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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
 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
  + 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
 + 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
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-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
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- name="address"/>\r
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- 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
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-  <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
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-       {mso-style-noshow:yes;\r
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-       {mso-style-noshow:yes;\r
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-       {mso-style-noshow:yes;\r
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-       {mso-style-update:auto;\r
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-       {mso-style-update:auto;\r
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-       {mso-style-update:auto;\r
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-       {mso-style-update:auto;\r
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-       {mso-style-parent:"Body Text";\r
-       mso-style-link:"List Char";\r
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-       {mso-style-parent:List;\r
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-p.MsoListNumber, li.MsoListNumber, div.MsoListNumber\r
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-p.MsoList2, li.MsoList2, div.MsoList2\r
-       {mso-style-parent:List;\r
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-       letter-spacing:-.25pt;\r
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-       {mso-style-parent:List;\r
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-       {mso-style-parent:List;\r
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-p.MsoListBullet2, li.MsoListBullet2, div.MsoListBullet2\r
-       {mso-style-parent:"List Bullet";\r
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-p.MsoListBullet3, li.MsoListBullet3, div.MsoListBullet3\r
-       {mso-style-parent:"List Bullet";\r
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-       letter-spacing:-.25pt;\r
-       mso-ansi-language:EN-US;\r
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-p.MsoListBullet4, li.MsoListBullet4, div.MsoListBullet4\r
-       {mso-style-parent:"List Bullet";\r
-       margin-top:0mm;\r
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-       letter-spacing:-.25pt;\r
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-       mso-fareast-language:EN-US;}\r
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-       {margin-top:0mm;\r
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-       mso-element:frame;\r
-       mso-element-frame-width:93.0pt;\r
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-       mso-element-anchor-vertical:paragraph;\r
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-       {mso-style-parent:"List Number";\r
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-       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
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-       margin-right:4.25pt;\r
-       margin-bottom:102.0pt;\r
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-p.CompanyName, li.CompanyName, div.CompanyName\r
-       {mso-style-name:"Company Name";\r
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-       margin-top:21.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:3.0pt;\r
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-       mso-fareast-language:EN-US;}\r
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-       margin-right:0mm;\r
-       margin-bottom:18.0pt;\r
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-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
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-p.FooterEven, li.FooterEven, div.FooterEven\r
-       {mso-style-name:"Footer Even";\r
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-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       text-align:center;\r
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-       tab-stops:center 216.0pt right 432.0pt;\r
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-p.FooterFirst, li.FooterFirst, div.FooterFirst\r
-       {mso-style-name:"Footer First";\r
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-       text-align:center;\r
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-       font-family:"Arial Black";\r
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-       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
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-       border:none;\r
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-       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
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-       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
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-       mso-bidi-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
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-p.HeaderEven, li.HeaderEven, div.HeaderEven\r
-       {mso-style-name:"Header Even";\r
-       mso-style-parent:Header;\r
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-       font-family:"Arial Black";\r
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-       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
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-       margin-bottom:.0001pt;\r
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-       mso-fareast-font-family:"Times New Roman";\r
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-       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
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-       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
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-       background:#E5E5E5;\r
-       mso-shading:windowtext;\r
-       mso-pattern:gray-10 auto;\r
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-       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
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-       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
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-       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
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-       margin-bottom:8.0pt;\r
-       margin-left:18.0pt;\r
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-       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
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-       mso-pagination:widow-orphan;\r
-       mso-list:l25 level1 lfo5;\r
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-       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
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-       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
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-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
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-\r
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-\r
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-\r
-<div style='mso-element:frame;mso-element-wrap:no-wrap-beside;mso-height-rule:\r
-exactly'>\r
-\r
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- <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
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-\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
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-\r
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-\r
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-\r
-<span lang=EN-US style='font-size:72.0pt;mso-bidi-font-size:10.0pt;font-family:\r
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-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
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-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
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-\r
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-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
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-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
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+  <o:LastPrinted>2006-03-05T19:42:00Z</o:LastPrinted>
+  <o:Created>2010-11-18T19:37:00Z</o:Created>
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-  lang=EN-US style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>\r
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-  <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
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-  </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
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-  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
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- <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
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-  style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></a> </span><span\r
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-  </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
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- </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
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- </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
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-  ["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
-<!--
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-  ["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
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-\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
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-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
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-\r
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-\r
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-\r
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-\r
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+@font-face
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+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
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+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
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+@font-face
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+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
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+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
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+       mso-generic-font-family:auto;
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+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
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+       mso-generic-font-family:auto;
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+       mso-font-pitch:variable;
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+       mso-generic-font-family:auto;
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+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:0 0 65536 0 -2147483648 0;}
+@font-face
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+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
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+@font-face
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+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
+       {font-family:"Kino MT";
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+       mso-font-charset:0;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
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+@font-face
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+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
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+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
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+       mso-generic-font-family:auto;
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+       mso-generic-font-family:auto;
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+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
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+       mso-generic-font-family:auto;
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+@font-face
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+       mso-generic-font-family:auto;
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+       mso-generic-font-family:auto;
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+       mso-font-signature:0 0 65536 0 -2147483648 0;}
+@font-face
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+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
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+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
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+       mso-font-charset:2;
+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:0 0 65536 0 -2147483648 0;}
+@font-face
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+       mso-generic-font-family:auto;
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+       mso-font-pitch:variable;
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+@font-face
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+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
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+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
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+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
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+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
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+       mso-generic-font-family:auto;
+       mso-font-pitch:variable;
+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
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+       mso-font-charset:0;
+       mso-generic-font-family:auto;
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+       mso-generic-font-family:auto;
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+       mso-font-signature:3 0 0 0 1 0;}
+@font-face
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+@font-face
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+       mso-font-signature:0 0 65536 0 -2147483648 0;}
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+       mso-font-signature:0 0 65536 0 -2147483648 0;}
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+       {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;
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+       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;
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+       mso-fareast-font-family:"Times New Roman";
+       mso-hansi-font-family:Cambria;
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+       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;}
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+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;
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+</head>
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+<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;
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+
+<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>
+
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+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>
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+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-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>
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+style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
+12.0pt;mso-fareast-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
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+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
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+
+<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
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+
+<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
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+12.0pt;mso-fareast-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>