><o:p>&nbsp;</o:p></span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494884'><span
+style='mso-bookmark:_Toc102494396'><span lang=AF>By default, all these
+directories are automatically created, following the dependencies suggested
+here. </span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494884'><span
+style='mso-bookmark:_Toc102494396'><span lang=AF>The first step is the
+determination of the HOME. By default the program tries to use HOME_4_TCOFFEE,
+then the HOME variable and TMP or TEMP if HOME is not set on your system or
+your account. It is your responsibility to make sure that one of these variables
+is set to some valid location where the T-Coffee process is allowed to read and
+write.</span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494884'><span
+style='mso-bookmark:_Toc102494396'><span lang=AF>If no valid location can be
+found for HOME_4_TCOFFEE, the program exits. If you are running T-Coffee on a
+server, we recommend to hard set the following locations, where your scratch is
+a valid location. </span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494884'><span
+style='mso-bookmark:_Toc102494396'><span lang=AF><o:p>&nbsp;</o:p></span></span></span></p>
+
+<p class=example><span style='mso-bookmark:_Toc102494884'><span
+style='mso-bookmark:_Toc102494396'>HOME_4_TCOFFEE=\94your scratch\94</span></span></p>
+
+<p class=example><span style='mso-bookmark:_Toc102494884'><span
+style='mso-bookmark:_Toc102494396'>TMP_4_TCOFFEE=\94your scratch\94</span></span></p>
+
+<p class=example><span style='mso-bookmark:_Toc102494884'><span
+style='mso-bookmark:_Toc102494396'>DIR_4_TCOFFEE=\94your scratch\94</span></span></p>
+
+<p class=example><span style='mso-bookmark:_Toc102494884'><span
+style='mso-bookmark:_Toc102494396'>CACHE_4_TCOFFEE=\94your scratch\94</span></span></p>
+
+<p class=example><span style='mso-bookmark:_Toc102494884'><span
+style='mso-bookmark:_Toc102494396'>NO_ERROR_REPORT_4_TCOFFEE=1</span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494884'><span
+style='mso-bookmark:_Toc102494396'><span lang=AF>Note that<span
+style="mso-spacerun: yes">&nbsp; </span>it is a good idea to have a cron job
+that cleans up this scratch area, once in a while. </span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494884'><span
+style='mso-bookmark:_Toc102494396'><span lang=AF><o:p>&nbsp;</o:p></span></span></span></p>
+
+<h3><span style='mso-bookmark:_Toc102494884'><span style='mso-bookmark:_Toc102494396'><a
+name="_Toc151732423">Output of the .dnd file.</a></span></span></h3>
+
+<p class=MyNormal><span lang=AF>A common source of error when running a server:
+T-Coffee MUST output the .dnd file because it re-reads it to carry out the
+progressive alignment. By default T-Coffee outputs this file in the directory where
+the process is running. If the T-Coffee process does not have permission to
+write in that directory, the computation will abort...</span></p>
+
+<p class=MyNormal><span lang=AF>To avoid this, simply specify the name of the
+output tree: </span></p>
+
+<p class=MyNormal><span lang=AF><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>-newtree=&lt;writable
+file (usually in /tmp)&gt;</span></p>
+
+<p class=MyNormal><span lang=AF>Chose the name so that two processes may not
+over-write each other dnd file. </span></p>
+
+<h3><a name="_Toc102494397"></a><a name="_Toc102494885"></a><a
+name="_Toc151732424"><span style='mso-bookmark:_Toc102494885'><span
+style='mso-bookmark:_Toc102494397'>Permissions</span></span></a></h3>
+
+<p class=MyNormal><span lang=AF>The t_coffee process MUST be allowed to write
+in some scratch area, even when it is ran by Mr nobody... Make sure the /tmp/
+partition is not protected.</span></p>
+
+<h3><a name="_Toc102494398"></a><a name="_Toc102494886"></a><a
+name="_Toc151732425"><span style='mso-bookmark:_Toc102494886'><span
+style='mso-bookmark:_Toc102494398'>Other Programs</span></span></a></h3>
+
+<p class=MyNormal><span lang=AF>T-Coffee may call various programs while it
+runs (lalign2list by defaults). Make sure your process knows where to find
+these executables.</span></p>
+
+<div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
+padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0cm;margin-right:
+4.25pt'>
+
+<p class=ChapterTitle><a name="_Toc101065353"></a><a name="_Toc102494887"><span
+style='mso-bookmark:_Toc101065353'>F</span></a>ormats</p>
+
+</div>
+
+<h2><a name="_Toc101065354"></a><a name="_Toc102494399"></a><a
+name="_Toc102494888"></a><a name="_Toc151732426"><span style='mso-bookmark:
+_Toc102494888'><span style='mso-bookmark:_Toc102494399'><span style='mso-bookmark:
+_Toc101065354'>Parameter files</span></span></span></a></h2>
+
+<p class=MyNormal><span lang=AF>Parameter files used with -parameters,
+-t_coffee_defaults, -dali_defaults... Must contain a valid parameter string
+where line breaks are allowed. These files cannot contain any comment, the
+recommended format is one parameter per line:</span></p>
+
+<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
+mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
+background:#E6E6E6'>
+
+<p class=examplefileCxSpFirst><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>&lt;parameter
+name&gt;=&lt;value1&gt;,&lt;value2&gt;....</p>
+
+<p class=examplefileCxSpLast><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>&lt;parameter
+name&gt;=.....</p>
+
+</div>
+
+<h2><a name="_Toc101065355"></a><a name="_Toc102494400"></a><a
+name="_Toc102494889"></a><a name="_Toc151732427"><span style='mso-bookmark:
+_Toc102494889'><span style='mso-bookmark:_Toc102494400'><span style='mso-bookmark:
+_Toc101065355'>Sequence Name Handling</span></span></span></a></h2>
+
+<p class=MyNormal><span lang=AF>Sequence name handling is meant to be fully
+consistent with ClustalW (Version 1.75). This implies that in some cases the
+names of your sequences may be edited when coming out of the program. Five
+rules apply:</span></p>
+
+<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
+
+<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
+mso-border-alt:solid windowtext .5pt;padding:1.0pt 1.0pt 1.0pt 1.0pt'>
+
+<p class=Noteboxtitle style='border:none;mso-border-alt:solid windowtext .5pt;
+padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'>Naming Your Sequences the
+Right Way</p>
+
+<p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
+padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'>1-No Space</p>
+
+<p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
+padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'>Names that do contain
+spaces, for instance:</p>
+
+<p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
+padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span style='mso-tab-count:
+1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>&gt;seq1
+human_myc</p>
+
+<p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
+padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'>will be turned into</p>
+
+<p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
+padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span style='mso-tab-count:
+1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>&gt;seq1</p>
+
+<p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
+padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'>It is your responsibility
+to make sure that the names you provide are not ambiguous after such an
+editing. This editing is consistent with Clustalw (Version 1.75)</p>
+
+<p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
+padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><o:p>&nbsp;</o:p></p>
+
+<p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
+padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'>2-No Strange Character</p>
+
+<p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
+padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'>Some non alphabetical characters
+are replaced with underscores. These are: ';:()'</p>
+
+<p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
+padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'>Other characters are legal
+and will be kept unchanged. This editing is meant to keep in line with Clustalw
+(Version 1.75).</p>
+
+<p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
+padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><o:p>&nbsp;</o:p></p>
+
+<p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
+padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'>3-&gt; is NEVER legal
+(except as a header token in a FASTA file)</p>
+
+<p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
+padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><o:p>&nbsp;</o:p></p>
+
+<p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
+padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'>4-Name length must be
+below 100 characters, although 15 is recommended for compatibility with other
+programs.</p>
+
+<p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
+padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'>5-Duplicated sequences
+will be renamed (i.e. sequences with the same name in the same dataset) are
+allowed but will be renamed according to their original order. When sequences
+come from multiple sources via the &#8211;in flag, consistency of the renaming
+is not guaranteed. You should avoid duplicated sequences as they will cause
+your input to differ from your output thus making it difficult to track data.</p>
+
+</div>
+
+<h2><a name="_Toc101065356"></a><a name="_Toc102494401"></a><a
+name="_Toc102494890"></a><a name="_Toc151732428"><span style='mso-bookmark:
+_Toc102494890'><span style='mso-bookmark:_Toc102494401'><span style='mso-bookmark:
+_Toc101065356'>Automatic Format Recognition</span></span></span></a></h2>
+
+<p class=MyNormal><span lang=AF>Most common formats are automatically
+recognized by t_coffee. See -in and the next section for more details. If your
+format is not recognized, use readseq or clustalw to switch to another format.
+We recommend Fasta.</span></p>
+
+<h2><a name="_Toc101065357"></a><a name="_Toc102494402"></a><a
+name="_Toc102494891"></a><a name="_Toc151732429"><span style='mso-bookmark:
+_Toc102494891'><span style='mso-bookmark:_Toc102494402'><span style='mso-bookmark:
+_Toc101065357'>Structures</span></span></span></a></h2>
+
+<p class=MyNormal><span lang=AF>PDB format is recognized by T-Coffee. T-Coffee
+uses extract_from_pdb (cf &#8211;other_pg flag). extract_from_pdb is a small
+embeded module that can be used on its own to extract information from pdb
+files.</span></p>
+
+<h2><a name="_Toc151732430">RNA Structures</a></h2>
+
+<p class=MyNormal><span lang=AF>RNA structures can either be coded as T-Coffee
+libraries, with each line indicating two paired residues, or as alifold output.
+The selex format is also partly supported (see the seq_reformat tutorial on RNA
+sequences handling).</span></p>
+
+<h2><a name="_Toc101065358"></a><a name="_Toc102494403"></a><a
+name="_Toc102494892"></a><a name="_Toc151732431"><span style='mso-bookmark:
+_Toc102494892'><span style='mso-bookmark:_Toc102494403'><span style='mso-bookmark:
+_Toc101065358'>Sequences</span></span></span></a></h2>
+
+<p class=MyNormal><span lang=AF>Sequences can come in the following formats:
+fasta, pir, swiss-prot, clustal aln, msf aln and t_coffee aln. These formats
+are the one automatically recognized. Please replace the '*' sign sometimes
+used for stop codons with an X.</span></p>
+
+<h2><a name="_Toc101065359"></a><a name="_Toc102494404"></a><a
+name="_Toc102494893"></a><a name="_Toc151732432"><span style='mso-bookmark:
+_Toc102494893'><span style='mso-bookmark:_Toc102494404'><span style='mso-bookmark:
+_Toc101065359'>Alignments</span></span></span></a></h2>
+
+<p class=MyNormal><span lang=AF>Alignments can come in the following formats:
+msf, ClustalW, Fasta, Pir and t_coffee. The t_coffee format is very similar to
+the ClustalW format, but slightly more flexible. Any interleaved format with
+sequence name on each line will be correctly parsed:</span></p>
+
+<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
+mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
+background:#E6E6E6'>
+
+<p class=examplefileCxSpFirst>&lt;empy line&gt; <span style='mso-tab-count:
+1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>[Facultative]n</p>
+
+<p class=examplefileCxSpMiddle>&lt;line of text&gt; <span style='mso-tab-count:
+1'>&nbsp;&nbsp; </span>[Required]</p>
+
+<p class=examplefileCxSpMiddle>&lt;line of text&gt;<span style='mso-tab-count:
+3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>[Facultative]n</p>
+
+<p class=examplefileCxSpMiddle>&lt;empty line&gt;<span style='mso-tab-count:
+3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>[Required]</p>
+
+<p class=examplefileCxSpMiddle>&lt;empty line&gt;<span style='mso-tab-count:
+3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>[Facultative]n</p>
+
+<p class=examplefileCxSpMiddle>&lt;seq1 name&gt;&lt;space&gt;&lt;seq1&gt;</p>
+
+<p class=examplefileCxSpMiddle>&lt;seq2 name&gt;&lt;space&gt;&lt;seq2&gt;</p>
+
+<p class=examplefileCxSpMiddle>&lt;seq3 name&gt;&lt;space&gt;&lt;seq3&gt;</p>
+
+<p class=examplefileCxSpMiddle>&lt;empty line&gt;<span style='mso-tab-count:
+3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>[Required]</p>
+
+<p class=examplefileCxSpMiddle>&lt;empty line&gt;<span style='mso-tab-count:
+3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>[Facultative]n</p>
+
+<p class=examplefileCxSpMiddle>&lt;seq1 name&gt;&lt;space&gt;&lt;seq1&gt;</p>
+
+<p class=examplefileCxSpMiddle>&lt;seq2 name&gt;&lt;space&gt;&lt;seq2&gt;</p>
+
+<p class=examplefileCxSpMiddle>&lt;seq3 name&gt;&lt;space&gt;&lt;seq3&gt;</p>
+
+<p class=examplefileCxSpMiddle>&lt;empty line&gt;<span style='mso-tab-count:
+3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>[Required]</p>
+
+<p class=examplefileCxSpLast>&lt;empty line&gt;<span style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>[Facultative]n</p>
+
+</div>
+
+<p class=MyNormal><span lang=AF>An empty line is a line that does NOT contain
+amino-acid. A line that contains the ClustalW annotation (.:*) is empty.</span></p>
+
+<p class=MyNormal><span lang=AF>Spaces are forbidden in the name. When the
+alignment is being read, non character signs are ignored in the sequence field
+(such as numbers, annotation\85).</span></p>
+
+<p class=Note><span style='mso-ansi-language:EN-US'>Note: a different number of
+lines in the different blocks will cause the program to crash or hang.<o:p></o:p></span></p>
+
+<h2><a name="_Toc101065360"></a><a name="_Toc102494405"></a><a
+name="_Toc102494894"></a><a name="_Toc151732433"><span style='mso-bookmark:
+_Toc102494894'><span style='mso-bookmark:_Toc102494405'><span style='mso-bookmark:
+_Toc101065360'>Libraries</span></span></span></a></h2>
+
+<h3><a name="_Toc102494406"></a><a name="_Toc102494895"></a><a
+name="_Toc151732434"><span style='mso-bookmark:_Toc102494895'><span
+style='mso-bookmark:_Toc102494406'>T-COFFEE_LIB_FORMAT_01</span></span></a></h3>
+
+<p class=MyNormal><span lang=AF>This is currently the only supported format.</span></p>
+
+<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
+mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
+background:#E6E6E6'>
+
+<p class=examplefileCxSpFirst>!&lt;space&gt; TC_LIB_FORMAT_01</p>
+
+<p class=examplefileCxSpMiddle>&lt;nseq&gt;</p>
+
+<p class=examplefileCxSpMiddle>&lt;seq1 name&gt; &lt;seq1 length&gt;
+&lt;seq1&gt;</p>
+
+<p class=examplefileCxSpMiddle>&lt;seq2 name&gt; &lt;seq2 length&gt;
+&lt;seq2&gt;</p>
+
+<p class=examplefileCxSpMiddle>&lt;seq3 name&gt; &lt;seq3 length&gt;
+&lt;seq3&gt;</p>
+
+<p class=examplefileCxSpMiddle>!Comment</p>
+
+<p class=examplefileCxSpMiddle>(!Comment)n</p>
+
+<p class=examplefileCxSpMiddle>#Si1 Si2</p>
+
+<p class=examplefileCxSpMiddle>Ri1 Ri2 V1 (V2, V3)</p>
+
+<p class=examplefileCxSpMiddle>#1 2</p>
+
+<p class=examplefileCxSpMiddle>12 13 99 (12/0 vs 13/1, weight 99)</p>
+
+<p class=examplefileCxSpMiddle>12 14 70</p>
+
+<p class=examplefileCxSpMiddle>15 16 56</p>
+
+<p class=examplefileCxSpMiddle>#1 3</p>
+
+<p class=examplefileCxSpMiddle>12 13 99 </p>
+
+<p class=examplefileCxSpMiddle>12 14 70</p>
+
+<p class=examplefileCxSpMiddle>15 16 56</p>
+
+<p class=examplefileCxSpLast>!&lt;space&gt;SEQ_1_TO_N </p>
+
+</div>
+
+<p class=MyNormal><span lang=AF>Si1: index of Sequence 1</span></p>
+
+<p class=MyNormal><span lang=AF>Ri1: index of residue 1 in seq1</span></p>
+
+<p class=MyNormal><span lang=AF>V1: Integer Value: Weight</span></p>
+
+<p class=MyNormal><span lang=AF>V2, V3: optional values</span></p>
+
+<p class=Note><span style='mso-ansi-language:EN-US'>Note 1: There is a space
+between the ! And SEQ_1_TO_N<o:p></o:p></span></p>
+
+<p class=Note><span style='mso-ansi-language:EN-US'>Note 2: The last line (!
+SEQ_1_TO_N) indicates that:<o:p></o:p></span></p>
+
+<p class=MyNormal><span lang=AF>Sequences and residues are numbered from 1 to
+N, unless the token SEQ_1_TO_N is omitted, in which case the sequences are
+numbered from 0 to N-1, and residues are from 1 to N.</span></p>
+
+<p class=MyNormal><span lang=AF>Residues do not need to be sorted, and neither
+do the sequences. The same pair can appear several times in the library. For
+instance, the following file would be legal:</span></p>
+
+<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
+mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
+background:#E6E6E6'>
+
+<p class=examplefileCxSpFirst>#1 2</p>
+
+<p class=examplefileCxSpMiddle>12 13 99</p>
+
+<p class=examplefileCxSpMiddle>#1 2</p>
+
+<p class=examplefileCxSpMiddle>15 16 99 </p>
+
+<p class=examplefileCxSpMiddle>#1 1</p>
+
+<p class=examplefileCxSpLast>12 14 70</p>
+
+</div>
+
+<p class=MyNormal><a name="_Toc102494407"></a><a name="_Toc102494896"><span
+style='mso-bookmark:_Toc102494407'><span lang=AF>It is also poosible to declare
+ranges of resdues rather than single pairs. For instance, the following:</span></span></a></p>
+
+<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
+mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
+background:#E6E6E6'>
+
+<p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc102494896'><span
+style='mso-bookmark:_Toc102494407'>#0 1</span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494896'><span
+style='mso-bookmark:_Toc102494407'>+BLOCK+<span style="mso-spacerun:
+yes">&nbsp; </span>10 12 14 99</span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494896'><span
+style='mso-bookmark:_Toc102494407'>+BLOCK+<span style="mso-spacerun:
+yes">&nbsp; </span>15 30 40 99</span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494896'><span
+style='mso-bookmark:_Toc102494407'>#0 2</span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494896'><span
+style='mso-bookmark:_Toc102494407'>15 16 99 </span></span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494896'><span
+style='mso-bookmark:_Toc102494407'>#0 1</span></span></p>
+
+<p class=examplefileCxSpLast><span style='mso-bookmark:_Toc102494896'><span
+style='mso-bookmark:_Toc102494407'>12 14 70</span></span></p>
+
+</div>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494896'><span
+style='mso-bookmark:_Toc102494407'><span lang=AF>The first statement BLOCK
+declares a BLOCK of length 10, that starts on position 12 of sequence 1 and
+position 14 of sequence 2 and where each pair of residues within the block has
+a score of 99. The second BLOCK starts on residue 30 of 1, residue 40 of 2 and
+extends for 15 residues.</span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494896'><span
+style='mso-bookmark:_Toc102494407'><span lang=AF>Blocks can overalp and be
+incompatible with one another, just like single constraints.</span></span></span></p>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc102494896'><span
+style='mso-bookmark:_Toc102494407'><span lang=AF><span style="mso-spacerun:
+yes">&nbsp; </span></span></span></span></p>
+
+<h3><span style='mso-bookmark:_Toc102494896'><span style='mso-bookmark:_Toc102494407'><a
+name="_Toc151732435">T-COFFEE_LIB_FORMAT_02</a></span></span></h3>
+
+<p class=MyNormal><span lang=AF>A simpler format is being developed, however it
+is not yet fully supported and is only mentioned here for development purpose.</span></p>
+
+<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
+mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
+background:#E6E6E6'>
+
+<p class=examplefileCxSpFirst>! TC_LIB_FORMAT_02</p>
+
+<p class=examplefileCxSpMiddle>#S1 SEQ1 [OPTIONAL]</p>
+
+<p class=examplefileCxSpMiddle>#S2 SEQ2 [OPTIONAL]</p>
+
+<p class=examplefileCxSpMiddle>...</p>
+
+<p class=examplefileCxSpMiddle>!comment [OPTIONAL]</p>
+
+<p class=examplefileCxSpMiddle>S1 R1 Ri1 S2 R2 Ri2 V1 (V2 V3)</p>
+
+<p class=examplefileCxSpMiddle>=&gt; N R1 Ri1 S2 R2 Ri2 V1 (V2 V3)</p>
+
+<p class=examplefileCxSpLast>...</p>
+
+</div>
+
+<p class=MyNormal><span lang=AF>S1, S2: name of sequence 1 and 2</span></p>
+
+<p class=MyNormal><span lang=AF>SEQ1: sequence of S1</span></p>
+
+<p class=MyNormal><span lang=AF>Ri1, Ri2: index of the residues in their
+respective sequence</span></p>
+
+<p class=MyNormal><span lang=AF>R1, R2: Residue type</span></p>
+
+<p class=MyNormal><span lang=AF>V1, V2, V3: integer Values (V2 and V3 are
+optional)</span></p>
+
+<p class=MyNormal><span lang=AF>Value1, Value 2 and Value3 are optional.</span></p>
+
+<h2><a name="_Toc101065361"></a><a name="_Toc102494408"></a><a
+name="_Toc102494897"></a><a name="_Toc151732436"><span style='mso-bookmark:
+_Toc102494897'><span style='mso-bookmark:_Toc102494408'><span style='mso-bookmark:
+_Toc101065361'>Library List</span></span></span></a><span style='mso-bookmark:
+_Toc101065361'></span></h2>
+
+<p class=MyNormal><span style='mso-bookmark:_Toc101065361'><span lang=AF>These
+are lists of pairs of sequences that must be used to compute a library. The
+format is:</span></span></p>
+
+<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
+mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
+background:#E6E6E6'>
+
+<p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc101065361'>&lt;nseq&gt;
+&lt;S1&gt; &lt;S2&gt;</span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065361'>2 hamg2
+globav</span></p>
+
+<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065361'>3 hamgw
+hemog singa</span></p>
+
+<p class=examplefileCxSpLast><span style='mso-bookmark:_Toc101065361'>...</span></p>
+
+</div>
+
+<h2><span style='mso-bookmark:_Toc101065361'><a name="_Toc102494409"></a><a
+name="_Toc102494898"></a><a name="_Toc151732437"><span style='mso-bookmark:
+_Toc102494898'><span style='mso-bookmark:_Toc102494409'>Substitution matrices.</span></span></a></span></h2>
+
+<p class=MyNormal><span lang=AF>If the required substitution matrix is not
+available, write your own in a file using the following format:</span></p>
+
+<h3><a name="_Toc101065362"></a><a name="_Toc102494410"></a><a
+name="_Toc102494899"></a><a name="_Toc151732438"><span style='mso-bookmark:
+_Toc102494899'><span style='mso-bookmark:_Toc102494410'><span style='mso-bookmark:
+_Toc101065362'>ClustalW Style</span> [Deprecated]</span></span></a></h3>
+
+<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
+mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
+background:#E6E6E6'>
+
+<p class=examplefileCxSpFirst># CLUSTALW_MATRIX FORMAT</p>
+
+<p class=examplefileCxSpMiddle>$</p>
+
+<p class=examplefileCxSpMiddle>v1</p>
+
+<p class=examplefileCxSpMiddle>v2 v3</p>
+
+<p class=examplefileCxSpMiddle>v4 v5 v6</p>
+
+<p class=examplefileCxSpMiddle>...</p>
+
+<p class=examplefileCxSpLast>$</p>
+
+</div>
+
+<p class=MyNormal><span lang=AF>v1, v2... are integers, possibly negatives.</span></p>
+
+<p class=MyNormal><span lang=AF>The order of the amino acids is:
+ABCDEFGHIKLMNQRSTVWXYZ, which means that v1 is the substitution value for A vs
+A, v2 for A vs B, v3 for B vs B, v4 for A vs C and so on.</span></p>
+
+<h3><a name="_Toc101065363"></a><a name="_Toc102494411"></a><a
+name="_Toc102494900"></a><a name="_Toc151732439"><span style='mso-bookmark:
+_Toc102494900'><span style='mso-bookmark:_Toc102494411'><span style='mso-bookmark:
+_Toc101065363'>BLAST Format [Recommended]</span></span></span></a></h3>
+
+<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
+mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
+background:#E6E6E6'>
+
+<p class=examplefileCxSpFirst># BLAST_MATRIX FORMAT</p>
+
+<p class=examplefileCxSpMiddle># ALPHABET=AGCT</p>
+
+<p class=examplefileCxSpMiddle><span style="mso-spacerun: yes">&nbsp;</span>A G
+C T</p>
+
+<p class=examplefileCxSpMiddle>A 0 1 2 3</p>
+
+<p class=examplefileCxSpMiddle>G 0 2 3 4</p>
+
+<p class=examplefileCxSpMiddle>C 1 1 2 3</p>
+
+<p class=examplefileCxSpLast>...</p>
+
+</div>
+
+<p class=MyNormal><span lang=AF>The alphabet can be freely defined</span></p>
+
+<h2><a name="_Toc101065364"></a><a name="_Toc102494412"></a><a
+name="_Toc102494901"></a><a name="_Toc151732440"><span style='mso-bookmark:
+_Toc102494901'><span style='mso-bookmark:_Toc102494412'><span style='mso-bookmark:
+_Toc101065364'>Sequences Weights</span></span></span></a></h2>
+
+<p class=MyNormal><span lang=AF>Create your own weight file, using the
+-seq_weight flag:</span></p>
+
+<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
+mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
+background:#E6E6E6'>
+
+<p class=examplefileCxSpFirst># SINGLE_SEQ_WEIGHT_FORMAT_01</p>
+
+<p class=examplefileCxSpMiddle>seq_name1 v1</p>
+
+<p class=examplefileCxSpMiddle>seq_name2 v2</p>
+
+<p class=examplefileCxSpLast>...</p>
+
+</div>
+
+<p class=MyNormal><span lang=AF>No duplicate allowed. Sequences not included in
+the set of sequences provided to t_coffee will be ignored. Order is free. V1 is
+a float. Un-weighted sequences will see their weight set to 1.</span></p>
+
+<span lang=AF style='font-size:11.0pt;font-family:"Times New Roman";mso-fareast-font-family:
+"Times New Roman";mso-bidi-font-family:"Courier New";mso-ansi-language:AF;
+mso-fareast-language:EN-US'><br clear=ALL style='page-break-before:always'>
+</span>
+
+<div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
+padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0cm;margin-right:
+4.25pt'>
+
+<p class=ChapterTitle>Known Problems</p>
+
+</div>
+
+<p class=MyNormal><span lang=AF>1-Sensitivity to sequence order: It is
+difficult to implement a MSA algorithm totally insensitive to the order of
+input of the sequences. In t_coffee, robustness is increased by sorting the
+sequences alphabetically before aligning them. Beware that this can result in
+confusing output where sequences with similar name are unexpectedly close to
+one another in the final alignment.</span></p>
+
+<p class=MyNormal><span lang=AF>2-Nucleotides sequences with long stretches of
+Ns will cause problems to lalign, especially when using Mocca. To avoid any
+problem, filter out these nucleotides before running mocca.</span></p>
+
+<p class=MyNormal><span lang=AF>3-Stop codons are sometimes coded with '*' in
+protein sequences. This will cause the program to crash or hang. Please replace
+the '*' signs with an X.</span></p>
+
+<p class=MyNormal><span lang=AF>4-Results can differ from one architecture to
+another, due rounding differences. This is caused by the tree estimation
+procedcure. If you want to make sure an alignment is reproducible, you should
+keep the associated dendrogram.</span></p>
+
+<p class=MyNormal><span lang=AF>5-Deploying the program on a </span></p>
+
+<div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
+padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0cm;margin-right:
+4.25pt'>
+
+<p class=ChapterTitle>Technical Notes</p>
+
+</div>
+
+<p class=MyNormal><span lang=AF>These notes are only meant for internal
+development.</span></p>
+
+<h2><a name="_Toc102494413"></a><a name="_Toc102494904"></a><a
+name="_Toc151732441"><span style='mso-bookmark:_Toc102494904'><span
+style='mso-bookmark:_Toc102494413'>Development</span></span></a></h2>
+
+<p class=MyNormal><span lang=AF>The following examples are only meant for
+internal development, and are used to insure stability from release to release</span></p>
+
+<h4><a name="_Toc151732442"><span lang=AF>profile2list</span></a></h4>
+
+<p class=MyNormal><span lang=AF>prf1: profile containing one structure</span></p>
+
+<p class=MyNormal><span lang=AF>prf2: profile containing one structure</span></p>
+
+<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT:
+t_coffee<span style="mso-spacerun: yes">&nbsp; </span>Rsample_profile1.aln,Rsample_profile2.aln
+-mode=3dcoffee -outfile=aligned_prf.aln</p>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><o:p>&nbsp;</o:p></p>
+
+</div>
+
+<h3><a name="_Toc102494414"></a><a name="_Toc102494905"></a><a
+name="_Toc151732443"><span style='mso-bookmark:_Toc102494905'><span
+style='mso-bookmark:_Toc102494414'>Command Line List</span></span></a></h3>
+
+<p class=MyNormal><span lang=AF>These command lines have been checked before
+every release (along with the other CL in this documentation:</span></p>
+
+<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
+
+<p class=MyNormal><span lang=AF>-external methods;</span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
+style='mso-tab-count:1'>&nbsp;&nbsp; </span>PROMPT: t_coffee sample_seq1.fasta
+&#8211;in=Mclustalw_pair,Mclustalw_msa,Mslow_pair &#8211;outfile=clustal_text</p>
+
+</div>
+
+<p class=MyNormal><span lang=AF>-fugue_client</span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+&#8211;in Ssample_seq5.fasta Pstruc4.pdb Mfugue_pair</p>
+
+</div>
+
+<p class=MyNormal><span lang=AF>-A list of command lines kindly provided by
+James Watson (used to crash the pg before version 3.40)</span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+-in Sseq.fas P2PTC Mfugue_pair</p>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+-in S2seqs.fas Mfugue_pair -template_file SELF_P_</p>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee -mode
+3dcoffee -in Sseq.fas P2PTC</p>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee -mode
+3dcoffee -in S2seqs.fas -template_file SELF_P_</p>
+
+</div>
+
+<p class=MyNormal><span lang=AF>-A list of command lines that crashed the
+program before 3.81</span></p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+sample_seq6.fasta &#8211;in Mfast_pair Msap_pair Mfugue_pair
+&#8211;template_file template_file6.template </p>
+
+</div>
+
+<p class=MsoBodyText><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>-A
+command line to read \93relaxed\94 pdb files...</p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+&#8211;in Msap_pair Ssample_seq7.fasta &#8211;template_file template_file7.template
+&#8211;weight 1001 &#8211;out_lib test_lib7.tc_lib &#8211;lib_only </p>
+
+</div>
+
+<p class=MsoBodyText><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>-Parsing
+of MARNA libraries</p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+&#8211;in Lmarna.tc_lib &#8211;outfile maran.test</p>
+
+</div>
+
+<p class=MsoBodyText><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>-Parsing
+of long sequence lines:</p>
+
+<div style='mso-element:para-border-div;border-top:solid black 1.0pt;
+border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
+solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
+background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
+
+<p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
+&#8211;in Asample_aln5.aln &#8211;outfile test.aln</p>
+
+</div>
+
+<p class=MsoBodyText><o:p>&nbsp;</o:p></p>
+
+<div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
+padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0cm;margin-right:
+4.25pt'>
+
+<p class=ChapterTitle><a name="_Toc102494906">To D</a>o\85</p>
+
+</div>
+
+<p class=MyNormal><span lang=AF>-implement UPGMA tree computation</span></p>
+
+<p class=MyNormal><span lang=AF>-implement seq2dpa_tree</span></p>
+
+<p class=MyNormal><span lang=AF>-debug dpa</span></p>
+
+<p class=MyNormal><span lang=AF>-Reconciliate sequences and template when
+reading the template</span></p>
+
+<p class=MyNormal><span lang=AF>-Add the server command lines to the checking
+procedure</span></p>
+
+<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoBodyText><o:p>&nbsp;</o:p></p>
+
+</div>
+
+</body>
+
+</html>