getting rid of ambiguous documentation folder. all prog_doc are now stored in website...

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4299 e3abac25-378b-4346-85de-24260fe3988d

diff --git a/binaries/help/AACon_manual.txt b/binaries/help/AACon_manual.txt
deleted file mode 100644 (file)
index e9b4b53..0000000
--- a/binaries/help/AACon_manual.txt
+++ /dev/null
@@ -1,94 +0,0 @@
-
-AA Conservation version 1.0b (2 September 2010)
-
-This program allows calculation of conservation of amino acids in
-multiple sequence alignments.
-It implements 17 different conservation scores as described by Valdar in
-his paper (Scoring Residue Conservation, PROTEINS: Structure, Function
-and  Bioinformatics 48:227-241 (2002)) and SMERFS scoring algorithm as described
-by Manning, Jefferson and Barton (The contrasting properties of conservation
-and correlated phylogeny in protein functional residue prediction,
-BMC Bioinformatics (2008)).
-
-The conservation algorithms supported are:
-
-KABAT, JORES, SCHNEIDER, SHENKIN, GERSTEIN, TAYLOR_GAPS, TAYLOR_NO_GAPS, 
-ZVELIBIL, KARLIN, ARMON, THOMPSON, NOT_LANCET, MIRNY, WILLIAMSON, 
-LANDGRAF, SANDER, VALDAR, SMERFS
-
-Input format is either a FASTA formatted file containing aligned sequences with 
-gaps or a Clustal alignment. The valid gap characters are *, -, space character,
-X and . (a dot). By default program prints the results to the command window. 
-If the output file is provided the results are printed to the file in two 
-possible formats with or without an alignment.
-If format is not specified, the program outputs conservation scores without 
-alignment. The scores are not normalized by default but they can be (see below).
-SMERFS default parameters are window width of 7, column score is set to
-the middle column (MID_SCORE), gap% cutoff of 0.1. Different parameters for SMERFS 
-can be provided (see below). Details of the program execution can be recorded to
-a separate file if an appropriate file path is provided.
-
-List of command line arguments:
-
--m=  precedes a comma separated list of method names
-     EXAMPLE: -m=KABAT,JORES,GERSTEIN
-     Optional, if no method is specified request for all is assumed. 
-
--i=  precedes a full path to the input FASTA file, required
-
--o=  precedes a full path to the output file, optional, if no output file is 
-     provided the program will output to the standard out.  
-
--t=  precedes the number of CPUs (CPU cores more precisely) to use. Optional, 
-        defaults to all processors available on the machine.  
-      
--f=  precedes the format  of the results in the output file
-     two different formats are possible:
-      RESULT_WITH_ALIGNMENT
-      RESULT_NO_ALIGNMENT
-     Optional, if not specified RESULT_NO_ALIGNMENT is assumed 
-
--d=  precedes a full path to a file where program execution details are to be 
-     listed. Optional, if not provided, no execution statistics is produced.  
-      
--g=  precedes comma separated list of gap characters provided by the user, if 
-     you're using an unusual gap character (not a -,., ,*,X) you have to 
-     provide it. If you you provide this list you have to list all the gaps 
-     accepted. Including those that were previously treated as a default. 
-     Optional.      
-      
--n   using this key causes the results to be normalized. 
-        Normalized results have values between 0 and 1. Please note however, that 
-        some results cannot be normalized. In such a case, the system returns not 
-        normalized value, and log the issue to the standard error stream. 
-        The following formula is used for normalization 
-                       n = (d - dmin)/(dmax - dmin)
-        Negative results first converted to positive by adding an absolute value of
-        the most negative result. Optional.
-
-SMERFS Only Parameters: 
-
--smerfsGT=  precedes SMERFS Gap Treshold - a gap percentage cutoff - 
-                       a float greater than 0 and smaller or equal 1. Optional defaults 
-                       to 0.1
-
--smerfsCS=  precedes SMERFS Column Score algorithm defines the window scores to 
-                       columns allocation , two methods are possible:
-               MID_SCORE - gives the window score to the middle column
-               MAX_SCORE - gives the column the highest score of all the windows it 
-               belongs to. Optional defaults to MID_SCORE.  
-
--smerfsWW=  precedes Window Width parameter - an integer and an odd number.
-            Optional, defaults to 7 
-         
-
-EXAMPLE HOW TO RUN THE PROGRAM:
-java -jar <jar name> -m=KABAT,SMERFS -i=prot1 -o=prot1_results -n
-
-As a result of the execution KABAT and SMERFS scores will be calculated. 
-Input comes form prot1 file and an output without an alignment is recorded to 
-prot1_results file. 
-
-Authors: Peter Troshin, Agnieszka Golicz, David Martin and Geoff Barton.
-Please visit http://www.compbio.dundee.ac.uk/aacon for further information.
- 
\ No newline at end of file

diff --git a/binaries/help/clustalw-help.txt b/binaries/help/clustalw-help.txt
deleted file mode 100644 (file)
index fd50671..0000000
--- a/binaries/help/clustalw-help.txt
+++ /dev/null
@@ -1,720 +0,0 @@
-\r
-\r
-\r
- CLUSTAL 2.0.12 Multiple Sequence Alignments\r
-\r
-\r
-\r
-\r
->> HELP NEW <<             NEW FEATURES/OPTIONS\r
-\r
-==UPGMA== \r
- The UPGMA algorithm has been added to allow faster tree construction. The user now\r
- has the choice of using Neighbour Joining or UPGMA. The default is still NJ, but the\r
- user can change this by setting the clustering parameter.\r
- \r
- -CLUSTERING=   :NJ or UPGMA\r
- \r
-==ITERATION==\r
-\r
- A remove first iteration scheme has been added. This can be used to improve the final\r
- alignment or improve the alignment at each stage of the progressive alignment. During the \r
- iteration step each sequence is removed in turn and realigned. If the resulting alignment \r
- is better than the  previous alignment it is kept. This process is repeated until the score\r
- converges (the  score is not improved) or until the maximum number of iterations is \r
- reached. The user can  iterate at each step of the progressive alignment by setting the \r
- iteration parameter to  TREE or just on the final alignment by seting the iteration \r
- parameter to ALIGNMENT. The default is no iteration. The maximum number of  iterations can \r
- be set using the numiter parameter. The default number of iterations is 3.\r
-  \r
- -ITERATION=    :NONE or TREE or ALIGNMENT\r
- \r
- -NUMITER=n     :Maximum number of iterations to perform\r
- \r
-==HELP==\r
- \r
- -FULLHELP      :Print out the complete help content\r
- \r
-==MISC==\r
-\r
- -MAXSEQLEN=n   :Maximum allowed sequence length\r
- \r
- -QUIET         :Reduce console output to minimum\r
- \r
- -STATS=file    :Log some alignents statistics to file\r
-\r
-\r
->> HELP 1 <<             General help for CLUSTAL W (2.0.12)\r
-\r
-Clustal W is a general purpose multiple alignment program for DNA or proteins.\r
-\r
-SEQUENCE INPUT:  all sequences must be in 1 file, one after another.  \r
-7 formats are automatically recognised: NBRF-PIR, EMBL-SWISSPROT, \r
-Pearson (Fasta), Clustal (*.aln), GCG-MSF (Pileup), GCG9-RSF and GDE flat file.\r
-All non-alphabetic characters (spaces, digits, punctuation marks) are ignored\r
-except "-" which is used to indicate a GAP ("." in MSF-RSF).  \r
-\r
-To do a MULTIPLE ALIGNMENT on a set of sequences, use item 1 from this menu to \r
-INPUT them; go to menu item 2 to do the multiple alignment.\r
-\r
-PROFILE ALIGNMENTS (menu item 3) are used to align 2 alignments.  Use this to\r
-add a new sequence to an old alignment, or to use secondary structure to guide \r
-the alignment process.  GAPS in the old alignments are indicated using the "-" \r
-character.   PROFILES can be input in ANY of the allowed formats; just \r
-use "-" (or "." for MSF-RSF) for each gap position.\r
-\r
-PHYLOGENETIC TREES (menu item 4) can be calculated from old alignments (read in\r
-with "-" characters to indicate gaps) OR after a multiple alignment while the \r
-alignment is still in memory.\r
-\r
-\r
-The program tries to automatically recognise the different file formats used\r
-and to guess whether the sequences are amino acid or nucleotide.  This is not\r
-always foolproof.\r
-\r
-FASTA and NBRF-PIR formats are recognised by having a ">" as the first \r
-character in the file.  \r
-\r
-EMBL-Swiss Prot formats are recognised by the letters\r
-ID at the start of the file (the token for the entry name field).  \r
-\r
-CLUSTAL format is recognised by the word CLUSTAL at the beginning of the file.\r
-\r
-GCG-MSF format is recognised by one of the following:\r
-       - the word PileUp at the start of the file. \r
-       - the word !!AA_MULTIPLE_ALIGNMENT or !!NA_MULTIPLE_ALIGNMENT\r
-         at the start of the file.\r
-       - the word MSF on the first line of the line, and the characters ..\r
-         at the end of this line.\r
-\r
-GCG-RSF format is recognised by the word !!RICH_SEQUENCE at the beginning of\r
-the file.\r
-\r
-\r
-If 85% or more of the characters in the sequence are from A,C,G,T,U or N, the\r
-sequence will be assumed to be nucleotide.  This works in 97.3% of cases\r
-but watch out!\r
-\r
-\r
->> HELP 2 <<             Help for multiple alignments\r
-\r
-If you have already loaded sequences, use menu item 1 to do the complete\r
-multiple alignment.  You will be prompted for 2 output files: 1 for the \r
-alignment itself; another to store a dendrogram that describes the similarity\r
-of the sequences to each other.\r
-\r
-Multiple alignments are carried out in 3 stages (automatically done from menu\r
-item 1 ...Do complete multiple alignments now):\r
-\r
-1) all sequences are compared to each other (pairwise alignments);\r
-\r
-2) a dendrogram (like a phylogenetic tree) is constructed, describing the\r
-approximate groupings of the sequences by similarity (stored in a file).\r
-\r
-3) the final multiple alignment is carried out, using the dendrogram as a guide.\r
-\r
-\r
-PAIRWISE ALIGNMENT parameters control the speed-sensitivity of the initial\r
-alignments.\r
-\r
-MULTIPLE ALIGNMENT parameters control the gaps in the final multiple alignments.\r
-\r
-\r
-RESET GAPS (menu item 7) will remove any new gaps introduced into the sequences\r
-during multiple alignment if you wish to change the parameters and try again.\r
-This only takes effect just before you do a second multiple alignment.  You\r
-can make phylogenetic trees after alignment whether or not this is ON.\r
-If you turn this OFF, the new gaps are kept even if you do a second multiple\r
-alignment. This allows you to iterate the alignment gradually.  Sometimes, the \r
-alignment is improved by a second or third pass.\r
-\r
-SCREEN DISPLAY (menu item 8) can be used to send the output alignments to the \r
-screen as well as to the output file.\r
-\r
-You can skip the first stages (pairwise alignments; dendrogram) by using an\r
-old dendrogram file (menu item 3); or you can just produce the dendrogram\r
-with no final multiple alignment (menu item 2).\r
-\r
-\r
-OUTPUT FORMAT: Menu item 9 (format options) allows you to choose from 6 \r
-different alignment formats (CLUSTAL, GCG, NBRF-PIR, PHYLIP, GDE, NEXUS, and FASTA).  \r
-\r
-\r
-\r
->> HELP 3 <<             Help for pairwise alignment parameters\r
-\r
-A distance is calculated between every pair of sequences and these are used to\r
-construct the dendrogram which guides the final multiple alignment. The scores\r
-are calculated from separate pairwise alignments. These can be calculated using\r
-2 methods: dynamic programming (slow but accurate) or by the method of Wilbur\r
-and Lipman (extremely fast but approximate). \r
-\r
-You can choose between the 2 alignment methods using menu option 8.  The\r
-slow-accurate method is fine for short sequences but will be VERY SLOW for \r
-many (e.g. >100) long (e.g. >1000 residue) sequences.   \r
-\r
-SLOW-ACCURATE alignment parameters:\r
-       These parameters do not have any affect on the speed of the alignments. \r
-They are used to give initial alignments which are then rescored to give percent\r
-identity scores.  These % scores are the ones which are displayed on the \r
-screen.  The scores are converted to distances for the trees.\r
-\r
-1) Gap Open Penalty:      the penalty for opening a gap in the alignment.\r
-2) Gap extension penalty: the penalty for extending a gap by 1 residue.\r
-3) Protein weight matrix: the scoring table which describes the similarity\r
-                          of each amino acid to each other.\r
-4) DNA weight matrix:     the scores assigned to matches and mismatches \r
-                          (including IUB ambiguity codes).\r
-\r
-\r
-FAST-APPROXIMATE alignment parameters:\r
-\r
-These similarity scores are calculated from fast, approximate, global align-\r
-ments, which are controlled by 4 parameters.   2 techniques are used to make\r
-these alignments very fast: 1) only exactly matching fragments (k-tuples) are\r
-considered; 2) only the 'best' diagonals (the ones with most k-tuple matches)\r
-are used.\r
-\r
-K-TUPLE SIZE:  This is the size of exactly matching fragment that is used. \r
-INCREASE for speed (max= 2 for proteins; 4 for DNA), DECREASE for sensitivity.\r
-For longer sequences (e.g. >1000 residues) you may need to increase the default.\r
-\r
-GAP PENALTY:   This is a penalty for each gap in the fast alignments.  It has\r
-little affect on the speed or sensitivity except for extreme values.\r
-\r
-TOP DIAGONALS: The number of k-tuple matches on each diagonal (in an imaginary\r
-dot-matrix plot) is calculated.  Only the best ones (with most matches) are\r
-used in the alignment.  This parameter specifies how many.  Decrease for speed;\r
-increase for sensitivity.\r
-\r
-WINDOW SIZE:  This is the number of diagonals around each of the 'best' \r
-diagonals that will be used.  Decrease for speed; increase for sensitivity.\r
-\r
-\r
->> HELP 4 <<             Help for multiple alignment parameters\r
-\r
-These parameters control the final multiple alignment. This is the core of the\r
-program and the details are complicated. To fully understand the use of the\r
-parameters and the scoring system, you will have to refer to the documentation.\r
-\r
-Each step in the final multiple alignment consists of aligning two alignments \r
-or sequences.  This is done progressively, following the branching order in \r
-the GUIDE TREE.  The basic parameters to control this are two gap penalties and\r
-the scores for various identical-non-indentical residues.  \r
-\r
-1) and 2) The GAP PENALTIES are set by menu items 1 and 2. These control the \r
-cost of opening up every new gap and the cost of every item in a gap. \r
-Increasing the gap opening penalty will make gaps less frequent. Increasing \r
-the gap extension penalty will make gaps shorter. Terminal gaps are not \r
-penalised.\r
-\r
-3) The DELAY DIVERGENT SEQUENCES switch delays the alignment of the most\r
-distantly related sequences until after the most closely related sequences have \r
-been aligned.   The setting shows the percent identity level required to delay\r
-the addition of a sequence; sequences that are less identical than this level\r
-to any other sequences will be aligned later.\r
-\r
-\r
-\r
-4) The TRANSITION WEIGHT gives transitions (A <--> G or C <--> T \r
-i.e. purine-purine or pyrimidine-pyrimidine substitutions) a weight between 0\r
-and 1; a weight of zero means that the transitions are scored as mismatches,\r
-while a weight of 1 gives the transitions the match score. For distantly related\r
-DNA sequences, the weight should be near to zero; for closely related sequences\r
-it can be useful to assign a higher score.\r
-\r
-\r
-5) PROTEIN WEIGHT MATRIX leads to a new menu where you are offered a choice of\r
-weight matrices. The default for proteins in version 1.8 is the PAM series \r
-derived by Gonnet and colleagues. Note, a series is used! The actual matrix\r
-that is used depends on how similar the sequences to be aligned at this \r
-alignment step are. Different matrices work differently at each evolutionary\r
-distance. \r
-\r
-6) DNA WEIGHT MATRIX leads to a new menu where a single matrix (not a series)\r
-can be selected. The default is the matrix used by BESTFIT for comparison of\r
-nucleic acid sequences.\r
-\r
-Further help is offered in the weight matrix menu.\r
-\r
-\r
-7)  In the weight matrices, you can use negative as well as positive values if\r
-you wish, although the matrix will be automatically adjusted to all positive\r
-scores, unless the NEGATIVE MATRIX option is selected.\r
-\r
-8) PROTEIN GAP PARAMETERS displays a menu allowing you to set some Gap Penalty\r
-options which are only used in protein alignments.\r
-\r
-\r
->> HELP A <<             Help for protein gap parameters.\r
-\r
-1) RESIDUE SPECIFIC PENALTIES are amino acid specific gap penalties that reduce\r
-or increase the gap opening penalties at each position in the alignment or\r
-sequence.  See the documentation for details.  As an example, positions that \r
-are rich in glycine are more likely to have an adjacent gap than positions that\r
-are rich in valine.\r
-\r
-2) 3) HYDROPHILIC GAP PENALTIES are used to increase the chances of a gap within\r
-a run (5 or more residues) of hydrophilic amino acids; these are likely to\r
-be loop or random coil regions where gaps are more common.  The residues that \r
-are "considered" to be hydrophilic are set by menu item 3.\r
-\r
-4) GAP SEPARATION DISTANCE tries to decrease the chances of gaps being too\r
-close to each other. Gaps that are less than this distance apart are penalised\r
-more than other gaps. This does not prevent close gaps; it makes them less\r
-frequent, promoting a block-like appearance of the alignment.\r
-\r
-5) END GAP SEPARATION treats end gaps just like internal gaps for the purposes\r
-of avoiding gaps that are too close (set by GAP SEPARATION DISTANCE above).\r
-If you turn this off, end gaps will be ignored for this purpose.  This is\r
-useful when you wish to align fragments where the end gaps are not biologically\r
-meaningful.\r
-\r
-\r
->> HELP 5 <<             Help for output format options.\r
-\r
-Six output formats are offered. You can choose any (or all 6 if you wish).  \r
-\r
-CLUSTAL format output is a self explanatory alignment format.  It shows the\r
-sequences aligned in blocks.  It can be read in again at a later date to\r
-(for example) calculate a phylogenetic tree or add a new sequence with a \r
-profile alignment.\r
-\r
-GCG output can be used by any of the GCG programs that can work on multiple\r
-alignments (e.g. PRETTY, PROFILEMAKE, PLOTALIGN).  It is the same as the GCG\r
-.msf format files (multiple sequence file); new in version 7 of GCG.\r
-\r
-PHYLIP format output can be used for input to the PHYLIP package of Joe \r
-Felsenstein.  This is an extremely widely used package for doing every \r
-imaginable form of phylogenetic analysis (MUCH more than the the modest intro-\r
-duction offered by this program).\r
-\r
-NBRF-PIR:  this is the same as the standard PIR format with ONE ADDITION.  Gap\r
-characters "-" are used to indicate the positions of gaps in the multiple \r
-alignment.  These files can be re-used as input in any part of clustal that\r
-allows sequences (or alignments or profiles) to be read in.  \r
-\r
-GDE:  this is the flat file format used by the GDE package of Steven Smith.\r
-\r
-NEXUS: the format used by several phylogeny programs, including PAUP and\r
-MacClade.\r
-\r
-GDE OUTPUT CASE: sequences in GDE format may be written in either upper or\r
-lower case.\r
-\r
-CLUSTALW SEQUENCE NUMBERS: residue numbers may be added to the end of the\r
-alignment lines in clustalw format.\r
-\r
-OUTPUT ORDER is used to control the order of the sequences in the output\r
-alignments.  By default, the order corresponds to the order in which the\r
-sequences were aligned (from the guide tree-dendrogram), thus automatically\r
-grouping closely related sequences. This switch can be used to set the order\r
-to the same as the input file.\r
-\r
-PARAMETER OUTPUT: This option allows you to save all your parameter settings\r
-in a parameter file. This file can be used subsequently to rerun Clustal W\r
-using the same parameters.\r
-\r
-\r
->> HELP 6 <<             Help for profile and structure alignments\r
-\r
-By PROFILE ALIGNMENT, we mean alignment using existing alignments. Profile \r
-alignments allow you to store alignments of your favourite sequences and add\r
-new sequences to them in small bunches at a time. A profile is simply an\r
-alignment of one or more sequences (e.g. an alignment output file from CLUSTAL\r
-W). Each input can be a single sequence. One or both sets of input sequences\r
-may include secondary structure assignments or gap penalty masks to guide the\r
-alignment. \r
-\r
-The profiles can be in any of the allowed input formats with "-" characters\r
-used to specify gaps (except for MSF-RSF where "." is used).\r
-\r
-You have to specify the 2 profiles by choosing menu items 1 and 2 and giving\r
-2 file names.  Then Menu item 3 will align the 2 profiles to each other. \r
-Secondary structure masks in either profile can be used to guide the alignment.\r
-\r
-Menu item 4 will take the sequences in the second profile and align them to\r
-the first profile, 1 at a time.  This is useful to add some new sequences to\r
-an existing alignment, or to align a set of sequences to a known structure.  \r
-In this case, the second profile would not be pre-aligned.\r
-\r
-\r
-The alignment parameters can be set using menu items 5, 6 and 7. These are\r
-EXACTLY the same parameters as used by the general, automatic multiple\r
-alignment procedure. The general multiple alignment procedure is simply a\r
-series of profile alignments. Carrying out a series of profile alignments on\r
-larger and larger groups of sequences, allows you to manually build up a\r
-complete alignment, if necessary editing intermediate alignments.\r
-\r
-SECONDARY STRUCTURE OPTIONS. Menu Option 0 allows you to set 2D structure\r
-parameters. If a solved structure is available, it can be used to guide the \r
-alignment by raising gap penalties within secondary structure elements, so \r
-that gaps will preferentially be inserted into unstructured surface loops.\r
-Alternatively, a user-specified gap penalty mask can be supplied directly.\r
-\r
-A gap penalty mask is a series of numbers between 1 and 9, one per position in \r
-the alignment. Each number specifies how much the gap opening penalty is to be \r
-raised at that position (raised by multiplying the basic gap opening penalty\r
-by the number) i.e. a mask figure of 1 at a position means no change\r
-in gap opening penalty; a figure of 4 means that the gap opening penalty is\r
-four times greater at that position, making gaps 4 times harder to open.\r
-\r
-The format for gap penalty masks and secondary structure masks is explained\r
-in the help under option 0 (secondary structure options).\r
-\r
-\r
->> HELP B <<             Help for secondary structure - gap penalty masks\r
-\r
-The use of secondary structure-based penalties has been shown to improve the\r
-accuracy of multiple alignment. Therefore CLUSTAL W now allows gap penalty \r
-masks to be supplied with the input sequences. The masks work by raising gap \r
-penalties in specified regions (typically secondary structure elements) so that\r
-gaps are preferentially opened in the less well conserved regions (typically \r
-surface loops).\r
-\r
-Options 1 and 2 control whether the input secondary structure information or\r
-gap penalty masks will be used.\r
-\r
-Option 3 controls whether the secondary structure and gap penalty masks should\r
-be included in the output alignment.\r
-\r
-Options 4 and 5 provide the value for raising the gap penalty at core Alpha \r
-Helical (A) and Beta Strand (B) residues. In CLUSTAL format, capital residues \r
-denote the A and B core structure notation. The basic gap penalties are\r
-multiplied by the amount specified.\r
-\r
-Option 6 provides the value for the gap penalty in Loops. By default this \r
-penalty is not raised. In CLUSTAL format, loops are specified by "." in the \r
-secondary structure notation.\r
-\r
-Option 7 provides the value for setting the gap penalty at the ends of \r
-secondary structures. Ends of secondary structures are observed to grow \r
-and-or shrink in related structures. Therefore by default these are given \r
-intermediate values, lower than the core penalties. All secondary structure \r
-read in as lower case in CLUSTAL format gets the reduced terminal penalty.\r
-\r
-Options 8 and 9 specify the range of structure termini for the intermediate \r
-penalties. In the alignment output, these are indicated as lower case. \r
-For Alpha Helices, by default, the range spans the end helical turn. For \r
-Beta Strands, the default range spans the end residue and the adjacent loop \r
-residue, since sequence conservation often extends beyond the actual H-bonded\r
-Beta Strand.\r
-\r
-CLUSTAL W can read the masks from SWISS-PROT, CLUSTAL or GDE format input\r
-files. For many 3-D protein structures, secondary structure information is\r
-recorded in the feature tables of SWISS-PROT database entries. You should\r
-always check that the assignments are correct - some are quite inaccurate.\r
-CLUSTAL W looks for SWISS-PROT HELIX and STRAND assignments e.g.\r
-\r
-FT   HELIX       100    115\r
-FT   STRAND      118    119\r
-\r
-The structure and penalty masks can also be read from CLUSTAL alignment format \r
-as comment lines beginning "!SS_" or "!GM_" e.g.\r
-\r
-!SS_HBA_HUMA    ..aaaAAAAAAAAAAaaa.aaaAAAAAAAAAAaaaaaaAaaa.........aaaAAAAAA\r
-!GM_HBA_HUMA    112224444444444222122244444444442222224222111111111222444444\r
-HBA_HUMA        VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGK\r
-\r
-Note that the mask itself is a set of numbers between 1 and 9 each of which is \r
-assigned to the residue(s) in the same column below. \r
-\r
-In GDE flat file format, the masks are specified as text and the names must\r
-begin with "SS_ or "GM_.\r
-\r
-Either a structure or penalty mask or both may be used. If both are included in\r
-an alignment, the user will be asked which is to be used.\r
-\r
-\r
->> HELP C <<             Help for secondary structure - gap penalty mask output options\r
-\r
-The options in this menu let you choose whether or not to include the masks\r
-in the CLUSTAL W output alignments. Showing both is useful for understanding\r
-how the masks work. The secondary structure information is itself very useful\r
-in judging the alignment quality and in seeing how residue conservation\r
-patterns vary with secondary structure.\r
-\r
-\r
->> HELP 7 <<             Help for phylogenetic trees\r
-\r
-1) Before calculating a tree, you must have an ALIGNMENT in memory. This can be\r
-input in any format or you should have just carried out a full multiple\r
-alignment and the alignment is still in memory. \r
-\r
-\r
-*************** Remember YOU MUST ALIGN THE SEQUENCES FIRST!!!! ***************\r
-\r
-\r
-The methods used are NJ (Neighbour Joining) and UPGMA. First\r
-you calculate distances (percent divergence) between all pairs of sequence from\r
-a multiple alignment; second you apply the NJ or UPGMA method to the distance matrix.\r
-\r
-2) EXCLUDE POSITIONS WITH GAPS? With this option, any alignment positions where\r
-ANY of the sequences have a gap will be ignored. This means that 'like' will be\r
-compared to 'like' in all distances, which is highly desirable. It also\r
-automatically throws away the most ambiguous parts of the alignment, which are\r
-concentrated around gaps (usually). The disadvantage is that you may throw away\r
-much of the data if there are many gaps (which is why it is difficult for us to\r
-make it the default).  \r
-\r
-\r
-\r
-3) CORRECT FOR MULTIPLE SUBSTITUTIONS? For small divergence (say <10%) this\r
-option makes no difference. For greater divergence, it corrects for the fact\r
-that observed distances underestimate actual evolutionary distances. This is\r
-because, as sequences diverge, more than one substitution will happen at many\r
-sites. However, you only see one difference when you look at the present day\r
-sequences. Therefore, this option has the effect of stretching branch lengths\r
-in trees (especially long branches). The corrections used here (for DNA or\r
-proteins) are both due to Motoo Kimura. See the documentation for details.  \r
-\r
-Where possible, this option should be used. However, for VERY divergent\r
-sequences, the distances cannot be reliably corrected. You will be warned if\r
-this happens. Even if none of the distances in a data set exceed the reliable\r
-threshold, if you bootstrap the data, some of the bootstrap distances may\r
-randomly exceed the safe limit.  \r
-\r
-4) To calculate a tree, use option 4 (DRAW TREE NOW). This gives an UNROOTED\r
-tree and all branch lengths. The root of the tree can only be inferred by\r
-using an outgroup (a sequence that you are certain branches at the outside\r
-of the tree .... certain on biological grounds) OR if you assume a degree\r
-of constancy in the 'molecular clock', you can place the root in the 'middle'\r
-of the tree (roughly equidistant from all tips).\r
-\r
-5) TOGGLE PHYLIP BOOTSTRAP POSITIONS\r
-By default, the bootstrap values are correctly placed on the tree branches of\r
-the phylip format output tree. The toggle allows them to be placed on the\r
-nodes, which is incorrect, but some display packages (e.g. TreeTool, TreeView\r
-and Phylowin) only support node labelling but not branch labelling. Care\r
-should be taken to note which branches and labels go together.\r
-\r
-6) OUTPUT FORMATS: four different formats are allowed. None of these displays\r
-the tree visually. Useful display programs accepting PHYLIP format include\r
-NJplot (from Manolo Gouy and supplied with Clustal W), TreeView (Mac-PC), and\r
-PHYLIP itself - OR get the PHYLIP package and use the tree drawing facilities\r
-there. (Get the PHYLIP package anyway if you are interested in trees). The\r
-NEXUS format can be read into PAUP or MacClade.\r
-\r
-\r
->> HELP 8 <<             Help for choosing a weight matrix\r
-\r
-For protein alignments, you use a weight matrix to determine the similarity of\r
-non-identical amino acids.  For example, Tyr aligned with Phe is usually judged \r
-to be 'better' than Tyr aligned with Pro.\r
-\r
-There are three 'in-built' series of weight matrices offered. Each consists of\r
-several matrices which work differently at different evolutionary distances. To\r
-see the exact details, read the documentation. Crudely, we store several\r
-matrices in memory, spanning the full range of amino acid distance (from almost\r
-identical sequences to highly divergent ones). For very similar sequences, it\r
-is best to use a strict weight matrix which only gives a high score to\r
-identities and the most favoured conservative substitutions. For more divergent\r
-sequences, it is appropriate to use "softer" matrices which give a high score\r
-to many other frequent substitutions.\r
-\r
-1) BLOSUM (Henikoff). These matrices appear to be the best available for \r
-carrying out database similarity (homology searches). The matrices used are:\r
-Blosum 80, 62, 45 and 30. (BLOSUM was the default in earlier Clustal W\r
-versions)\r
-\r
-2) PAM (Dayhoff). These have been extremely widely used since the late '70s.\r
-We use the PAM 20, 60, 120 and 350 matrices.\r
-\r
-3) GONNET. These matrices were derived using almost the same procedure as the\r
-Dayhoff one (above) but are much more up to date and are based on a far larger\r
-data set. They appear to be more sensitive than the Dayhoff series. We use the\r
-GONNET 80, 120, 160, 250 and 350 matrices. This series is the default for\r
-Clustal W version 1.8.\r
-\r
-We also supply an identity matrix which gives a score of 1.0 to two identical \r
-amino acids and a score of zero otherwise. This matrix is not very useful.\r
-Alternatively, you can read in your own (just one matrix, not a series).\r
-\r
-A new matrix can be read from a file on disk, if the filename consists only\r
-of lower case characters. The values in the new weight matrix must be integers\r
-and the scores should be similarities. You can use negative as well as positive\r
-values if you wish, although the matrix will be automatically adjusted to all\r
-positive scores.\r
-\r
-\r
-\r
-For DNA, a single matrix (not a series) is used. Two hard-coded matrices are \r
-available:\r
-\r
-\r
-1) IUB. This is the default scoring matrix used by BESTFIT for the comparison\r
-of nucleic acid sequences. X's and N's are treated as matches to any IUB\r
-ambiguity symbol. All matches score 1.9; all mismatches for IUB symbols score 0.\r
- \r
- \r
-2) CLUSTALW(1.6). The previous system used by Clustal W, in which matches score\r
-1.0 and mismatches score 0. All matches for IUB symbols also score 0.\r
-\r
-INPUT FORMAT  The format used for a new matrix is the same as the BLAST program.\r
-Any lines beginning with a # character are assumed to be comments. The first\r
-non-comment line should contain a list of amino acids in any order, using the\r
-1 letter code, followed by a * character. This should be followed by a square\r
-matrix of integer scores, with one row and one column for each amino acid. The\r
-last row and column of the matrix (corresponding to the * character) contain\r
-the minimum score over the whole matrix.\r
-\r
-\r
->> HELP 9 <<             Help for command line parameters\r
-\r
-                DATA (sequences)\r
-\r
--INFILE=file.ext                             :input sequences.\r
--PROFILE1=file.ext  and  -PROFILE2=file.ext  :profiles (old alignment).\r
-\r
-\r
-                VERBS (do things)\r
-\r
--OPTIONS            :list the command line parameters\r
--HELP  or -CHECK    :outline the command line params.\r
--FULLHELP           :output full help content.\r
--ALIGN              :do full multiple alignment.\r
--TREE               :calculate NJ tree.\r
--PIM                :output percent identity matrix (while calculating the tree)\r
--BOOTSTRAP(=n)      :bootstrap a NJ tree (n= number of bootstraps; def. = 1000).\r
--CONVERT            :output the input sequences in a different file format.\r
-\r
-\r
-                PARAMETERS (set things)\r
-\r
-***General settings:****\r
--INTERACTIVE :read command line, then enter normal interactive menus\r
--QUICKTREE   :use FAST algorithm for the alignment guide tree\r
--TYPE=       :PROTEIN or DNA sequences\r
--NEGATIVE    :protein alignment with negative values in matrix\r
--OUTFILE=    :sequence alignment file name\r
--OUTPUT=     :GCG, GDE, PHYLIP, PIR or NEXUS\r
--OUTORDER=   :INPUT or ALIGNED\r
--CASE        :LOWER or UPPER (for GDE output only)\r
--SEQNOS=     :OFF or ON (for Clustal output only)\r
--SEQNO_RANGE=:OFF or ON (NEW: for all output formats)\r
--RANGE=m,n   :sequence range to write starting m to m+n\r
--MAXSEQLEN=n :maximum allowed input sequence length\r
--QUIET       :Reduce console output to minimum\r
--STATS=      :Log some alignents statistics to file\r
-\r
-***Fast Pairwise Alignments:***\r
--KTUPLE=n    :word size\r
--TOPDIAGS=n  :number of best diags.\r
--WINDOW=n    :window around best diags.\r
--PAIRGAP=n   :gap penalty\r
--SCORE       :PERCENT or ABSOLUTE\r
-\r
-\r
-***Slow Pairwise Alignments:***\r
--PWMATRIX=    :Protein weight matrix=BLOSUM, PAM, GONNET, ID or filename\r
--PWDNAMATRIX= :DNA weight matrix=IUB, CLUSTALW or filename\r
--PWGAPOPEN=f  :gap opening penalty        \r
--PWGAPEXT=f   :gap opening penalty\r
-\r
-\r
-***Multiple Alignments:***\r
--NEWTREE=      :file for new guide tree\r
--USETREE=      :file for old guide tree\r
--MATRIX=       :Protein weight matrix=BLOSUM, PAM, GONNET, ID or filename\r
--DNAMATRIX=    :DNA weight matrix=IUB, CLUSTALW or filename\r
--GAPOPEN=f     :gap opening penalty        \r
--GAPEXT=f      :gap extension penalty\r
--ENDGAPS       :no end gap separation pen. \r
--GAPDIST=n     :gap separation pen. range\r
--NOPGAP        :residue-specific gaps off  \r
--NOHGAP        :hydrophilic gaps off\r
--HGAPRESIDUES= :list hydrophilic res.    \r
--MAXDIV=n      :% ident. for delay\r
--TYPE=         :PROTEIN or DNA\r
--TRANSWEIGHT=f :transitions weighting\r
--ITERATION=    :NONE or TREE or ALIGNMENT\r
--NUMITER=n     :maximum number of iterations to perform\r
--NOWEIGHTS     :disable sequence weighting\r
-\r
-\r
-***Profile Alignments:***\r
--PROFILE      :Merge two alignments by profile alignment\r
--NEWTREE1=    :file for new guide tree for profile1\r
--NEWTREE2=    :file for new guide tree for profile2\r
--USETREE1=    :file for old guide tree for profile1\r
--USETREE2=    :file for old guide tree for profile2\r
-\r
-\r
-***Sequence to Profile Alignments:***\r
--SEQUENCES   :Sequentially add profile2 sequences to profile1 alignment\r
--NEWTREE=    :file for new guide tree\r
--USETREE=    :file for old guide tree\r
-\r
-\r
-***Structure Alignments:***\r
--NOSECSTR1     :do not use secondary structure-gap penalty mask for profile 1 \r
--NOSECSTR2     :do not use secondary structure-gap penalty mask for profile 2\r
--SECSTROUT=STRUCTURE or MASK or BOTH or NONE   :output in alignment file\r
--HELIXGAP=n    :gap penalty for helix core residues \r
--STRANDGAP=n   :gap penalty for strand core residues\r
--LOOPGAP=n     :gap penalty for loop regions\r
--TERMINALGAP=n :gap penalty for structure termini\r
--HELIXENDIN=n  :number of residues inside helix to be treated as terminal\r
--HELIXENDOUT=n :number of residues outside helix to be treated as terminal\r
--STRANDENDIN=n :number of residues inside strand to be treated as terminal\r
--STRANDENDOUT=n:number of residues outside strand to be treated as terminal \r
-\r
-\r
-***Trees:***\r
--OUTPUTTREE=nj OR phylip OR dist OR nexus\r
--SEED=n        :seed number for bootstraps.\r
--KIMURA        :use Kimura's correction.   \r
--TOSSGAPS      :ignore positions with gaps.\r
--BOOTLABELS=node OR branch :position of bootstrap values in tree display\r
--CLUSTERING=   :NJ or UPGMA\r
-\r
-\r
->> HELP 0 <<             Help for tree output format options\r
-\r
-Four output formats are offered: 1) Clustal, 2) Phylip, 3) Just the distances\r
-4) Nexus\r
-\r
-None of these formats displays the results graphically. Many packages can\r
-display trees in the the PHYLIP format 2) below. It can also be imported into\r
-the PHYLIP programs RETREE, DRAWTREE and DRAWGRAM for graphical display. \r
-NEXUS format trees can be read by PAUP and MacClade.\r
-\r
-1) Clustal format output. \r
-This format is verbose and lists all of the distances between the sequences and\r
-the number of alignment positions used for each. The tree is described at the\r
-end of the file. It lists the sequences that are joined at each alignment step\r
-and the branch lengths. After two sequences are joined, it is referred to later\r
-as a NODE. The number of a NODE is the number of the lowest sequence in that\r
-NODE.   \r
-\r
-2) Phylip format output.\r
-This format is the New Hampshire format, used by many phylogenetic analysis\r
-packages. It consists of a series of nested parentheses, describing the\r
-branching order, with the sequence names and branch lengths. It can be used by\r
-the RETREE, DRAWGRAM and DRAWTREE programs of the PHYLIP package to see the\r
-trees graphically. This is the same format used during multiple alignment for\r
-the guide trees. \r
-\r
-Use this format with NJplot (Manolo Gouy), supplied with Clustal W. Some other\r
-packages that can read and display New Hampshire format are TreeView (Mac/PC),\r
-TreeTool (UNIX), and Phylowin.\r
-\r
-3) The distances only.\r
-This format just outputs a matrix of all the pairwise distances in a format\r
-that can be used by the Phylip package. It used to be useful when one could not\r
-produce distances from protein sequences in the Phylip package but is now\r
-redundant (Protdist of Phylip 3.5 now does this).\r
-\r
-4) NEXUS FORMAT TREE. This format is used by several popular phylogeny programs,\r
-including PAUP and MacClade. The format is described fully in:\r
-Maddison, D. R., D. L. Swofford and W. P. Maddison.  1997.\r
-NEXUS: an extensible file format for systematic information.\r
-Systematic Biology 46:590-621.\r
-\r
-5) TOGGLE PHYLIP BOOTSTRAP POSITIONS\r
-By default, the bootstrap values are placed on the nodes of the phylip format\r
-output tree. This is inaccurate as the bootstrap values should be associated\r
-with the tree branches and not the nodes. However, this format can be read and\r
-displayed by TreeTool, TreeView and Phylowin. An option is available to\r
-correctly place the bootstrap values on the branches with which they are\r
-associated.\r

diff --git a/binaries/help/iupred.txt b/binaries/help/iupred.txt
deleted file mode 100644 (file)
index e023ac9..0000000
--- a/binaries/help/iupred.txt
+++ /dev/null
@@ -1,45 +0,0 @@
-INTERPRETATION OF THE OUTPUT:\r
-\r
-In the case of long and short types of disorder the output  gives the\r
-likelihood of disorder for each residue, i.e. it is a value between 0 and 1,\r
-and higher values indicate higher probability of disorder. Residues with values\r
-above 0.5 can be regarded as disordered, and at this cutoff 5% of globular\r
-proteins is expected to be predicted to disordered (false positives).\r
- \r
-For the prediction type of globular domains it gives the number of globular\r
-domains and list their start and end position in the sequence. This is followed\r
-by the submitted sequence with residues of globular domains indicated by\r
-uppercase letters. \r
-\r
-\r
-SHORT SUMMARY OF THE METHOD\r
-\r
-Intrinsically unstructured/disordered proteins have no single well-defined\r
-tertiary structure in their native, functional state. Our server recognizes\r
-such regions from the amino acid sequence based on the estimated pairwise\r
-energy content. The underlying assumption is that globular proteins make a\r
-large number of interresidue interactions, providing the stabilizing energy to\r
-overcome the entropy loss during folding. In contrast, IUPs have special\r
-sequences that do not have the capacity to form sufficient interresidue\r
-interactions. Taking a set of globular proteins with known structure, we have\r
-developed a simple formalism that allows the estimation of the pairwise\r
-interaction energies of these proteins. It uses a quadratic expression in the\r
-amino acid composition, which takes into account that the contribution of an\r
-amino acid to order/disorder depends not only its own chemical type, but also\r
-on its sequential environment, including its potential interaction partners.\r
-Applying this calculation for IUP sequences, their estimated energies are\r
-clearly shifted towards less favorable energies compared to globular proteins,\r
-enabling the predicion of protein disorder on this ground. \r
-\r
-       \r
-References\r
-\r
-"The Pairwise Energy Content Estimated from Amino Acid Composition \r
-Discriminates between Folded and Intrinsically Unstructured Proteins"\r
-Zsuzsanna Dosztanyi, Veronika Csizmok, Peter Tompa and Istvan Simon\r
-J. Mol. Biol. (2005) 347, 827-839.\r
-\r
-"IUPred: web server for the prediction of intrinsically unstructured \r
-regions of proteins based on estimated energy content"\r
-Zsuzsanna Dosztanyi, Veronika Csizmok, Peter Tompa and Istvan Simon\r
-Bioinformatics (2005) 21, 3433-3434.\r

diff --git a/binaries/help/mafft_manual.htm b/binaries/help/mafft_manual.htm
deleted file mode 100644 (file)
index 3848d71..0000000
--- a/binaries/help/mafft_manual.htm
+++ /dev/null
@@ -1,721 +0,0 @@
-<html><head>\r
-<meta http-equiv="content-type" content="text/html; charset=ISO-8859-1"><title>Manpage of MAFFT</title>\r
-<link rel="stylesheet" type="text/css" href="mafft_manual_files/tt.css">\r
-</head><body>\r
-<h1>MAFFT</h1>\r
-Section: Mafft Manual (1)<br>Updated: 2007-06-09<br><a href="#index">Index</a>\r
-<a href="http://align.bmr.kyushu-u.ac.jp/mafft/software/">Return to Main Contents</a><hr>\r
-\r
-\r
-\r
-\r
-\r
-<a name="lbAB">&nbsp;</a>\r
-<h2>NAME</h2>\r
-\r
-<dl compact="compact"><dt></dt><dd>\r
-mafft - Multiple alignment program for amino acid or nucleotide sequences\r
-</dd></dl>\r
-\r
-<a name="lbAC">&nbsp;</a>\r
-<h2>SYNOPSIS</h2>\r
-\r
-<dl compact="compact"><dt></dt><dd>\r
-<dl compact="compact">\r
-<dt>\r
-<b>mafft</b> [<b>options</b>] <i>input</i> [&gt;&nbsp;<i>output</i>]\r
-</dt><dt>\r
-<b>linsi</b> <i>input</i> [&gt;&nbsp;<i>output</i>]\r
-</dt><dt>\r
-<b>ginsi</b> <i>input</i> [&gt;&nbsp;<i>output</i>]\r
-</dt><dt>\r
-<b>einsi</b> <i>input</i> [&gt;&nbsp;<i>output</i>]\r
-</dt><dt>\r
-<b>fftnsi</b> <i>input</i> [&gt;&nbsp;<i>output</i>]\r
-</dt><dt>\r
-<b>fftns</b> <i>input</i> [&gt;&nbsp;<i>output</i>]\r
-</dt><dt>\r
-<b>nwns</b> <i>input</i> [&gt;&nbsp;<i>output</i>]\r
-</dt><dt>\r
-<b>nwnsi</b> <i>input</i> [&gt;&nbsp;<i>output</i>]\r
-</dt><dt>\r
-<b>mafft-profile</b> <i>group1</i> <i>group2</i> [&gt;&nbsp;<i>output</i>]\r
-</dt><dt>\r
-<p>\r
-<i>input</i>, <i>group1</i> and <i>group2</i> must be in FASTA format.\r
-</p></dt></dl>\r
-</dd></dl>\r
-\r
-<a name="lbAD">&nbsp;</a>\r
-<h2>DESCRIPTION</h2>\r
-\r
-<dl compact="compact"><dt></dt><dd>\r
-<b>MAFFT</b> is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods.\r
-</dd></dl>\r
-<a name="lbAE">&nbsp;</a>\r
-<h3>Accuracy-oriented methods:</h3>\r
-\r
-<p>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-*L-INS-i (probably most accurate; recommended for &lt;200 sequences;\r
-iterative refinement method incorporating local pairwise alignment\r
-information):\r
-<dl compact="compact">\r
-<dt>\r
-<b>mafft</b> <b>--localpair</b> <b>--maxiterate</b>&nbsp;<i>1000</i> <i>input</i> [&gt;&nbsp;<i>output</i>]\r
-</dt><dt>\r
-<b>linsi</b> <i>input</i> [&gt;&nbsp;<i>output</i>]\r
-</dt></dl>\r
-</dd></dl>\r
-\r
-<p>\r
-</p><dl compact="compact"><dt></dt><dd>*G-INS-i (suitable for sequences\r
-of similar lengths; recommended for &lt;200 sequences; iterative\r
-refinement method incorporating global pairwise alignment information):\r
-<dl compact="compact">\r
-<dt>\r
-<b>mafft</b> <b>--globalpair</b> <b>--maxiterate</b>&nbsp;<i>1000</i> <i>input</i> [&gt;&nbsp;<i>output</i>]\r
-</dt><dt>\r
-<b>ginsi</b> <i>input</i> [&gt;&nbsp;<i>output</i>]\r
-</dt></dl>\r
-</dd></dl>\r
-\r
-<p>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-*E-INS-i (suitable for sequences containing large unalignable regions; recommended for &lt;200 sequences):\r
-<dl compact="compact">\r
-<dt>\r
-<b>mafft</b> <b>--ep</b>&nbsp;<i>0</i> <b>--genafpair</b> <b>--maxiterate</b>&nbsp;<i>1000</i> <i>input</i> [&gt;&nbsp;<i>output</i>]\r
-</dt><dt>\r
-<b>einsi</b> <i>input</i> [&gt;&nbsp;<i>output</i>]\r
-</dt><dd>\r
-<p>\r
-</p></dd><dd>For E-INS-i, the\r
-<b>--ep</b>\r
-<i>0</i>\r
-option is recommended to allow large gaps.\r
-</dd></dl>\r
-</dd></dl>\r
-\r
-<a name="lbAF">&nbsp;</a>\r
-<h3>Speed-oriented methods:</h3>\r
-\r
-<p>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-*FFT-NS-i (iterative refinement method; two cycles only):\r
-<dl compact="compact">\r
-<dt>\r
-<b>mafft</b> <b>--retree</b>&nbsp;<i>2</i> <b>--maxiterate</b>&nbsp;<i>2</i> <i>input</i> [&gt;&nbsp;<i>output</i>]\r
-</dt><dt>\r
-<b>fftnsi</b> <i>input</i> [&gt;&nbsp;<i>output</i>]\r
-</dt></dl>\r
-</dd></dl>\r
-\r
-<p>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-*FFT-NS-i (iterative refinement method; max. 1000 iterations):\r
-<dl compact="compact">\r
-<dt>\r
-<b>mafft</b> <b>--retree</b>&nbsp;<i>2</i> <b>--maxiterate</b>&nbsp;<i>1000</i> <i>input</i> [&gt;&nbsp;<i>output</i>]\r
-</dt></dl>\r
-</dd></dl>\r
-\r
-<p>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-*FFT-NS-2 (fast; progressive method):\r
-<dl compact="compact">\r
-<dt>\r
-<b>mafft</b> <b>--retree</b>&nbsp;<i>2</i> <b>--maxiterate</b>&nbsp;<i>0</i> <i>input</i> [&gt;&nbsp;<i>output</i>]\r
-</dt><dt>\r
-<b>fftns</b> <i>input</i> [&gt;&nbsp;<i>output</i>]\r
-</dt></dl>\r
-</dd></dl>\r
-\r
-<p>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-*FFT-NS-1 (very fast; recommended for &gt;2000 sequences; progressive method with a rough guide tree):\r
-<dl compact="compact">\r
-<dt>\r
-<b>mafft</b> <b>--retree</b>&nbsp;<i>1</i> <b>--maxiterate</b>&nbsp;<i>0</i> <i>input</i> [&gt;&nbsp;<i>output</i>]\r
-</dt></dl>\r
-</dd></dl>\r
-\r
-<p>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-*NW-NS-i (iterative refinement method without FFT approximation; two cycles only):\r
-<dl compact="compact">\r
-<dt>\r
-<b>mafft</b> <b>--retree</b>&nbsp;<i>2</i> <b>--maxiterate</b>&nbsp;<i>2</i> <b>--nofft</b>&nbsp;<i>input</i> [&gt;&nbsp;<i>output</i>]\r
-</dt><dt>\r
-<b>nwnsi</b> <i>input</i> [&gt;&nbsp;<i>output</i>]\r
-</dt></dl>\r
-</dd></dl>\r
-\r
-<p>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-*NW-NS-2 (fast; progressive method without the FFT approximation):\r
-<dl compact="compact">\r
-<dt>\r
-<b>mafft</b> <b>--retree</b>&nbsp;<i>2</i> <b>--maxiterate</b>&nbsp;<i>0</i> <b>--nofft</b>&nbsp;<i>input</i> [&gt;&nbsp;<i>output</i>]\r
-</dt><dt>\r
-<b>nwns</b> <i>input</i> [&gt;&nbsp;<i>output</i>]\r
-</dt></dl>\r
-</dd></dl>\r
-\r
-<p>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-*NW-NS-PartTree-1 (recommended for ~10,000 to ~50,000 sequences; progressive method with the PartTree algorithm):\r
-<dl compact="compact">\r
-<dt>\r
-<b>mafft</b> <b>--retree</b>&nbsp;<i>1</i> <b>--maxiterate</b>&nbsp;<i>0</i> <b>--nofft</b>&nbsp;<b>--parttree</b> <i>input</i> [&gt;&nbsp;<i>output</i>]\r
-</dt></dl>\r
-</dd></dl>\r
-\r
-<a name="lbAG">&nbsp;</a>\r
-<h3>Group-to-group alignments</h3>\r
-\r
-<dl compact="compact">\r
-<dt>\r
-</dt><dl compact="compact"><dt></dt><dd>\r
-<b>mafft-profile</b> <i>group1</i> <i>group2</i> [&gt;&nbsp;<i>output</i>]\r
-<p>\r
-</p></dd><dd>or:\r
-<p>\r
-<b>mafft</b> <b>--maxiterate</b>&nbsp;<i>1000</i> <b>--seed</b>&nbsp;<i>group1</i> <b>--seed</b>&nbsp;<i>group2</i> /dev/null [&gt;&nbsp;<i>output</i>]\r
-</p></dd></dl>\r
-\r
-\r
-\r
-</dl>\r
-<a name="lbAH">&nbsp;</a>\r
-<h2>OPTIONS</h2>\r
-\r
-<a name="lbAI">&nbsp;</a>\r
-<h3>Algorithm</h3>\r
-\r
-<dl compact="compact"><dt></dt><dd>\r
-<p>\r
-\r
-<b>--auto</b>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Automatically selects an appropriate strategy from L-INS-i, FFT-NS-i and FFT-NS-2, according to data \r
-size.  Default: off (always FFT-NS-2)\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--6merpair</b>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Distance is calculated based on the number of shared 6mers.  Default: on\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--globalpair</b>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-All pairwise alignments are computed with the Needleman-Wunsch\r
-algorithm.  More accurate but slower \r
-than --6merpair.  Suitable for a set of\r
-globally alignable sequences.  Applicable to \r
-up to ~200 sequences.  A combination with --maxiterate 1000 is recommended (G-INS-i).  Default: off (6mer distance is used)\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--localpair</b>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-All pairwise alignments are computed with the Smith-Waterman\r
-algorithm.  More accurate but slower\r
-than --6merpair.  Suitable for a set of \r
-locally alignable sequences.  Applicable to \r
-up to ~200 sequences.  A combination with --maxiterate 1000 is recommended (L-INS-i).  Default: off (6mer distance is used)\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--genafpair</b>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-All pairwise alignments are computed with a local\r
-algorithm with the generalized affine gap cost\r
-(Altschul 1998).  More accurate but slower\r
-than --6merpair.  Suitable when large internal gaps\r
-are expected.  Applicable to \r
-up to ~200 sequences.  A combination with --maxiterate 1000 is recommended (E-INS-i).  Default: off (6mer distance is used)\r
-</dd></dl>\r
-\r
-\r
-\r
-\r
-\r
-\r
-\r
-<p>\r
-\r
-<b>--fastapair</b>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-All pairwise alignments are computed with FASTA (Pearson and Lipman 1988).\r
-FASTA is required.  Default: off (6mer distance is used)\r
-</dd></dl>\r
-\r
-\r
-\r
-\r
-\r
-\r
-\r
-<p>\r
-\r
-<b>--weighti</b> <i>number</i>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Weighting factor for the consistency term calculated from pairwise alignments.  Valid when \r
-either of --blobalpair, --localpair,  --genafpair, --fastapair or \r
---blastpair is selected.  Default: 2.7\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--retree</b> <i>number</i>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Guide tree is built <i>number</i> times in the \r
-progressive stage.  Valid with 6mer distance.  Default: 2\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--maxiterate</b> <i>number</i>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-<i>number</i> cycles of iterative refinement are performed.  Default: 0\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--fft</b>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Use FFT approximation in group-to-group alignment.  Default: on\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--nofft</b>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Do not use FFT approximation in group-to-group alignment.  Default: off\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--noscore</b>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Alignment score is not checked in the iterative refinement stage.  Default: off (score is checked)\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--memsave</b>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Use the Myers-Miller (1988) algorithm.  Default: automatically turned on when the alignment length exceeds 10,000 (aa/nt).\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--parttree</b>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Use a fast tree-building method (PartTree, Katoh and Toh 2007) with\r
-the 6mer distance.  Recommended for a large number (&gt; ~10,000) \r
-of sequences are input.  Default: off\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--dpparttree</b>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-The PartTree algorithm is used with distances based on DP.  Slightly\r
-more accurate and slower than --parttree.  Recommended for a large\r
-number (&gt; ~10,000) of sequences are input.   Default: off\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--fastaparttree</b>\r
-</p><dl compact="compact"><dt></dt><dd>The PartTree algorithm is used\r
-with distances based on FASTA. Slightly more accurate and slower than\r
---parttree. Recommended for a large number (&gt; ~10,000) of sequences\r
-are input. FASTA is required. Default: off\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--partsize</b> <i>number</i>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-The number of partitions in the PartTree algorithm.  Default: 50\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--groupsize</b> <i>number</i>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Do not make alignment larger than <i>number</i> sequences. Valid only with the --*parttree options.  Default: the number of input sequences\r
-</dd></dl>\r
-\r
-</dd></dl>\r
-\r
-<a name="lbAJ">&nbsp;</a>\r
-<h3>Parameter</h3>\r
-\r
-<dl compact="compact"><dt></dt><dd>\r
-<p>\r
-\r
-<b>--op</b> <i>number</i>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Gap opening penalty at group-to-group alignment.  Default: 1.53\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--ep</b> <i>number</i>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Offset value, which works like gap extension penalty, for\r
-group-to-group alignment.  Deafult: 0.123\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--lop</b> <i>number</i>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Gap opening penalty at local pairwise \r
-alignment.  Valid when\r
-the --localpair or --genafpair option is selected.  Default: -2.00\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--lep</b> <i>number</i>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Offset value at local pairwise alignment.  Valid when\r
-the --localpair or --genafpair option is selected.  Default: 0.1\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--lexp</b> <i>number</i>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Gap extension penalty at local pairwise alignment.  Valid when\r
-the --localpair or --genafpair option is selected.  Default: -0.1\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--LOP</b> <i>number</i>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Gap opening penalty to skip the alignment.  Valid when the\r
---genafpair option is selected.   Default: -6.00\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--LEXP</b> <i>number</i>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Gap extension penalty to skip the alignment.  Valid when the\r
---genafpair option is selected.   Default: 0.00\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--bl</b> <i>number</i>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-BLOSUM <i>number</i> matrix (Henikoff and Henikoff 1992) is used.  <i>number</i>=30, 45, 62 or 80.  Default: 62\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--jtt</b> <i>number</i>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-JTT PAM <i>number</i> (Jones et al. 1992) matrix is used.  <i>number</i>&gt;0.  Default: BLOSUM62\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--tm</b> <i>number</i>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Transmembrane PAM <i>number</i> (Jones et al. 1994) matrix is used.  <i>number</i>&gt;0.  Default: BLOSUM62\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--aamatrix</b> <i>matrixfile</i>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Use a user-defined AA scoring matrix.  The format of <i>matrixfile</i> is\r
-the same to that of BLAST.  Ignored when nucleotide sequences are input.   Default: BLOSUM62\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--fmodel</b>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Incorporate the AA/nuc composition information into\r
-the scoring matrix.  Deafult: off\r
-</dd></dl>\r
-\r
-</dd></dl>\r
-\r
-<a name="lbAK">&nbsp;</a>\r
-<h3>Output</h3>\r
-\r
-<dl compact="compact"><dt></dt><dd>\r
-<p>\r
-\r
-<b>--clustalout</b>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Output format: clustal format.  Default: off (fasta format)\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--inputorder</b>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Output order: same as input.  Default: on\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--reorder</b>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Output order: aligned.  Default: off (inputorder)\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--treeout</b>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Guide tree is output to the <i>input</i>.tree file.  Default: off\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--quiet</b>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Do not report progress.  Default: off\r
-</dd></dl>\r
-\r
-</dd></dl>\r
-\r
-<a name="lbAL">&nbsp;</a>\r
-<h3>Input</h3>\r
-\r
-<dl compact="compact"><dt></dt><dd>\r
-<p>\r
-\r
-<b>--nuc</b>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Assume the sequences are nucleotide.  Deafult: auto\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--amino</b>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Assume the sequences are amino acid.  Deafult: auto\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--seed</b> <i>alignment1</i> [<b>--seed</b> <i>alignment2</i> <b>--seed</b> <i>alignment3</i> ...]\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Seed alignments given in <i>alignment_n</i> (fasta format) are aligned with \r
-sequences in <i>input</i>.  The alignment within every seed is preserved.  \r
-</dd></dl>\r
-\r
-</dd></dl>\r
-\r
-<a name="lbAM">&nbsp;</a>\r
-<h2>FILES</h2>\r
-\r
-<dl compact="compact"><dt></dt><dd>\r
-<p>\r
-\r
-Mafft stores the input sequences and other files in a temporary directory, which by default is located in\r
-<i>/tmp</i>.\r
-</p></dd></dl>\r
-\r
-<a name="lbAN">&nbsp;</a>\r
-<h2>ENVIONMENT</h2>\r
-\r
-<dl compact="compact"><dt></dt><dd>\r
-<p>\r
-\r
-<b>MAFFT_BINARIES</b>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Indicates the location of the binary files used by mafft. By default, they are searched in\r
-<i>/usr/local/lib/mafft</i>, but on Debian systems, they are searched in\r
-<i>/usr/lib/mafft</i>.\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>FASTA_4_MAFFT</b>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-This variable can be set to indicate to mafft the location to the fasta34 program if it is not in the PATH.\r
-</dd></dl>\r
-\r
-</dd></dl>\r
-\r
-<a name="lbAO">&nbsp;</a>\r
-<h2>SEE ALSO</h2>\r
-\r
-<dl compact="compact"><dt></dt><dd>\r
-<p>\r
-\r
-</p><p>\r
-<b><a href="http://align.bmr.kyushu-u.ac.jp/mafft/software/manual/mafft-homologs2.1.html">mafft-homologs</a></b>(1)\r
-</p></dd></dl>\r
-\r
-<a name="lbAP">&nbsp;</a>\r
-<h2>REFERENCES</h2>\r
-\r
-<dl compact="compact"><dt></dt><dd>\r
-</dd></dl>\r
-<a name="lbAQ">&nbsp;</a>\r
-<h3>In English</h3>\r
-\r
-<p>\r
-</p><dl compact="compact"><dt></dt><dd>*Katoh and Toh (Bioinformatics\r
-23:372-374, 2007) PartTree: an algorithm to build an approximate tree\r
-from a large number of unaligned sequences (describes the PartTree\r
-algorithm).\r
-</dd></dl>\r
-\r
-<p>\r
-</p><dl compact="compact"><dt></dt><dd>*Katoh, Kuma, Toh and Miyata\r
-(Nucleic Acids Res. 33:511-518, 2005) MAFFT version 5: improvement in\r
-accuracy of multiple sequence alignment (describes [ancestral versions\r
-of] the G-INS-i, L-INS-i and E-INS-i strategies)\r
-</dd></dl>\r
-\r
-<p>\r
-</p><dl compact="compact"><dt></dt><dd>*Katoh, Misawa, Kuma and Miyata\r
-(Nucleic Acids Res. 30:3059-3066, 2002) MAFFT: a novel method for rapid\r
-multiple sequence alignment based on fast Fourier transform (describes\r
-the FFT-NS-1, FFT-NS-2 and FFT-NS-i strategies)\r
-</dd></dl>\r
-\r
-<a name="lbAR">&nbsp;</a>\r
-<h3>In Japanese</h3>\r
-\r
-<p>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-*Katoh and Misawa (Seibutsubutsuri 46:312-317, 2006) Multiple Sequence Alignments: the Next Generation\r
-</dd></dl>\r
-\r
-<p>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-*Katoh and Kuma (Kagaku to Seibutsu 44:102-108, 2006) Jissen-teki Multiple Alignment\r
-</dd></dl>\r
-\r
-\r
-<a name="lbAS">&nbsp;</a>\r
-<h2>AUTHORS</h2>\r
-\r
-<dl compact="compact"><dt></dt><dd>\r
-<p>\r
-\r
-<b>Kazutaka Katoh</b> &lt;katoh_at_bioreg.kyushu-u.ac.jp&gt;\r
-</p><p>\r
-</p><dl compact="compact">\r
-<dt></dt><dd>\r
-Wrote Mafft.\r
-</dd></dl>\r
-<p>\r
-\r
-<b>Charles Plessy</b> &lt;charles-debian-nospam_at_plessy.org&gt;\r
-</p><p>\r
-</p><dl compact="compact">\r
-<dt></dt><dd>\r
-Wrote this manpage in DocBook XML for the Debian distribution, using Mafft's homepage as a template.\r
-</dd></dl>\r
-</dd></dl>\r
-\r
-<a name="lbAT">&nbsp;</a>\r
-<h2>COPYRIGHT</h2>\r
-\r
-<dl compact="compact"><dt></dt><dd>\r
-Copyright © 2002-2007 Kazutaka Katoh (mafft)\r
-<br>\r
-\r
-Copyright © 2007 Charles Plessy (this manpage)\r
-<br>\r
-\r
-<p>\r
-\r
-Mafft and its manpage are offered under the following conditions:\r
-</p><p>Redistribution and use in source and binary forms, with or\r
-without modification, are permitted provided that the following\r
-conditions are met:\r
-</p><p>\r
-</p><dl compact="compact"><dt></dt><dd>\r
- 1.Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.\r
-</dd></dl>\r
-\r
-<p>\r
-</p><dl compact="compact"><dt></dt><dd> 2.Redistributions in binary\r
-form must reproduce the above copyright notice, this list of conditions\r
-and the following disclaimer in the documentation and/or other\r
-materials provided with the distribution.\r
-</dd></dl>\r
-\r
-<p>\r
-</p><dl compact="compact"><dt></dt><dd> 3.The name of the author may\r
-not be used to endorse or promote products derived from this software\r
-without specific prior written permission.\r
-</dd></dl>\r
-\r
-<p>THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR\r
-IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED\r
-WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\r
-DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT,\r
-INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES\r
-(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR\r
-SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)\r
-HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,\r
-STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING\r
-IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE\r
-POSSIBILITY OF SUCH DAMAGE.\r
-<br>\r
-\r
-</p></dd></dl>\r
-\r
-<p>\r
-\r
-</p><hr>\r
-<a name="index">&nbsp;</a><h2>Index</h2>\r
-<dl>\r
-<dt><a href="#lbAB">NAME</a></dt><dd>\r
-</dd><dt><a href="#lbAC">SYNOPSIS</a></dt><dd>\r
-</dd><dt><a href="#lbAD">DESCRIPTION</a></dt><dd>\r
-<dl>\r
-<dt><a href="#lbAE">Accuracy-oriented methods:</a></dt><dd>\r
-</dd><dt><a href="#lbAF">Speed-oriented methods:</a></dt><dd>\r
-</dd><dt><a href="#lbAG">Group-to-group alignments</a></dt><dd>\r
-</dd></dl>\r
-</dd><dt><a href="#lbAH">OPTIONS</a></dt><dd>\r
-<dl>\r
-<dt><a href="#lbAI">Algorithm</a></dt><dd>\r
-</dd><dt><a href="#lbAJ">Parameter</a></dt><dd>\r
-</dd><dt><a href="#lbAK">Output</a></dt><dd>\r
-</dd><dt><a href="#lbAL">Input</a></dt><dd>\r
-</dd></dl>\r
-</dd><dt><a href="#lbAM">FILES</a></dt><dd>\r
-</dd><dt><a href="#lbAN">ENVIONMENT</a></dt><dd>\r
-</dd><dt><a href="#lbAO">SEE ALSO</a></dt><dd>\r
-</dd><dt><a href="#lbAP">REFERENCES</a></dt><dd>\r
-<dl>\r
-<dt><a href="#lbAQ">In English</a></dt><dd>\r
-</dd><dt><a href="#lbAR">In Japanese</a></dt><dd>\r
-</dd></dl>\r
-</dd><dt><a href="#lbAS">AUTHORS</a></dt><dd>\r
-</dd><dt><a href="#lbAT">COPYRIGHT</a></dt><dd>\r
-</dd></dl>\r
-<hr>\r
-This document was created by\r
-man2html,\r
-using the manual pages.<br>\r
-Time: 02:26:04 GMT, August 14, 2007\r
-</body></html>
\ No newline at end of file

diff --git a/binaries/help/muscle3.6.html b/binaries/help/muscle3.6.html
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-  <o:Author>Bob Edgar</o:Author>\r
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-ol\r
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-ul\r
-       {margin-bottom:0in;}\r
--->\r
-</style>\r
-<!--[if gte mso 10]>\r
-<style>\r
- /* Style Definitions */\r
- table.MsoNormalTable\r
-       {mso-style-name:"Table Normal";\r
-       mso-tstyle-rowband-size:0;\r
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-       font-size:10.0pt;\r
-       font-family:"Times New Roman";}\r
-</style>\r
-<![endif]-->\r
-</head>\r
-\r
-<body lang=EN-US link=blue vlink=purple style='tab-interval:.25in'>\r
-\r
-<div class=Section1>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=MsoNormal align=right style='text-align:right'><span style='font-size:\r
-24.0pt;font-family:"Arial Black"'>MUSCLE User Guide<o:p></o:p></span></p>\r
-\r
-<p class=MsoNormal align=right style='text-align:right'><u>&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;&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;&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;&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;&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;&nbsp;&nbsp;<o:p></o:p></u></p>\r
-\r
-<p class=MsoNormal align=right style='text-align:right'><b><span\r
-style='font-family:Arial'><o:p>&nbsp;</o:p></span></b></p>\r
-\r
-<p class=MsoNormal><span style='font-family:Arial'><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MsoNormal><span style='font-family:Arial'><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MsoNormal><span style='font-family:Arial'><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MsoNormal><span style='font-family:Arial'><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MsoNormal><span style='font-family:Arial'><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MsoNormal><span style='font-family:Arial'>Multiple sequence comparison\r
-by log-expectation<o:p></o:p></span></p>\r
-\r
-<p class=MsoNormal><span class=GramE><span style='font-family:Arial'>by</span></span><span\r
-style='font-family:Arial'> Robert C. Edgar<o:p></o:p></span></p>\r
-\r
-<p class=MsoNormal><span style='font-family:Arial'><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MsoNormal><span style='font-family:Arial'>Version 3.6<o:p></o:p></span></p>\r
-\r
-<p class=MsoNormal><span style='font-family:Arial'>September 2005<o:p></o:p></span></p>\r
-\r
-<p class=MsoNormal><span style='font-family:Arial'><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MsoNormal><span style='font-family:Arial'><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MsoNormal><span style='font-family:Arial'><a\r
-href="http://www.drive5.com/muscle">http://www.drive5.com/muscle</a><o:p></o:p></span></p>\r
-\r
-<p class=MsoNormal><span class=GramE><span style='font-family:Arial'>email</span></span><span\r
-style='font-family:Arial'>: muscle (at) drive5.com<o:p></o:p></span></p>\r
-\r
-<p class=MsoNormal><span style='font-family:Arial'><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MsoNormal><span style='font-family:Arial'>MUSCLE is updated regularly.\r
-Send me an e-mail if you would like to be notified of new releases.<o:p></o:p></span></p>\r
-\r
-<p class=MsoNormal><span style='font-family:Arial'><span\r
-style='mso-spacerun:yes'> </span><o:p></o:p></span></p>\r
-\r
-<p class=MsoNormal><span style='font-family:Arial'><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MsoNormal><i><span style='font-family:Arial'>Citation:<o:p></o:p></span></i></p>\r
-\r
-<p class=MsoNormal><span style='font-family:Arial'><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MsoNormal><span style='font-family:Arial'><a\r
-href="http://nar.oupjournals.org/cgi/content/full/32/5/1792?ijkey=48Nmt1tta0fMg&amp;keytype=ref">Edgar,\r
-Robert C. (2004), MUSCLE: multiple sequence alignment with high accuracy and\r
-high throughput, <i>Nucleic Acids Research</i> <b>32</b>(5), 1792-97</a>.<o:p></o:p></span></p>\r
-\r
-<p class=MsoNormal><span style='font-family:Arial'><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MsoNormal><i><span style='font-family:Arial'>For a complete\r
-description of the algorithm, see also:<o:p></o:p></span></i></p>\r
-\r
-<p class=MsoNormal><span style='font-family:Arial'><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MsoNormal><span style='font-family:Arial'><a\r
-href="http://www.biomedcentral.com/1471-2105/5/113">Edgar, Robert C (2004), <span\r
-style='mso-bidi-font-weight:bold'>MUSCLE: a multiple sequence alignment method\r
-with reduced time and <span class=GramE>space</span> complexity</span>. <i\r
-style='mso-bidi-font-style:normal'>BMC Bioinformatics</i>, <b style='mso-bidi-font-weight:\r
-normal'>5</b>(1):113</a>.<br clear=all style='page-break-before:always'>\r
-</span><b><span style='font-size:16.0pt;font-family:Arial'>Table of Contents<o:p></o:p></span></b></p>\r
-\r
-<p class=MsoToc1 style='tab-stops:right dotted 431.5pt'><!--[if supportFields]><span\r
-style='font-family:Arial'><span style='mso-element:field-begin'></span><span\r
-style='mso-spacerun:yes'> </span>TOC \o &quot;1-3&quot; \h \z \u <span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954755">1\r
-Introduction<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 _Toc113954755 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>3</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700350035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc1 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954756">2\r
-Quick Start<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 _Toc113954756 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>3</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700350036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954757">2.1\r
-Installation<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 _Toc113954757 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>3</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700350037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954758">2.2\r
-Making an alignment<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 _Toc113954758 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>3</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700350038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954759">2.3\r
-Large alignments<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 _Toc113954759 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>3</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700350039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954760">2.4\r
-Faster speed<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 _Toc113954760 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>4</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700360030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954761">2.5\r
-Huge alignments<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 _Toc113954761 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>4</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700360031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954762">2.6\r
-Accuracy: caveat emptor<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
-_Toc113954762 \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'>4</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700360032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954763">2.7\r
-Pipelining<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 _Toc113954763 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>4</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700360033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954764">2.8\r
-Refining an existing alignment<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 _Toc113954764 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>4</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700360034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954765">2.9\r
-Using a pre-computed guide tree<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 _Toc113954765 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>4</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700360035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954766">2.10\r
-Profile-profile alignment<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
-_Toc113954766 \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'>5</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700360036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954767">2.11\r
-Adding sequences to an existing alignment<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 _Toc113954767 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>5</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700360037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954768">2.12\r
-Sequence clustering<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 _Toc113954768 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>5</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700360038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954769">2.13\r
-Specifying a substitution 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 _Toc113954769 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='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>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700360039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954770">2.14\r
-Refining a long alignment<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
-_Toc113954770 \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'>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>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700370030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc1 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954771">3\r
-File Formats<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 _Toc113954771 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='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>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700370031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954772">3.1\r
-Input files<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 _Toc113954772 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='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>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700370032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954773">3.1.1\r
-Amino acid sequences<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 _Toc113954773 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='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>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700370033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954774">3.1.2\r
-Nucleotide sequences<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 _Toc113954774 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='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>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700370034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954775">3.1.3\r
-Determining sequence type<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
-_Toc113954775 \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'>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>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700370035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954776">3.2\r
-Output files<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 _Toc113954776 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='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>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700370036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954777">3.2.1\r
-Sequence grouping<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 _Toc113954777 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='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>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700370037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954778">3.3\r
-CLUSTALW format<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 _Toc113954778 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='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>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700370038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954779">3.4\r
-MSF format<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 _Toc113954779 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='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>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700370039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954780">3.5\r
-HTML format<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 _Toc113954780 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='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>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700380030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954781">3.6\r
-Phylip format<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 _Toc113954781 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='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>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700380031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc1 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954782">4\r
-Using MUSCLE<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 _Toc113954782 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='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>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700380032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954783">4.1\r
-How the algorithm works<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
-_Toc113954783 \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'>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>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700380033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954784">4.2\r
-Command-line options<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 _Toc113954784 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='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>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700380034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954785">4.3\r
-The maxiters option<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 _Toc113954785 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='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>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700380035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954786">4.4\r
-The maxtrees option<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 _Toc113954786 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='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>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700380036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954787">4.5\r
-The maxhours option<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 _Toc113954787 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='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>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700380037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954788">4.6\r
-The maxmb option<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 _Toc113954788 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='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>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700380038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954789">4.7\r
-The profile scoring function<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 _Toc113954789 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='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>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700380039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954790">4.8\r
-Diagonal optimization<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 _Toc113954790 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='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>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700390030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954791">4.9\r
-Anchor optimization<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 _Toc113954791 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='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>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700390031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954792">4.10\r
-Log file<span style='color:windowtext;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:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc113954792 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='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>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700390032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954793">4.11\r
-Progress messages<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 _Toc113954793 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='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>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700390033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954794">4.12\r
-Running out of memory<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 _Toc113954794 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>12</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700390034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954795">4.13\r
-Troubleshooting<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 _Toc113954795 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>12</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700390035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954796">4.14\r
-Technical support<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 _Toc113954796 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>12</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700390036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc1 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954797">5\r
-Command Line Reference<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 _Toc113954797 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='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>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700390037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoNormal><!--[if supportFields]><span style='font-family:Arial'><span\r
-style='mso-element:field-end'></span></span><![endif]--><span style='font-family:\r
-Arial'><o:p>&nbsp;</o:p></span></p>\r
-\r
-<b><span style='font-size:16.0pt;font-family:Arial;mso-fareast-font-family:\r
-"MS Mincho";mso-bidi-font-family:"Times New Roman";mso-font-kerning:16.0pt;\r
-mso-ansi-language:EN-US;mso-fareast-language:JA;mso-bidi-language:AR-SA'><br\r
-clear=all style='page-break-before:always'>\r
-</span></b>\r
-\r
-<h1 style='margin-left:0in;text-indent:0in'><a name="_Toc113954755"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial;mso-bidi-font-family:Arial'><span\r
-style='mso-list:Ignore'>1 </span></span><![endif]>Introduction</a></h1>\r
-\r
-<p class=MsoNormal>MUSCLE is a program for creating multiple alignments of\r
-amino acid or nucleotide sequences. A range of options is provided that give\r
-you the choice of optimizing accuracy, speed, or some compromise between the\r
-two. Default parameters are those that give the best average accuracy in our\r
-tests. Using versions current at the time of writing, my tests show that MUSCLE\r
-can achieve both better average accuracy and better speed than CLUSTALW or T&#8209;Coffee,\r
-depending on the chosen options. Many command line options are provided to vary\r
-the internals of the algorithm; some of these will primarily be of interest to\r
-algorithm developers who wish to better understand which features of the algorithm\r
-are important in different circumstances.</p>\r
-\r
-<h1 style='margin-left:0in;text-indent:0in'><a name="_Toc113954756"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial;mso-bidi-font-family:Arial'><span\r
-style='mso-list:Ignore'>2 </span></span><![endif]>Quick Start</a></h1>\r
-\r
-<p class=MsoNormal>The MUSCLE algorithm is delivered as a command-line program\r
-called <i>muscle</i>. If you are running under Linux or <span class=GramE>Unix</span>\r
-you will be working at a shell prompt. If you are running under Windows, you should\r
-be in a command window (nostalgically known to us older people as a DOS prompt).\r
-If you don't know how to use command-line programs, you should get help from a\r
-local guru.</p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954757"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2.1 </span></span><![endif]>Installation</a></h2>\r
-\r
-<p class=MsoNormal>Copy the <i>muscle</i> binary file to a directory that is\r
-accessible from your computer. That's it\97there are no configuration files,\r
-libraries, environment variables or other settings to worry about. If you are\r
-using Windows, then the binary file is named <i>muscle.exe</i>. From now on <i>muscle</i>\r
-should be understood to mean &quot;<i>muscle</i> if you are using Linux or <span\r
-class=GramE>Unix</span>, <i>muscle.exe</i> if you are using Windows&quot;.<o:p></o:p></p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954758"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2.2 </span></span><![endif]>Making\r
-an alignment</a></h2>\r
-\r
-<p class=MsoNormal>Make a FASTA file containing some sequences. (If you are not\r
-familiar with FASTA format, it is described in detail later in this Guide.) For\r
-now, just to make things fast, limit the number of sequence in the file to no\r
-more than 50 and the sequence length to be no more than 500. Call the input\r
-file <span class=SpellE><i>seqs.fa</i></span>. (An example file named <span\r
-class=SpellE><i>seqs.fa</i></span> is distributed with the standard MUSCLE\r
-package). Make sure the directory containing the <i>muscle</i> binary is in\r
-your path. (If it isn't, you can run it by typing the full path name, and the\r
-following example command lines must be changed accordingly). Now type:</p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=Code>muscle -in seqs.fa -out seqs.afa</p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=MsoNormal>You should see some progress messages. If <i>muscle</i> completes\r
-successfully, it will create a file <span class=SpellE><i>seqs.afa</i></span>\r
-containing the alignment. By default, output is created in &quot;aligned\r
-FASTA&quot; format (hence the <i>.<span class=SpellE>afa</span></i> extension).\r
-This is just like regular FASTA except that gaps are added in order to align\r
-the sequences. This is a nice format for computers but not very readable for\r
-people, so to look at the alignment you will want an alignment viewer such as <span\r
-class=SpellE>Belvu</span>, or a script that converts FASTA to a more readable format.\r
-You can also use the \96<span class=SpellE><i>clw</i></span> command-line option\r
-to request output in CLUSTALW format, which is easier to understand for people.\r
-If <i>muscle</i> gives an error message and you don't know how to fix it,\r
-please read the Troubleshooting section.<o:p></o:p></p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=MsoNormal>The default settings are designed to give the best accuracy,\r
-so this may be all you need to know.</p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954759"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2.3 </span></span><![endif]>Large\r
-alignments</a></h2>\r
-\r
-<p class=MsoNormal>If you have a large number of sequences (a few thousand), or\r
-they are very long, then the default settings of may be too slow for practical\r
-use. A good compromise between speed and accuracy is to run just the first two\r
-iterations of the algorithm. On average, this gives accuracy comparable to\r
-T-Coffee and speeds much faster than CLUSTALW. This is done by the option <i>\96maxiters\r
-2</i>, as in the following example.</p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=Code>muscle -in seqs.fa -out seqs.afa -maxiters 2</p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954760"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2.4 </span></span><![endif]>Faster\r
-speed</a></h2>\r
-\r
-<p class=MsoNormal>The <i>\96<span class=SpellE>diags</span></i> option enables\r
-an optimization for speed by finding common words (6-mers in a compressed amino\r
-acid alphabet) between the two sequences as seeds for diagonals. This is\r
-related to optimizations in programs such as BLAST and FASTA: you get faster speed,\r
-but sometimes lower average accuracy. For large numbers of closely related\r
-sequences, this option works very well.</p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=MsoNormal>If you want the fastest possible speed, then the following\r
-example shows the applicable options for proteins.</p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=Code>muscle -in seqs.fa -out seqs.afa -maxiters 1 -diags -sv\r
--distance1 kbit20_3</p>\r
-\r
-<p class=Code><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=MsoNormal>For nucleotides, use:</p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=Code>muscle -in seqs.fa -out seqs.afa -maxiters 1 -diags</p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=MsoNormal>At the time of writing, <i>muscle</i> with these options is faster\r
-than any other multiple sequence alignment <span class=GramE>program</span>\r
-that I have tested. The alignments are not bad, especially when the sequences\r
-are closely related. However, as you might expect, this blazing speed comes at\r
-the cost of the lowest average accuracy of the options that <i>muscle</i>\r
-provides.</p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954761"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2.5 </span></span><![endif]>Huge\r
-alignments</a></h2>\r
-\r
-<p class=MsoNormal>If you have a <i>very</i> large number of sequences (several\r
-thousand), or they are very long, then the <i>kbit20_3</i> option may cause\r
-problems because it needs a relatively large amount of memory. Better is to use\r
-the default distance measure, which is roughly 2× or 3× slower but needs less\r
-memory, like this:</p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=Code>muscle -in seqs.fa -out seqs.afa -maxiters 1 -diags1 -sv</p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954762"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2.6 </span></span><![endif]>Accuracy:\r
-caveat emptor</a></h2>\r
-\r
-<p class=MsoNormal>Why do I keep using the clumsy phrase &quot;average\r
-accuracy&quot; instead of just saying &quot;accuracy&quot;? That's because the\r
-quality of alignments produced by MUSCLE varies, as do those produced other programs\r
-such as CLUSTALW and T-Coffee. The state of the art leaves plenty of room for\r
-improvement. Sometimes the fastest speed options to <i>muscle</i> give\r
-alignments that are better than T-Coffee, though the reverse will more often be\r
-the case. With challenging sets of sequences, it is a good idea to make several\r
-different alignments using different <i>muscle</i> options and to try other programs\r
-too. Regions where different alignments agree are more believable than regions\r
-where they disagree. <o:p></o:p></p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954763"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2.7 </span></span><![endif]>Pipelining</a></h2>\r
-\r
-<p class=MsoNormal>Input can be taken from standard input, and output can be\r
-written to standard output. This is the default, so our first example would\r
-also work like this:</p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=Code>muscle &lt; seqs.fa &gt; seqs.afa</p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954764"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2.8 </span></span><![endif]>Refining\r
-an existing alignment</a></h2>\r
-\r
-<p class=MsoNormal>You can ask <i>muscle</i> to try to improve an existing\r
-alignment by using the \96<i>refine</i> option. The input file must then be a\r
-FASTA file containing an alignment. All sequences must be of equal length, gaps\r
-can be specified using dots &quot;.&quot; or dashes &quot;\96&quot;. For example:</p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=Code>muscle -in seqs.afa -out refined.afa -refine</p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954765"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2.9 </span></span><![endif]>Using\r
-a pre-computed guide tree</a></h2>\r
-\r
-<p class=MsoNormal>The \96<span class=SpellE><i>usetree</i></span> option allows\r
-you to provide your own guide tree. For example,</p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=Code>muscle -in seqs.fa -out seqs.afa -usetree mytree.phy</p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=MsoNormal>The tree must by in <span class=SpellE>Newick</span> format,\r
-as used by the <span class=SpellE>Phylip</span> package (hence the <i>.<span\r
-class=SpellE>phy</span></i> extension). The <span class=SpellE>Newick</span>\r
-format is described here:</p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=MsoNormal><span style='mso-tab-count:1'>        </span><a\r
-href="http://evolution.genetics.washington.edu/phylip/newicktree.html">http://evolution.genetics.washington.edu/phylip/newicktree.html</a></p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=MsoNormal><span class=GramE><b>WARNING</b>.</span> Do not use this\r
-option just because you believe that you have an accurate evolutionary tree for\r
-your sequences. The best guide tree for multiple <span class=GramE>alignment</span>\r
-is <i>not</i> in general the correct evolutionary tree. This can be understood\r
-by the following argument. Alignment accuracy decreases with lower sequence\r
-identity. It follows that given a set of <span class=GramE>profiles,</span> the\r
-two that can be aligned most accurately will tend to be the pair with the\r
-highest identity, i.e. at the shortest evolutionary distance. This is exactly\r
-the pair selected by the nearest-neighbor criterion which MUSCLE uses by\r
-default. When mutation rates are variable, the <i>evolutionary </i>neighbor may\r
-not be the <i>nearest </i>neighbor. This explains why a nearest-neighbor tree\r
-may be superior to the true evolutionary tree for guiding a progressive alignment.</p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=MsoNormal>You will get a warning if you use the \96<span class=SpellE><i>usetree</i></span>\r
-option. To disable the warning, use \ad<i>\96<span class=SpellE>usetree_nowarn</span></i>\r
-instead, </p>\r
-\r
-<p class=MsoNormal>e.g.:</p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=Code>muscle -in seqs.fa -out seqs.afa -usetree_nowarn mytree.phy</p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954766"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2.10 </span></span><![endif]>Profile-profile\r
-alignment</a></h2>\r
-\r
-<p class=MsoNormal>A fundamental step in the MUSCLE algorithm is aligning two\r
-multiple sequence alignments. This operation is sometimes called\r
-&quot;profile-profile alignment&quot;. If you have two existing alignments of\r
-related sequences you can use the <i>\96profile</i> option of MUSCLE to align\r
-those two sequences. Typical usage is:</p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=Code>muscle -profile -in1 one.afa -in2 two.afa -out both.afa</p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=MsoNormal>The alignments in <span class=SpellE><i>one.afa</i></span>\r
-and <span class=SpellE><i>two.afa</i></span>, which must be in aligned FASTA\r
-format, are aligned to each other, keeping input columns intact and inserting\r
-columns of gaps where needed. Output is stored in <span class=SpellE><i>both.afa</i></span>.</p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=MsoNormal>MUSCLE does not compute a similarity measure or measure of\r
-statistical significance (such as an E-value), so this option is not useful for\r
-discriminating homologs from unrelated sequences. For this task, I recommend <span\r
-class=SpellE>Sadreyev</span> &amp; <span class=SpellE>Grishin's</span> COMPASS\r
-program.</p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954767"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2.11 </span></span><![endif]>Adding\r
-sequences to an existing alignment</a></h2>\r
-\r
-<p class=MsoNormal>To add a sequence to an existing alignment that you wish to\r
-keep intact, use profile-profile alignment with the new sequence as a profile.\r
-For example, if you have an existing alignment <span class=SpellE><i>existing_aln.afa</i></span>\r
-and want to add a new sequence in <span class=SpellE><i>new_seq.fa</i></span>,\r
-use the following commands:</p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=Code>muscle -profile -in1 existing_aln.afa -in2 new_seq.fa -out\r
-combined.afa<o:p></o:p></p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=MsoNormal>If you have more than one new <span class=GramE>sequences</span>,\r
-you can align them first then add them, for example:</p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=Code>muscle -in new_seqs.fa -out new_seqs.afa</p>\r
-\r
-<p class=Code>muscle -profile -in1 existing_aln.afa -in2 new_seqs.fa -out\r
-combined.afas</p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954768"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2.12 </span></span><![endif]>Sequence\r
-clustering</a></h2>\r
-\r
-<p class=MsoNormal>The first stage in MUSCLE is a fast clustering algorithm.\r
-This may be of use in other applications. Typical usage is:</p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=Code>muscle -cluster -in seqs.fa -tree1 tree.phy -maxiters 1</p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=MsoNormal>The sequences will be clustered, and a tree written to <span\r
-class=SpellE><i>tree.phy</i></span>. Options \96<i>weight1</i>, \96<i>distance1</i>,\r
-\96<i>cluster1</i> and \96<i>root1</i> can be applied if desired. Note that by\r
-default, UPGMA clustering is used. You can use</p>\r
-\r
-<p class=MsoNormal><span style='mso-spacerun:yes'> </span><span class=GramE>\96<span\r
-class=SpellE><i>neighborjoining</i></span> if you prefer, but note that this is\r
-substantially slower than UPGMA for large numbers of sequences, and is also\r
-slightly less accurate.</span> See discussion of \96<span class=SpellE><i>usetree</i></span>\r
-above.</p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954769"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2.13 </span></span><![endif]>Specifying\r
-a substitution matrix</a></h2>\r
-\r
-<p class=MsoNormal>You can specify your own substitution matrix by using the <i>-matrix</i>\r
-option. This reads a protein substitution matrix in NCBI or WU-BLAST format.\r
-The alphabet is assumed to be amino acid, and sum-of-pairs scoring is used. The\r
-\ad<i>-<span class=SpellE>gapopen</span></i>, <i>-<span class=SpellE>gapextend</span></i>\r
-and -<i>center</i> parameters should be specified; normally you will specify a\r
-zero value for the center. Note that gap penalties MUST be negative. The\r
-environment variable MUSCLE_MXPATH can be used to specify a path where the\r
-matrices are stored. For example,</p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=Code>muscle -in seqs.fa -out seqs.afa -matrix blosum62 -gapopen -12.0</p>\r
-\r
-<p class=Code><span style='mso-tab-count:1'>   </span><span\r
-style='mso-spacerun:yes'> </span>-gapextend -1.0 -center 0.0</p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=MsoNormal>You can hack a nucleotide matrix by pretending that AGCT are\r
-amino acids and making a 20x20 matrix out of the original 4x4 matrix. Let me\r
-know if this isn't clear, I can help you through it.<o:p></o:p></p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954770"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2.14 </span></span><![endif]>Refining\r
-a long alignment</a></h2>\r
-\r
-<p class=MsoNormal>A long alignment can be refined using the \96<span\r
-class=SpellE><i>refinew</i></span> option, which is primarily designed for\r
-refining whole-genome nucleotide alignments. Usage is:</p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=Code>muscle -in input.afa -out output.afa</p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=MsoNormal>MUSCLE divides the input alignment into non-overlapping\r
-windows and re-aligns each window from scratch, i.e. all gap characters are\r
-discarded. The \96<span class=SpellE><i>refinewindow</i></span> option may be\r
-used to change the window length, which <span class=GramE>is</span> 200 columns\r
-by default.<o:p></o:p></p>\r
-\r
-<h1 style='margin-left:0in;text-indent:0in'><a name="_Toc113954771"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial;mso-bidi-font-family:Arial'><span\r
-style='mso-list:Ignore'>3 </span></span><![endif]>File Formats</a></h1>\r
-\r
-<p class=MsoNormal>MUSCLE uses FASTA format for both input and output. For\r
-output only, it also offers CLUSTALW, MSF, HTML, <span class=SpellE>Phylip</span>\r
-sequential and <span class=SpellE>Phylip</span> interleaved formats. See the\r
-following command-line options: &#8209;<span class=SpellE><i>clw</i></span>, &#8209;<span\r
-class=SpellE><i>clwstrict</i></span><i>, </i>\96<span class=SpellE><i>msf</i></span>,\r
-\96<i>html</i>, \96<i>phys</i>, \96<span class=SpellE><i>phyi</i></span><i>,</i> &#8209;<span\r
-class=SpellE><i>clwout</i></span>, &#8209;<span class=SpellE><i>clwstrictout</i></span><i>,\r
-</i>\96<span class=SpellE><i>msfout</i></span>, \96<span class=SpellE><i>htmlout</i></span>,\r
-\96<span class=SpellE><i>physout</i></span><i> </i>and \96<span class=SpellE><i>phyiout</i></span>.<o:p></o:p></p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954772"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>3.1 </span></span><![endif]>Input\r
-files</a></h2>\r
-\r
-<p class=MsoNormal>Input files must be in FASTA format. These are plain text\r
-files (word processing files such as Word documents are not understood!). <span\r
-class=GramE>Unix</span>, Windows and DOS text files are supported (end-of-line\r
-may be NL or CR NL). There is no explicit limit on the length of a sequence,\r
-however if you are running a 32-bit version of <i>muscle</i> then the maximum\r
-will be very roughly 10,000 letters due to maximum addressable size of tables\r
-required in memory. Each sequence starts with an annotation line, which is\r
-recognized by having a greater-than symbol &quot;&gt;&quot; as its first\r
-character. There is no limit on the length of an annotation line (this is new\r
-as of version 3.5), and there is no requirement that the annotation be unique. The\r
-sequence itself follows on one or more subsequent lines, and is terminated\r
-either by the next annotation line or by the end of the file. </p>\r
-\r
-<h3 style='margin-left:0in;text-indent:0in'><a name="_Toc113954773"><![if !supportLists]><span\r
-style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman"'><span\r
-style='mso-list:Ignore'>3.1.1 </span></span><![endif]>Amino acid sequences</a></h3>\r
-\r
-<p class=MsoNormal>The standard single-letter amino acid alphabet is used. Upper\r
-and lower case is allowed, the case is not significant. The special characters\r
-X, B, Z and U are understood. X means &quot;unknown amino acid&quot;, B is D or\r
-N, Z is E or Q. U is understood to be the 21st amino acid <span class=SpellE>Selenocysteine</span>.\r
-White space (spaces, tabs and the end-of-line characters CR and NL) is allowed\r
-inside sequence data. Dots &quot;.&quot; and dashes &quot;\96&quot; in sequences\r
-are allowed and are discarded unless the input is expected to be aligned (e.g.\r
-for the \96<i>refine</i> option). </p>\r
-\r
-<h3 style='margin-left:0in;text-indent:0in'><a name="_Toc113954774"><![if !supportLists]><span\r
-style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman"'><span\r
-style='mso-list:Ignore'>3.1.2 </span></span><![endif]>Nucleotide sequences</a></h3>\r
-\r
-<p class=MsoNormal>The usual letters A, G, C, T and U stand for nucleotides.\r
-The letters T and U are equivalent as far as MUSCLE is concerned. N is the\r
-wildcard meaning &quot;unknown nucleotide&quot;. R means A or G, Y means C or\r
-T/U. Other wildcards, such as those used by RFAM, are not understood in this\r
-version and will be replaced by Ns. If you would like support for other DNA /\r
-RNA alphabets, please let me know.</p>\r
-\r
-<h3 style='margin-left:0in;text-indent:0in'><a name="_Toc113954775"><![if !supportLists]><span\r
-style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman"'><span\r
-style='mso-list:Ignore'>3.1.3 </span></span><![endif]>Determining sequence type</a></h3>\r
-\r
-<p class=MsoNormal>By default, MUSCLE looks at the first 100 letters in the\r
-input sequence data (excluding gaps). If 95% or more of those letters are valid\r
-nucleotides (AGCTUN), then the file is treated as nucleotides, otherwise as\r
-amino acids. This method almost always guesses correctly, but you can make sure\r
-by specifying the sequence type on the command line. This is done using the \96<span\r
-class=SpellE><i>seqtype</i></span> option, which can take the following values:</p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=MsoNormal><span style='mso-tab-count:1'>        </span>\96\ad<span\r
-class=SpellE><i>seqtype</i></span><i> protein</i><span style='mso-tab-count:\r
-4'>                          </span>Amino acid</p>\r
-\r
-<p class=MsoNormal><span style='mso-tab-count:1'>        </span>\96<span\r
-class=SpellE>s<i>eqtype</i></span><i> <span class=SpellE>nucleo</span></i><span\r
-style='mso-tab-count:4'>                          </span>Nucleotide</p>\r
-\r
-<p class=MsoNormal><span style='mso-tab-count:1'>        </span><span\r
-class=GramE>\96<span class=SpellE><i>seqtype</i></span><i> auto</i><span\r
-style='mso-tab-count:4'>                               </span>Automatic\r
-detection (default).</span><o:p></o:p></p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954776"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>3.2 </span></span><![endif]>Output\r
-files</a></h2>\r
-\r
-<p class=MsoNormal>By default, output is also written in FASTA format. All\r
-letters are upper-case and gaps are represented by dashes &quot;\96&quot;. Output\r
-is written to the following destination(s):</p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=MsoNormal><span style='mso-tab-count:1'>        </span>If no other\r
-output option is given, then standard output.</p>\r
-\r
-<p class=MsoNormal><span style='mso-tab-count:1'>        </span>If <i>-out</i> <i>&lt;filename&gt;</i>\r
-is given, to the specified file.</p>\r
-\r
-<p class=MsoNormal><span style='mso-tab-count:1'>        </span><span\r
-class=GramE>For all of the <i>-<span class=SpellE>xxxout</span></i> options\r
-(e.g. -<span class=SpellE><i>fastaout</i></span>, -<span class=SpellE><i>clwout</i></span>),\r
-to the specified files.</span><o:p></o:p></p>\r
-\r
-<h3 style='margin-left:0in;text-indent:0in'><a name="_Toc113954777"><![if !supportLists]><span\r
-style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman"'><span\r
-style='mso-list:Ignore'>3.2.1 </span></span><![endif]>Sequence grouping</a></h3>\r
-\r
-<p class=MsoNormal>By default, MUSCLE re-arranges sequences so that similar\r
-sequences are adjacent in the output file. (This is done by ordering sequences\r
-according to a prefix traversal of the guide tree). This makes the alignment\r
-easier to evaluate by eye. If you want to the sequences to be output in the\r
-same order as the input file, you can use the \96<i>stable</i> option.</p>\r
-\r
-<h3 style='margin-left:0in;text-indent:0in'><![if !supportLists]><span\r
-style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman"'><span\r
-style='mso-list:Ignore'>3.2.2 </span></span><![endif]>Output to multiple file\r
-formats</h3>\r
-\r
-<p class=MsoNormal>You can request output to more than one file format by using\r
-the -<span class=SpellE><i>xxxout</i></span> options. For example, to get both\r
-FASTA and CLUSTALW formats:</p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=Code>muscle -in seqs.fa -fastaout seqs.afa -clwout seqs.aln<o:p></o:p></p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954778"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>3.3 </span></span><![endif]>CLUSTALW\r
-format</a></h2>\r
-\r
-<p class=MsoNormal>You can request CLUSTALW output by using the \96<span\r
-class=SpellE><i>clw</i></span> option. This should be compatible with CLUSTALW,\r
-with the exception of the program name in the file header. You can ask MUSCLE\r
-to impersonate CLUSTALW by writing &quot;CLUSTAL W (1.81)&quot; as the program\r
-name by using \96<span class=SpellE><i>clwstrict</i></span> or <i>&#8209;<span\r
-class=SpellE>clwstrictout</span></i>. Note that MUSCLE allows duplicate\r
-sequence labels, while CLUSTALW forbids duplicates. If you use the \96<i>stable</i>\r
-option of <i>muscle</i>, then the order of the input sequences is preserved and\r
-sequences can be unambiguously identified even if the labels differ. If you\r
-have problems parsing MUSCLE output with scripts designed for CLUSTALW, please\r
-let me know and I'll do my best to provide a fix.<o:p></o:p></p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954779"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>3.4 </span></span><![endif]>MSF\r
-format</a></h2>\r
-\r
-<p class=MsoNormal>MSF format, as used in the GCG package, is requested by\r
-using the \96<span class=SpellE><i>msf</i></span> option. As with CLUSTALW\r
-format, this is easier for people to read than FASTA. As of MUSCLE 3.52, the\r
-MSF format has been tweaked to be more compatible with GCG. The following\r
-differences remain.</p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=MsoNormal>(a) MUSCLE truncates at the first white space or after 63\r
-characters, which ever comes first. The GCG package apparently truncates after\r
-10 characters. If this is a problem for you, please let me know and I'll add an\r
-option to truncate after 10 in a future version.</p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=MsoNormal>(b) MUSCLE allows duplicate sequence labels, while GCG\r
-forbids duplicates. If you use the \96<i>stable</i> option of <i>muscle</i>, then\r
-the order of the input sequences is preserved and sequences can be\r
-unambiguously identified even if the labels differ.</p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=MsoNormal>Thanks to Eric Martel for help with improving GCG\r
-compatibility.<o:p></o:p></p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954780"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>3.5 </span></span><![endif]>HTML\r
-format</a></h2>\r
-\r
-<p class=MsoNormal>I've added an experimental feature starting in version 3.4. To\r
-get a Web page as output, use the \96<i>html</i> option. The alignment is colored\r
-using a color scheme from Eric <span class=SpellE>Sonnhammer's</span> <span\r
-class=SpellE>Belvu</span> editor, which is my personal favorite. A drawback of\r
-this option is that the Web page typically contains a very large number of HTML\r
-tags, which can be slow to display in the Internet Explorer browser. The\r
-Netscape browser works much better. If you have any ideas about good ways to\r
-make Web pages, please let me know.</p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954781"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>3.6 </span></span><![endif]></a><span\r
-class=SpellE><span style='mso-bookmark:_Toc113954781'>Phylip</span></span><span\r
-style='mso-bookmark:_Toc113954781'> format</span></h2>\r
-\r
-<p class=MsoNormal>The <span class=SpellE>Phylip</span> package supports two\r
-different multiple sequence alignment file formats, called sequential and\r
-interleaved respectively.<o:p></o:p></p>\r
-\r
-<h1 style='margin-left:0in;text-indent:0in'><a name="_Toc113954782"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial;mso-bidi-font-family:Arial'><span\r
-style='mso-list:Ignore'>4 </span></span><![endif]>Using MUSCLE</a></h1>\r
-\r
-<p class=MsoNormal>In this section we give more details of the MUSCLE algorithm\r
-and the more important options offered by the <i>muscle</i> implementation.<o:p></o:p></p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954783"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>4.1 </span></span><![endif]>How\r
-the algorithm works</a></h2>\r
-\r
-<p class=MsoNormal>I won't give a complete description of the MUSCLE algorithm\r
-here\97for that, you will have to read the papers. (See citations on title page\r
-above). But hopefully a summary will help explain what some of the command-line\r
-options do and how they might be useful in your work.</p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=MsoNormal>The first step is to calculate a tree. In CLUSTALW, this is\r
-done as follows. Each pair of input sequences is aligned, and used to compute\r
-the pair-wise identity of the pair. Identities are converted to a measure of\r
-distance. Finally, the distance matrix is converted to a tree using a\r
-clustering method (CLUSTALW uses neighbor-joining). If you have 1,000\r
-sequences, there are (1,000 <span style='font-family:Symbol;mso-ascii-font-family:\r
-"Times New Roman";mso-hansi-font-family:"Times New Roman";mso-char-type:symbol;\r
-mso-symbol-font-family:Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:\r
-Symbol'>´</span></span> 999)/2 = 499,500 pairs, so aligning every pair can take\r
-a while. MUSCLE uses a much faster, but somewhat more approximate, method to\r
-compute distances: it counts the number of short sub-sequences (known as <i>k</i>-<span\r
-class=SpellE>mers</span>, <i>k</i>-<span class=SpellE>tuples</span> or words)\r
-that two sequences have in common, without constructing an alignment. This is\r
-typically around 3,000 times faster that <span class=SpellE>CLUSTALW's</span>\r
-method, but the trees will generally be less accurate. We call this step &quot;<i>k</i>-<span\r
-class=SpellE>mer</span> clustering&quot;.<o:p></o:p></p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=MsoNormal>The second step is to use the tree to construct what is\r
-known as a progressive alignment. At each node of the binary tree, a pair-wise\r
-alignment is constructed, progressing from the leaves towards the root. The\r
-first alignment will be made from two sequences. Later alignments will be one\r
-of the three following types: sequence-sequence, profile-sequence or\r
-profile-profile, where &quot;profile&quot; means the multiple <span\r
-class=GramE>alignment</span> of the sequences under a given internal node of\r
-the tree. This is very similar to what CLUSTALW does once it has built a tree.</p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=MsoNormal style='page-break-after:avoid'>Now we have a multiple\r
-alignment, which has been built very quickly compared with conventional\r
-methods, mainly because of the distance calculation using <i>k</i>-<span\r
-class=SpellE>mers</span> rather than alignments. The quality of this alignment\r
-is typically pretty good\97it will often tie or beat a T-Coffee alignment on our\r
-tests. However, on average, we find that it can be improved by proceeding\r
-through the following steps.</p>\r
-\r
-<p class=MsoNormal style='page-break-after:avoid'><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=MsoNormal style='page-break-after:avoid'>From the multiple <span\r
-class=GramE>alignment</span>, we can now compute the pair-wise identities of\r
-each pair of sequences. This gives us a new distance matrix, from which we\r
-estimate a new tree. We compare the old and new trees, and re-align subgroups\r
-where needed to produce a progressive multiple alignment from the new tree. If\r
-the two trees are identical, there is nothing to do; if there are no subtrees\r
-that agree (very unusual), then the whole progressive alignment procedure must\r
-be repeated from scratch. Typically we find that the tree is pretty stable near\r
-the leaves, but some re-alignments are needed closer the root. This procedure\r
-(compute pair-wise identities, estimate new tree, compare trees, re-align) is\r
-iterated until the tree stabilizes or until a specified maximum number of\r
-iterations has been done. We call this process &quot;tree refinement&quot;,\r
-although it also tends to improve the alignment.</p>\r
-\r
-<p class=MsoNormal style='page-break-after:avoid'><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=MsoNormal style='page-break-after:avoid'>We now keep the tree fixed\r
-and move to a new procedure which is designed to improve the multiple\r
-alignment. The set of sequences is divided into two subsets (i.e., we make a\r
-bipartition on the set of sequences). A profile is constructed for each of the\r
-two subsets based on the current multiple <span class=GramE>alignment</span>.\r
-These two profiles are then re-aligned to each other using the same pair-wise\r
-alignment algorithm as used in the progressive stage. If this improves an\r
-&quot;objective score&quot; that measures the quality of the alignment, then\r
-the new multiple <span class=GramE>alignment</span> is kept, otherwise it is\r
-discarded. By default, the objective score is the classic sum-of-pairs score\r
-that takes the (sequence weighted) average of the pair-wise alignment score of\r
-every pair of sequences in the alignment. Bipartitions are chosen by deleting\r
-an edge in the guide tree, each of the two resulting subtrees defines a subset\r
-of sequences. This procedure is called &quot;tree dependent refinement&quot;. <span\r
-class=GramE>One iteration</span> of tree dependent refinement tries\r
-bipartitions produced by deleting every edge of the tree in depth order moving\r
-from the leaves towards the center of the tree. Iterations continue until\r
-convergence or up to a specified maximum.</p>\r
-\r
-<p class=MsoNormal style='page-break-after:avoid'><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=MsoNormal style='page-break-after:avoid'>For convenience, the major\r
-steps in MUSCLE are described as &quot;iterations&quot;, though the first three\r
-iterations all do quite different things and may take very different lengths of\r
-time to complete. The tree-dependent refinement iterations 3, 4 ... are true\r
-iterations and will take similar lengths of time. </p>\r
-\r
-<p class=MsoNormal style='page-break-after:avoid'><o:p>&nbsp;</o:p></p>\r
-\r
-<table class=MsoTableGrid border=0 cellspacing=0 cellpadding=0\r
- style='border-collapse:collapse;mso-yfti-tbllook:480;mso-padding-alt:0in 5.4pt 0in 5.4pt'>\r
- <tr style='mso-yfti-irow:0'>\r
-  <td width=89 valign=top style='width:66.6pt;border:none;border-bottom:solid windowtext 1.0pt;\r
-  mso-border-bottom-alt:solid windowtext .5pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'><b><span style='font-size:\r
-  9.0pt;font-family:Arial'>Iteration<o:p></o:p></span></b></p>\r
-  </td>\r
-  <td width=461 valign=top style='width:4.8in;border:none;border-bottom:solid windowtext 1.0pt;\r
-  mso-border-bottom-alt:solid windowtext .5pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'><b><span style='font-size:\r
-  9.0pt;font-family:Arial'>Actions<o:p></o:p></span></b></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:1'>\r
-  <td width=89 valign=top style='width:66.6pt;border:none;mso-border-top-alt:\r
-  solid windowtext .5pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>1</p>\r
-  </td>\r
-  <td width=461 valign=top style='width:4.8in;border:none;mso-border-top-alt:\r
-  solid windowtext .5pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>Distance matrix by <i>k</i>-<span\r
-  class=SpellE>mer</span> clustering, estimate tree, progressive alignment\r
-  according to this tree.</p>\r
-  <p class=MsoNormal style='page-break-after:avoid'><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:2'>\r
-  <td width=89 valign=top style='width:66.6pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>2</p>\r
-  </td>\r
-  <td width=461 valign=top style='width:4.8in;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>Distance matrix by\r
-  pair-wise identities from current multiple alignment, estimate tree,\r
-  progressive alignment according to new tree, repeat until convergence or specified\r
-  maximum number of times.</p>\r
-  <p class=MsoNormal style='page-break-after:avoid'><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:3;mso-yfti-lastrow:yes'>\r
-  <td width=89 valign=top style='width:66.6pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>3, 4 ...</p>\r
-  </td>\r
-  <td width=461 valign=top style='width:4.8in;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>Tree-dependent refinement. <span\r
-  class=GramE>One iteration</span> visits every edge in the tree one time.</p>\r
-  </td>\r
- </tr>\r
-</table>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954784"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>4.2 </span></span><![endif]>Command-line\r
-options</a></h2>\r
-\r
-<p class=MsoNormal>There are two types of command-line options: value options\r
-and flag options. Value options are followed by the value of the given\r
-parameter, for example \96<i>in &lt;filename&gt;</i>; flag options just stand for\r
-themselves, such as \96<span class=SpellE><i>msf</i></span>. All options are a\r
-dash (not two dashes!) followed by a long name; there are no single-letter\r
-equivalents. Value options must be separated from their values by white space\r
-in the command line. Thus, <i>muscle</i> does not follow <span class=GramE>Unix</span>,\r
-Linux or <span class=SpellE>Posix</span> standards, for which we apologize. The\r
-order in which options are given is irrelevant unless two options contradict,\r
-in which case the right-most option silently wins.<o:p></o:p></p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954785"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>4.3 </span></span><![endif]>The\r
-maxiters option</a></h2>\r
-\r
-<p class=MsoNormal>You can control the number of iterations that MUSCLE does by\r
-specifying the <i>\96maxiters</i> option. If you specify 1, 2 or 3, then this is\r
-exactly the number of iterations that will be performed. If the value is\r
-greater than 3, then <i>muscle</i> will continue up to the maximum you specify\r
-or until convergence is reached, which ever happens sooner. The default is 16.\r
-If you have a large number of sequences, refinement may be rather slow.</p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954786"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>4.4 </span></span><![endif]>The\r
-</a><span class=SpellE><span style='mso-bookmark:_Toc113954786'>maxtrees</span></span><span\r
-style='mso-bookmark:_Toc113954786'> option</span></h2>\r
-\r
-<p class=MsoNormal>This option controls the maximum number of new trees to\r
-create in iteration 2. Our experience suggests that a point of diminishing\r
-returns is typically reached after the first tree, so the default value is 1.\r
-If a larger value is given, the process will repeat until convergence or until\r
-this number of trees has been created, which ever comes first.</p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954787"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>4.5 </span></span><![endif]>The\r
-</a><span class=SpellE><span style='mso-bookmark:_Toc113954787'>maxhours</span></span><span\r
-style='mso-bookmark:_Toc113954787'> option</span></h2>\r
-\r
-<p class=MsoNormal>If you have a large alignment, <i>muscle</i> may take a long\r
-time to complete. It is sometimes convenient to say &quot;I want the best\r
-alignment I can get in 24 hours&quot; rather than specifying a set of options\r
-that will take an unknown length of time. This is done by using <i>\96<span\r
-class=SpellE>maxhours</span></i>, which specifies a floating-point number of\r
-hours. If this time is exceeded, <i>muscle</i> will write out current alignment\r
-and stop. For example,</p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=Code>muscle -in huge.fa -out huge.afa -maxiters 9999 -maxhours 24.0</p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=MsoNormal>Note that the actual time may exceed the specified limit by\r
-a few minutes while <i>muscle</i> finishes up on a step. It is also possible\r
-for no alignment to be produced if the time limit is too small.</p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954788"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>4.6 </span></span><![endif]>The\r
-</a><span class=SpellE><span style='mso-bookmark:_Toc113954788'>maxmb</span></span><span\r
-style='mso-bookmark:_Toc113954788'> option</span></h2>\r
-\r
-<p class=MsoNormal>If the amount of memory needed by MUSCLE exceeds available\r
-physical RAM, then the operating system will probably begin paging (i.e.,\r
-swapping memory to and from hard disk), causing MUSCLE to run very slowly. This\r
-is especially problematic when MUSCLE is used for batch processing, where one or\r
-two very large alignments can cause a batch to effectively hang. Starting in\r
-version 3.52, MUSCLE attempts to limit the amount of memory used. If the limit\r
-is exceeded, MUSCLE quits, saving the best alignment so far produced (if any).\r
-MUSCLE attempts to determine the amount of physical RAM by making an\r
-appropriate operating system call. Under Linux and Windows, this works well. On\r
-other systems, particularly other flavors of <span class=GramE>Unix</span>,\r
-MUSCLE doesn't know how to query the system and assumes that there is 500 Mb of\r
-RAM. To override this default, you can specify the maximum number of megabytes\r
-to allocate by using the \96<span class=SpellE><i>maxmb</i></span> option, for\r
-example to set a limit of 1.5 <span class=SpellE><span class=GramE>Gb</span></span>:</p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=Code>muscle -in huge.fa -out huge.afa -maxhours 1.0 -maxmb 1500</p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=MsoNormal>This feature has been hacked on top of code that wasn't\r
-really designed for it. So it doesn't always work perfectly, but is better than\r
-nothing. The ideal solution would be to implement linear space dynamic\r
-programming code (e.g., the Myers-Miller algorithm) for situations where memory\r
-is tight. One day I might do this if there is sufficient interest. If you are\r
-interested in contributing the code, e.g. for a class project, please let me\r
-know, I'll be glad to provide support.<o:p></o:p></p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954789"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>4.7 </span></span><![endif]>The\r
-profile scoring function</a></h2>\r
-\r
-<p class=MsoNormal>Three different protein profile scoring functions are\r
-supported, the log-expectation score (\96<i>le</i> option) and a sum of pairs\r
-score using either the PAM200 matrix (\96<i>sp</i>) or the VTML240 matrix (\96<span\r
-class=SpellE><i>sv</i></span>). The log-expectation score is the default as it\r
-gives better results on our tests, but is typically somewhere between two or\r
-three times slower than the sum-of-pairs score. For nucleotides, \96<span\r
-class=SpellE><i>spn</i></span> is currently the only option (which is of course\r
-the default for nucleotide data, so you don't need to specify this option).<o:p></o:p></p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954790"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>4.8 </span></span><![endif]>Diagonal\r
-optimization</a></h2>\r
-\r
-<p class=MsoNormal>Creating a pair-wise alignment by dynamic programming\r
-requires computing an <i>L</i><sub>1</sub> <span style='font-family:Symbol;\r
-mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman";\r
-mso-char-type:symbol;mso-symbol-font-family:Symbol'><span style='mso-char-type:\r
-symbol;mso-symbol-font-family:Symbol'>´</span></span> <i>L</i><sub>2</sub>\r
-matrix, where <i>L</i><sub>1</sub> and <i>L</i><sub>2</sub> are the sequence\r
-lengths. A trick used in algorithms such as BLAST is to reduce the size of this\r
-matrix by using fast methods to find &quot;diagonals&quot;, i.e. short regions\r
-of high similarity between the two sequences. This speeds up the algorithm at\r
-the expense of some reduction in accuracy. MUSCLE uses a technique called <i>k</i>-<span\r
-class=SpellE>mer</span> extension to find diagonals. It is disabled by default\r
-because of the slight reduction in average accuracy and can be turned on by\r
-specifying the \96<span class=SpellE><i>diags</i></span> option. To enable\r
-diagonal optimization in the first iteration, use \96<i>diags1</i>, to enable\r
-diagonal optimization in the second iteration, use \96<i>diags2</i>. These are\r
-provided separately because it would be a reasonable strategy to enable\r
-diagonals in the first iteration but not the second (because the main goal of\r
-the first iteration is to construct a multiple alignment quickly in order to\r
-improve the distance matrix, which is not very sensitive to alignment quality;\r
-whereas the goal of the second iteration is to make the best possible\r
-progressive alignment).<o:p></o:p></p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954791"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>4.9 </span></span><![endif]>Anchor\r
-optimization</a></h2>\r
-\r
-<p class=MsoNormal>Tree-dependent refinement (iterations 3, 4 <span\r
-class=GramE>... )</span> can be speeded up by dividing the alignment vertically\r
-into blocks. Block boundaries are found by identifying high-scoring columns\r
-(e.g., a perfectly conserved column of Cs or Ws would be a candidate). Each\r
-vertical block is then refined independently before reassembling the complete\r
-alignment, which is faster because of the <i>L</i><sup>2</sup> factor in\r
-dynamic programming (e.g., suppose the alignment is split into two vertical\r
-blocks, then 2 <span style='font-family:Symbol;mso-ascii-font-family:"Times New Roman";\r
-mso-hansi-font-family:"Times New Roman";mso-char-type:symbol;mso-symbol-font-family:\r
-Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:Symbol'>´</span></span>\r
-0.5<sup>2</sup> = 0.5, so the dynamic programming time is roughly halved). The\r
-\96<span class=SpellE><i>noanchors</i></span> option is used to disable this\r
-feature. This option has no effect if <i>\96maxiters 1</i> or \96<i>maxiters 2</i>\r
-is specified. On benchmark tests, enabling anchors has little or no effect on\r
-accuracy, but if you want to be very conservative and are striving for the best\r
-possible accuracy then \96<span class=SpellE><i>noanchors</i></span> is a\r
-reasonable choice.<o:p></o:p></p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954792"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>4.10 </span></span><![endif]>Log\r
-file</a></h2>\r
-\r
-<p class=MsoNormal>You can specify a log file by using \96<i>log &lt;filename&gt;</i>\r
-or \96<span class=SpellE><i>loga</i></span><i> &lt;filename&gt;</i>. Using \96<i>log</i>\r
-causes any existing file to be deleted, \96<span class=SpellE><i>loga</i></span>\r
-appends to any existing file. A message will be written to the log file when <i>muscle</i>\r
-starts and stops. Error and warning messages will also be written to the log.\r
-If \96<i>verbose</i> is specified, then more information will be written,\r
-including the command line used to invoke <i>muscle</i>, the resulting internal\r
-parameter settings, and also progress messages. The content and format of\r
-verbose log file output is subject to change in future versions. </p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=MsoNormal>The use of a log file may seem contrary to <span\r
-class=GramE>Unix</span> conventions for using standard output and standard\r
-error. I like these conventions, but never found a fully satisfactory way to\r
-use them. I like progress messages (see below), but they mess up a file if you\r
-re-direct standard error and there are errors or warning messages too. I could\r
-try to detect whether a standard file handle is a <span class=SpellE><span\r
-class=GramE><i>tty</i></span></span> device or a disk file and change behavior\r
-accordingly, but I regard this as too complicated and too hard for the user to\r
-understand. On Windows it can be hard to re-direct standard file handles,\r
-especially when working in a GUI debugger. Maybe one day I will figure out a\r
-better solution (suggestions welcomed).</p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=MsoNormal>I highly recommend using \96<i>verbose </i>and \ad\96<i>log[a]</i>,\r
-especially when running <i>muscle</i> in a batch mode. This enables you to\r
-verify whether a particular alignment was completed and to review any errors or\r
-warnings that occurred.<o:p></o:p></p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954793"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>4.11 </span></span><![endif]>Progress\r
-messages</a></h2>\r
-\r
-<p class=MsoNormal>By default, <i>muscle</i> writes progress messages to\r
-standard error periodically so that you know it's doing something and get some\r
-feedback about the time and memory requirements for the alignment. Here is a\r
-typical progress message.</p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=Code>00:00:23<span style='mso-spacerun:yes'>     </span>25 Mb (5%)<span\r
-style='mso-spacerun:yes'>  </span>Iter<span style='mso-spacerun:yes'>  \r
-</span>2<span style='mso-spacerun:yes'>  </span>87.20%<span\r
-style='mso-spacerun:yes'>  </span>Build guide tree</p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=MsoNormal style='page-break-after:avoid'>The fields are as follows.</p>\r
-\r
-<p class=MsoNormal style='page-break-after:avoid'><o:p>&nbsp;</o:p></p>\r
-\r
-<table class=MsoTableGrid border=0 cellspacing=0 cellpadding=0\r
- style='border-collapse:collapse;mso-yfti-tbllook:480;mso-padding-alt:0in 5.4pt 0in 5.4pt'>\r
- <tr style='mso-yfti-irow:0'>\r
-  <td width=118 valign=top style='width:88.2pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=Code style='page-break-after:avoid'>00:00:23</p>\r
-  </td>\r
-  <td width=408 valign=top style='width:306.05pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>Elapsed time since <i>muscle</i>\r
-  started.<o:p></o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:1'>\r
-  <td width=118 valign=top style='width:88.2pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=Code style='page-break-after:avoid'>25 Mb (5%)</p>\r
-  </td>\r
-  <td width=408 valign=top style='width:306.05pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>Peak memory use in megabytes\r
-  (i.e., not the current usage, but the maximum amount of memory used since <i>muscle</i>\r
-  started). The number in parentheses is the fraction of physical memory (see \96<span\r
-  class=SpellE><i>maxmb</i></span> option for more discussion).<o:p></o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:2'>\r
-  <td width=118 valign=top style='width:88.2pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=Code style='page-break-after:avoid'>Iter 2</p>\r
-  </td>\r
-  <td width=408 valign=top style='width:306.05pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>Iteration currently in\r
-  progress.</p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:3'>\r
-  <td width=118 valign=top style='width:88.2pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=Code style='page-break-after:avoid'>87.20%</p>\r
-  </td>\r
-  <td width=408 valign=top style='width:306.05pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>How much of the current step\r
-  has been completed (percentage).</p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:4;mso-yfti-lastrow:yes'>\r
-  <td width=118 valign=top style='width:88.2pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=Code>Build...</p>\r
-  </td>\r
-  <td width=408 valign=top style='width:306.05pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>A brief description of the current step.</p>\r
-  </td>\r
- </tr>\r
-</table>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=MsoNormal>The \96<i>quiet</i> command-line option disables writing\r
-progress messages to standard error. If the \96<i>verbose</i> command-line option\r
-is specified, a progress message will be written to the log file when <span\r
-class=GramE>each iteration</span> completes. So \96<i>quiet</i> and \96<i>verbose</i>\r
-are not contradictory.</p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954794"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>4.12 </span></span><![endif]>Running\r
-out of memory</a></h2>\r
-\r
-<p class=MsoNormal>The <i>muscle</i> code tries to deal gracefully with\r
-low-memory conditions by using the following technique. A block of &quot;emergency\r
-reserve&quot; memory is allocated when <i>muscle</i> starts. If a later request\r
-to allocate memory fails, this reserve block is made available, and <i>muscle</i>\r
-attempts to save the current alignment. With luck, the reserved memory will be\r
-enough to allow <i>muscle</i> to save the alignment and exit gracefully with an\r
-informative error message. See also the \96<span class=SpellE><i>maxmb</i></span>\r
-option.<o:p></o:p></p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954795"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>4.13 </span></span><![endif]>Troubleshooting</a></h2>\r
-\r
-<p class=MsoNormal>Here is some general advice on what to do if <i>muscle</i>\r
-fails and you don't understand what happened. The code is designed to fail\r
-gracefully with an informative error message when something goes wrong, but\r
-there will no doubt be situations I haven't anticipated (not to mention bugs).</p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=MsoNormal>Check the MUSCLE web site for updates, bug reports and other\r
-relevant information.</p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=MsoNormal style='page-break-after:avoid'><span style='mso-tab-count:\r
-1'>        </span><a href="http://www.drive5.com/muscle">http://www.drive5.com/muscle</a><i><o:p></o:p></i></p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=MsoNormal>Check the input file to make sure it is in valid FASTA\r
-format. Try giving it to another sequence analysis program that can accept\r
-large FASTA files (e.g., the NCBI <span class=SpellE><i>formatdb</i></span>\r
-utility) to see if you get an informative error message. Try dividing the file\r
-into two halves and using each half individually as input. If one half fails\r
-and the other <span class=GramE>does</span> not, repeat until the problem is\r
-localized as far as possible.</p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=MsoNormal>Use \96<i>log</i> or \96<span class=SpellE><i>loga</i></span>\r
-and \96\ad<i>verbose</i> and check the log file to see if there are any messages\r
-that give you a hint about the problem. Look at the peak memory requirements\r
-(reported in progress messages) to see if you may be exceeding the physical or\r
-virtual memory capacity of your computer.</p>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<p class=MsoNormal>If <i>muscle</i> crashes without giving an error message, or\r
-hangs, then you may need to refer to the source code or use a debugger. A\r
-&quot;debug&quot; version, <i>muscled</i>, may be provided. This is built from\r
-the same source code but with the DEBUG macro defined and without compiler\r
-optimizations. This version runs much more slowly (perhaps by a factor of three\r
-or more), but does a lot more internal checking and may be able to catch\r
-something that is going wrong in the code. The \96\ad<i>core</i> option specifies\r
-that <i>muscle</i> should not catch exceptions. When \96<i>core</i> is specified,\r
-an exception may result in a debugger trap or a core dump, depending on the\r
-execution environment. The \96<span class=SpellE><i>nocore</i></span> option has\r
-the opposite effect. In <i>muscle</i>, \96<span class=SpellE><i>nocore</i></span>\r
-is the default, \96\ad<i>core</i> is the default in <i>muscled</i>.</p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954796"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>4.14 </span></span><![endif]>Technical\r
-support</a></h2>\r
-\r
-<p class=MsoNormal>I am happy to provide support. But I am busy, and am\r
-offering this program at no charge, so I ask you to make a reasonable effort to\r
-figure things out for yourself before contacting me.</p>\r
-\r
-<h1 style='margin-left:0in;text-indent:0in'><a name="_Toc113954797"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial;mso-bidi-font-family:Arial'><span\r
-style='mso-list:Ignore'>5 </span></span><![endif]>Command Line Reference</a></h1>\r
-\r
-<p class=MsoNormal style='page-break-after:avoid'><o:p>&nbsp;</o:p></p>\r
-\r
-<table class=MsoTableGrid border=0 cellspacing=0 cellpadding=0\r
- style='border-collapse:collapse;mso-yfti-tbllook:480;mso-padding-alt:0in 5.4pt 0in 5.4pt'>\r
- <thead>\r
-  <tr style='mso-yfti-irow:0'>\r
-   <td width=110 valign=top style='width:82.85pt;border:none;border-bottom:\r
-   solid windowtext 1.0pt;mso-border-bottom-alt:solid windowtext .5pt;\r
-   padding:0in 5.4pt 0in 5.4pt'>\r
-   <p class=MsoNormal style='page-break-after:avoid'><b><span style='font-size:\r
-   9.0pt;font-family:Arial'>Value option<o:p></o:p></span></b></p>\r
-   </td>\r
-   <td width=113 valign=top style='width:84.8pt;border:none;border-bottom:solid windowtext 1.0pt;\r
-   mso-border-bottom-alt:solid windowtext .5pt;padding:0in 5.4pt 0in 5.4pt'>\r
-   <p class=MsoNormal style='page-break-after:avoid'><b><span style='font-size:\r
-   9.0pt;font-family:Arial'>Legal values<o:p></o:p></span></b></p>\r
-   </td>\r
-   <td width=103 valign=top style='width:77.35pt;border:none;border-bottom:\r
-   solid windowtext 1.0pt;mso-border-bottom-alt:solid windowtext .5pt;\r
-   padding:0in 5.4pt 0in 5.4pt'>\r
-   <p class=MsoNormal style='page-break-after:avoid'><b><span style='font-size:\r
-   9.0pt;font-family:Arial'>Default<o:p></o:p></span></b></p>\r
-   </td>\r
-   <td width=264 valign=top style='width:197.8pt;border:none;border-bottom:\r
-   solid windowtext 1.0pt;mso-border-bottom-alt:solid windowtext .5pt;\r
-   padding:0in 5.4pt 0in 5.4pt'>\r
-   <p class=MsoNormal style='page-break-after:avoid'><b><span style='font-size:\r
-   9.0pt;font-family:Arial'>Description<o:p></o:p></span></b></p>\r
-   </td>\r
-  </tr>\r
- </thead>\r
- <tr style='mso-yfti-irow:1'>\r
-  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'>anchorspacing</span></span><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>Integer</p>\r
-  </td>\r
-  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
-  8.0pt;font-family:"Courier New"'>32<o:p></o:p></span></p>\r
-  </td>\r
-  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>Minimum spacing between\r
-  anchor columns.</p>\r
-  <p class=MsoNormal style='page-break-after:avoid'><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:2'>\r
-  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
-  8.0pt;font-family:"Courier New"'>center<o:p></o:p></span></p>\r
-  </td>\r
-  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>Floating point</p>\r
-  </td>\r
-  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>[1]<o:p></o:p></p>\r
-  </td>\r
-  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>Center parameter. Should be\r
-  negative.</p>\r
-  <p class=MsoNormal style='page-break-after:avoid'><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:3'>\r
-  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
-  8.0pt;font-family:"Courier New"'>cluster1<o:p></o:p></span></p>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
-  8.0pt;font-family:"Courier New"'>cluster2<o:p></o:p></span></p>\r
-  </td>\r
-  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'>upgma</span></span><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'>upgmb</span></span><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'>neighborjoining</span></span><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'>upgmb</span></span><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>Clustering method. <span\r
-  class=GramE>cluster1</span> is used in iteration 1 and 2, cluster2 in later\r
-  iterations.</p>\r
-  <p class=MsoNormal style='page-break-after:avoid'><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:4'>\r
-  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'>clwout</span></span><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
-  8.0pt;font-family:"Courier New"'>File name<o:p></o:p></span></p>\r
-  </td>\r
-  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
-  8.0pt;font-family:"Courier New"'>None<o:p></o:p></span></p>\r
-  </td>\r
-  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>Write output in CLUSTALW\r
-  format to given file name.</p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:5'>\r
-  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'>clwout</span></span><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
-  8.0pt;font-family:"Courier New"'>File name<o:p></o:p></span></p>\r
-  </td>\r
-  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
-  8.0pt;font-family:"Courier New"'>None<o:p></o:p></span></p>\r
-  </td>\r
-  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>As <i>-<span class=SpellE>clwout</span></i>,\r
-  except that header is strictly compatible with CLUSTALW 1.81.</p>\r
-  <p class=MsoNormal style='page-break-after:avoid'><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:6'>\r
-  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'>diagbreak</span></span><span style='font-size:\r
-  8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>Integer<o:p></o:p></p>\r
-  </td>\r
-  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>1</p>\r
-  </td>\r
-  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>Maximum distance between two diagonals that allows them to\r
-  merge into one diagonal.</p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:7'>\r
-  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'>diaglength</span></span><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>Integer<o:p></o:p></p>\r
-  </td>\r
-  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
-  8.0pt;font-family:"Courier New"'>24<o:p></o:p></span></p>\r
-  </td>\r
-  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>Minimum length of diagonal.</p>\r
-  <p class=MsoNormal style='page-break-after:avoid'><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:8'>\r
-  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'>diagmargin</span></span><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>Integer<o:p></o:p></p>\r
-  </td>\r
-  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
-  8.0pt;font-family:"Courier New"'>5<o:p></o:p></span></p>\r
-  </td>\r
-  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>Discard this many positions\r
-  at ends of diagonal.</p>\r
-  <p class=MsoNormal style='page-break-after:avoid'><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:9'>\r
-  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>distance1<o:p></o:p></span></p>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><o:p>&nbsp;</o:p></span></p>\r
-  </td>\r
-  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>kmer6_6<o:p></o:p></span></p>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>kmer20_3<o:p></o:p></span></p>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>kmer20_4<o:p></o:p></span></p>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>kbit20_3<o:p></o:p></span></p>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>kmer4_6<o:p></o:p></span></p>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><o:p>&nbsp;</o:p></span></p>\r
-  </td>\r
-  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>Kmer6_6\r
-  (amino) or Kmer4_6 (<span class=SpellE>nucleo</span>)</span></p>\r
-  </td>\r
-  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>Distance measure for iteration 1.</p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:10'>\r
-  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>distance2<o:p></o:p></span></p>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><o:p>&nbsp;</o:p></span></p>\r
-  </td>\r
-  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>kmer6_6<o:p></o:p></span></p>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>kmer20_3<o:p></o:p></span></p>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>kmer20_4<o:p></o:p></span></p>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>kbit20_3<o:p></o:p></span></p>\r
-  <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'>pctid_kimura</span></span><span style='font-size:\r
-  8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
-  <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'>pctid_log</span></span><span style='font-size:\r
-  8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><o:p>&nbsp;</o:p></span></p>\r
-  </td>\r
-  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'>pctid_kimura</span></span></p>\r
-  </td>\r
-  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>Distance measure for iterations 2, 3 ...</p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:11'>\r
-  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'>fastaout</span></span><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>File\r
-  name<o:p></o:p></span></p>\r
-  </td>\r
-  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>None<o:p></o:p></span></p>\r
-  </td>\r
-  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>Write output in FASTA format to the given file.</p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:12'>\r
-  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'>gapopen</span></span><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>Floating point</p>\r
-  </td>\r
-  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>[1]<o:p></o:p></p>\r
-  </td>\r
-  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>The <span class=GramE>gap open</span> score. Must be\r
-  negative.</p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:13'>\r
-  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>hydro<o:p></o:p></span></p>\r
-  </td>\r
-  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>Integer<o:p></o:p></p>\r
-  </td>\r
-  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>5</span><o:p></o:p></p>\r
-  </td>\r
-  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>Window size for determining whether a region is\r
-  hydrophobic.</p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:14'>\r
-  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'>hydrofactor</span></span><span style='font-size:\r
-  8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>Floating point</p>\r
-  </td>\r
-  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>1.2<o:p></o:p></span></p>\r
-  </td>\r
-  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>Multiplier for gap open/close penalties in hydrophobic\r
-  regions.</p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:15'>\r
-  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>in<o:p></o:p></span></p>\r
-  </td>\r
-  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>Any file name</p>\r
-  </td>\r
-  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>standard input</p>\r
-  </td>\r
-  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>Where to find the input sequences.</p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:16'>\r
-  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>in1<o:p></o:p></span></p>\r
-  </td>\r
-  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>Any file name</p>\r
-  </td>\r
-  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>None</p>\r
-  </td>\r
-  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>Where to find an input alignment.</p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:17'>\r
-  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>in2<o:p></o:p></span></p>\r
-  </td>\r
-  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>Any file name</p>\r
-  </td>\r
-  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>None</p>\r
-  </td>\r
-  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>Where to find an input alignment.</p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:18'>\r
-  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>log<o:p></o:p></span></p>\r
-  </td>\r
-  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>File name<o:p></o:p></p>\r
-  </td>\r
-  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>None.<o:p></o:p></p>\r
-  </td>\r
-  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>Log file name (delete existing file).</p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:19'>\r
-  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'>loga</span></span><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>File name</p>\r
-  </td>\r
-  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>None.</p>\r
-  </td>\r
-  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>Log file name (append to existing file).</p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:20'>\r
-  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>matrix<o:p></o:p></span></p>\r
-  </td>\r
-  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>File name</p>\r
-  </td>\r
-  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>None</p>\r
-  </td>\r
-  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>File name for substitution matrix in NCBI or WU-BLAST\r
-  format. If you specify your own matrix, you should also specify:</p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  <p class=MsoNormal>-<span class=SpellE>gapopen</span> &lt;g&gt;, -<span\r
-  class=SpellE>gapextend</span> &lt;e&gt; -center 0.0</p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  <p class=MsoNormal>Note that &lt;g&gt; and &lt;e&gt; MUST be negative.</p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:21'>\r
-  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'>maxhours</span></span><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>Floating point</p>\r
-  </td>\r
-  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>None.</p>\r
-  </td>\r
-  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>Maximum time to run in hours. The actual time may exceed\r
-  the requested limit by a few minutes. Decimals are allowed, so 1.5 means one hour\r
-  and 30 minutes.</p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:22'>\r
-  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'>maxiters</span></span><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>Integer 1, 2 ...</p>\r
-  </td>\r
-  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>16<o:p></o:p></span></p>\r
-  </td>\r
-  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>Maximum number of iterations.</p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:23'>\r
-  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'>maxmb</span></span><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>Integer</p>\r
-  </td>\r
-  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>80%\r
-  of Physical RAM, or 500 Mb if not known.<o:p></o:p></span></p>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><o:p>&nbsp;</o:p></span></p>\r
-  </td>\r
-  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>Maximum memory to allocate in Mb.</p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:24'>\r
-  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'>maxtrees</span></span><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>Integer</p>\r
-  </td>\r
-  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>1<o:p></o:p></span></p>\r
-  </td>\r
-  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>Maximum number of new trees to build in iteration 2.</p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:25'>\r
-  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'>minbestcolscore</span></span><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>Floating point </p>\r
-  </td>\r
-  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>[1]</p>\r
-  </td>\r
-  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>Minimum score a column must\r
-  have to be an anchor.</p>\r
-  <p class=MsoNormal style='page-break-after:avoid'><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:26'>\r
-  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'>minsmoothscore</span></span><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>Floating point</p>\r
-  </td>\r
-  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>[1]</p>\r
-  </td>\r
-  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>Minimum smoothed score a\r
-  column must have to be an anchor.</p>\r
-  <p class=MsoNormal style='page-break-after:avoid'><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:27'>\r
-  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'>msaout</span></span><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>File name</p>\r
-  </td>\r
-  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>None</p>\r
-  </td>\r
-  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>Write output to given file\r
-  name in MSF format.</p>\r
-  <p class=MsoNormal style='page-break-after:avoid'><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:28'>\r
-  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'>objscore</span></span><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>sp<o:p></o:p></span></p>\r
-  <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'>ps</span></span><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'><o:p></o:p></span></p>\r
-  <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'>dp</span></span><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'><o:p></o:p></span></p>\r
-  <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'>xp</span></span><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'><o:p></o:p></span></p>\r
-  <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'>spf</span></span><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'><o:p></o:p></span></p>\r
-  <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'>spm</span></span><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'>spm</span></span><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>Objective score used by tree dependent refinement.</p>\r
-  <p class=MsoNormal><span class=GramE>sp=</span>sum-of-pairs score.</p>\r
-  <p class=MsoNormal><span class=SpellE>spf</span>=sum-of-pairs score (dimer\r
-  approximation)</p>\r
-  <p class=MsoNormal><span class=SpellE>spm</span>=sp for &lt; 100 <span\r
-  class=SpellE>seqs</span>, otherwise <span class=SpellE>spf</span></p>\r
-  <p class=MsoNormal><span class=SpellE><span class=GramE>dp</span></span><span\r
-  class=GramE>=</span>dynamic programming score.</p>\r
-  <p class=MsoNormal><span class=SpellE><span class=GramE>ps</span></span><span\r
-  class=GramE>=</span>average profile-sequence score.</p>\r
-  <p class=MsoNormal><span class=SpellE><span class=GramE>xp</span></span><span\r
-  class=GramE>=</span>cross profile score.</p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:29'>\r
-  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>out<o:p></o:p></span></p>\r
-  </td>\r
-  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>File name</p>\r
-  </td>\r
-  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>standard output</p>\r
-  </td>\r
-  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>Where to write the alignment.</p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:30'>\r
-  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'>phyiout</span></span><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>File name</p>\r
-  </td>\r
-  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>None</p>\r
-  </td>\r
-  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>Write output in <span class=SpellE>Phylip</span>\r
-  interleaved format to given file name.</p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:31'>\r
-  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'>physout</span></span><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>File name</p>\r
-  </td>\r
-  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>None</p>\r
-  </td>\r
-  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>Write output in <span class=SpellE>Phylip</span>\r
-  sequential format to given file name.</p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:32'>\r
-  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'>refinewindow</span></span><span style='font-size:\r
-  8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>Integer</p>\r
-  </td>\r
-  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>200</p>\r
-  </td>\r
-  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>Length of window for <i>-<span class=SpellE>refinew</span></i>.</p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:33'>\r
-  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>root1<o:p></o:p></span></p>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>root2<o:p></o:p></span></p>\r
-  </td>\r
-  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>pseudo<o:p></o:p></span></p>\r
-  <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'>midlongestspan</span></span><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
-  <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'>minavgleafdist</span></span><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'>psuedo</span></span><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>Method used to root tree; root1 is used in iteration 1 and\r
-  2, root2 in later iterations.</p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:34'>\r
-  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'>scorefile</span></span><span style='font-size:\r
-  8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>File\r
-  name<o:p></o:p></span></p>\r
-  </td>\r
-  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>None<o:p></o:p></span></p>\r
-  </td>\r
-  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>File name where to write a score file. This contains one\r
-  line for each column in the alignment. The line contains the letters in the\r
-  column followed by the average BLOSUM62 score over pairs of letters in the column.</p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:35'>\r
-  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'>seqtype</span></span><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>protein<o:p></o:p></span></p>\r
-  <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'>nucleo</span></span><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'><o:p></o:p></span></p>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>auto<o:p></o:p></span></p>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><o:p>&nbsp;</o:p></span></p>\r
-  </td>\r
-  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>auto<o:p></o:p></span></p>\r
-  </td>\r
-  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>Sequence type.</p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:36'>\r
-  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'>smoothscoreceil</span></span><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>Floating point</p>\r
-  </td>\r
-  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>[1]</p>\r
-  </td>\r
-  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>Maximum <span class=GramE>value of column score</span> for\r
-  smoothing purposes.</p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:37'>\r
-  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'>smoothwindow</span></span><span style='font-size:\r
-  8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>Integer<o:p></o:p></p>\r
-  </td>\r
-  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>7<o:p></o:p></span></p>\r
-  </td>\r
-  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>Window used for anchor column smoothing.</p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:38'>\r
-  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'>spscore</span></span><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>File name<o:p></o:p></p>\r
-  </td>\r
-  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><o:p>&nbsp;</o:p></span></p>\r
-  </td>\r
-  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>Compute SP objective score of multiple <span class=GramE>alignment</span>.</p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:39'>\r
-  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>SUEFF<o:p></o:p></span></p>\r
-  </td>\r
-  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>Floating point value between 0 and 1.</p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
-  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>0.1<o:p></o:p></span></p>\r
-  </td>\r
-  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>Constant used in UPGMB clustering. Determines the relative\r
-  fraction of average linkage (SUEFF) vs. nearest-neighbor linkage (1 \96 SUEFF).<br\r
-  style='mso-special-character:line-break'>\r
-  <![if !supportLineBreakNewLine]><br style='mso-special-character:line-break'>\r
-  <![endif]></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:40'>\r
-  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>tree1<o:p></o:p></span></p>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>tree2<o:p></o:p></span></p>\r
-  </td>\r
-  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>File name</p>\r
-  </td>\r
-  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>None<o:p></o:p></p>\r
-  </td>\r
-  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>Save tree produced in first or second iteration to given\r
-  file in <span class=SpellE>Newick</span> (<span class=SpellE>Phylip</span>-compatible)\r
-  format.</p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:41'>\r
-  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'>usetree</span></span><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>File name</p>\r
-  </td>\r
-  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>None<o:p></o:p></p>\r
-  </td>\r
-  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>Use given tree as guide tree. Must by in <span\r
-  class=SpellE>Newick</span> (<span class=SpellE>Phyip</span>-compatible)\r
-  format.</p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:42;mso-yfti-lastrow:yes'>\r
-  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
-  8.0pt;font-family:"Courier New"'>weight1<o:p></o:p></span></p>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
-  8.0pt;font-family:"Courier New"'>weight2<o:p></o:p></span></p>\r
-  </td>\r
-  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
-  8.0pt;font-family:"Courier New"'>none<o:p></o:p></span></p>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'>henikoff</span></span><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'>henikoffpb</span></span><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'>gsc</span></span><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'>clustalw</span></span><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'>threeway</span></span></p>\r
-  </td>\r
-  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'>clustalw</span></span><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
-  <p class=MsoNormal style='page-break-after:avoid'><o:p>&nbsp;</o:p></p>\r
-  </td>\r
-  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>Sequence weighting scheme.</p>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span class=GramE>weight1</span>\r
-  is used in iterations 1 and 2.</p>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span class=GramE>weight2</span>\r
-  is used for tree-dependent refinement.</p>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span class=GramE>none=</span>all\r
-  sequences have equal weight.</p>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
-  class=GramE>henikoff</span></span><span class=GramE>=</span>Henikoff &amp;\r
-  Henikoff weighting scheme.</p>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
-  class=GramE>henikoffpb</span></span><span class=GramE>=</span>Modified\r
-  Henikoff scheme as used in PSI-BLAST.</p>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
-  class=GramE>clustalw</span></span><span class=GramE>=</span>CLUSTALW method.</p>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
-  class=GramE>threeway</span></span><span class=GramE>=</span>Gotoh three-way\r
-  method.</p>\r
-  <p class=MsoNormal style='page-break-after:avoid'><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
-</table>\r
-\r
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-\r
-<table class=MsoTableGrid border=0 cellspacing=0 cellpadding=0\r
- style='border-collapse:collapse;mso-yfti-tbllook:480;mso-padding-alt:0in 5.4pt 0in 5.4pt'>\r
- <thead>\r
-  <tr style='mso-yfti-irow:0'>\r
-   <td width=137 valign=top style='width:102.6pt;border:none;border-bottom:\r
-   solid windowtext 1.0pt;mso-border-bottom-alt:solid windowtext .5pt;\r
-   padding:0in 5.4pt 0in 5.4pt'>\r
-   <p class=MsoNormal style='page-break-after:avoid'><b><span style='font-size:\r
-   9.0pt;font-family:Arial'>Flag option<o:p></o:p></span></b></p>\r
-   </td>\r
-   <td width=106 valign=top style='width:1.1in;border:none;border-bottom:solid windowtext 1.0pt;\r
-   mso-border-bottom-alt:solid windowtext .5pt;padding:0in 5.4pt 0in 5.4pt'>\r
-   <p class=MsoNormal style='page-break-after:avoid'><b><span style='font-size:\r
-   9.0pt;font-family:Arial'>Set by default?<o:p></o:p></span></b></p>\r
-   </td>\r
-   <td width=348 valign=top style='width:261.0pt;border:none;border-bottom:\r
-   solid windowtext 1.0pt;mso-border-bottom-alt:solid windowtext .5pt;\r
-   padding:0in 5.4pt 0in 5.4pt'>\r
-   <p class=MsoNormal style='page-break-after:avoid'><b><span style='font-size:\r
-   9.0pt;font-family:Arial'>Description<o:p></o:p></span></b></p>\r
-   </td>\r
-  </tr>\r
- </thead>\r
- <tr style='mso-yfti-irow:1;height:6.25pt'>\r
-  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
-  8.0pt;font-family:"Courier New"'>anchors<o:p></o:p></span></p>\r
-  </td>\r
-  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>yes<o:p></o:p></p>\r
-  </td>\r
-  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>Use anchor optimization in\r
-  tree dependent refinement iterations.</p>\r
-  <p class=MsoNormal style='page-break-after:avoid'><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:2;height:6.25pt'>\r
-  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'>brenner</span></span><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>no</p>\r
-  </td>\r
-  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>Use Steven Brenner's method\r
-  for computing the root alignment.</p>\r
-  <p class=MsoNormal style='page-break-after:avoid'><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:3;height:6.25pt'>\r
-  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
-  8.0pt;font-family:"Courier New"'>cluster<o:p></o:p></span></p>\r
-  </td>\r
-  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>no</p>\r
-  </td>\r
-  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>Perform fast clustering of\r
-  input sequences. Use the \96<i>tree1</i> option to save the tree.</p>\r
-  <p class=MsoNormal style='page-break-after:avoid'><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:4;height:6.25pt'>\r
-  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
-  8.0pt;font-family:"Courier New"'>dimer<o:p></o:p></span></p>\r
-  </td>\r
-  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>no</p>\r
-  </td>\r
-  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>Use dimer approximation for\r
-  the SP score (faster, slightly less accurate).</p>\r
-  <p class=MsoNormal style='page-break-after:avoid'><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:5;height:6.25pt'>\r
-  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'>clw</span></span><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>no<o:p></o:p></p>\r
-  </td>\r
-  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>Write output in CLUSTALW\r
-  format (default is FASTA).</p>\r
-  <p class=MsoNormal style='page-break-after:avoid'><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:6;height:6.25pt'>\r
-  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'>clwstrict</span></span><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>no</p>\r
-  </td>\r
-  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>Write output in CLUSTALW\r
-  format with the &quot;CLUSTAL W (1.81)&quot; header rather than the MUSCLE\r
-  version. This is useful when a post-processing step is picky about the file\r
-  header.</p>\r
-  <p class=MsoNormal style='page-break-after:avoid'><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:7;height:6.25pt'>\r
-  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
-  8.0pt;font-family:"Courier New"'>core<o:p></o:p></span></p>\r
-  </td>\r
-  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>yes in muscle,</p>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span class=GramE>no</span>\r
-  in muscled.<o:p></o:p></p>\r
-  </td>\r
-  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>Do not catch exceptions.</p>\r
-  <p class=MsoNormal style='page-break-after:avoid'><o:p>&nbsp;</o:p></p>\r
-  <p class=MsoNormal style='page-break-after:avoid'><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:8;height:6.25pt'>\r
-  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'>diags</span></span><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>no<o:p></o:p></p>\r
-  </td>\r
-  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>Use diagonal optimizations.\r
-  Faster, especially for closely related sequences, but may be less accurate.</p>\r
-  <p class=MsoNormal style='page-break-after:avoid'><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:9;height:6.25pt'>\r
-  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
-  8.0pt;font-family:"Courier New"'>diags1<o:p></o:p></span></p>\r
-  </td>\r
-  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>no</p>\r
-  </td>\r
-  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>Use diagonal optimizations\r
-  in first iteration.</p>\r
-  <p class=MsoNormal style='page-break-after:avoid'><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:10;height:6.25pt'>\r
-  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
-  8.0pt;font-family:"Courier New"'>diags2<o:p></o:p></span></p>\r
-  </td>\r
-  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>no</p>\r
-  </td>\r
-  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>Use diagonal optimizations\r
-  in second iteration.</p>\r
-  <p class=MsoNormal style='page-break-after:avoid'><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:11;height:6.25pt'>\r
-  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'>fasta</span></span><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>yes<o:p></o:p></p>\r
-  </td>\r
-  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>Write output in FASTA\r
-  format.</p>\r
-  <p class=MsoNormal style='page-break-after:avoid'><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:12;height:6.25pt'>\r
-  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
-  8.0pt;font-family:"Courier New"'>group<o:p></o:p></span></p>\r
-  </td>\r
-  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>yes<o:p></o:p></p>\r
-  </td>\r
-  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>Group similar sequences\r
-  together in the output. This is the default. See also \96<i>stable</i>.</p>\r
-  <p class=MsoNormal style='page-break-after:avoid'><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:13;height:6.25pt'>\r
-  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
-  8.0pt;font-family:"Courier New"'>html<o:p></o:p></span></p>\r
-  </td>\r
-  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>no<o:p></o:p></p>\r
-  </td>\r
-  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'>Write output in HTML format\r
-  (default is FASTA).</p>\r
-  <p class=MsoNormal style='page-break-after:avoid'><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:14'>\r
-  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
-  8.0pt;font-family:"Courier New"'>le</span></p>\r
-  </td>\r
-  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>maybe<o:p></o:p></p>\r
-  </td>\r
-  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt'>\r
-  <p class=MsoNormal>Use log-expectation profile score (VTML240). Alternatives\r
-  are to use \96<i>sp</i> or <i>\96<span class=SpellE>sv</span></i>. This is the\r
-  default for amino acid sequences.<o:p></o:p></p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:15;height:6.25pt'>\r
-  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'>msf</span></span><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal>no<o:p></o:p></p>\r
-  </td>\r
-  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal>Write output in MSF format (default is FASTA). Designed to\r
-  be compatible with the GCG package.</p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:16;height:6.25pt'>\r
-  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'>noanchors</span></span><span style='font-size:\r
-  8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal>no<o:p></o:p></p>\r
-  </td>\r
-  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal>Disable anchor optimization. Default is \96<i>anchors</i>.<o:p></o:p></p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:17;height:6.25pt'>\r
-  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'>nocore</span></span><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal>no in muscle,</p>\r
-  <p class=MsoNormal><span class=GramE>yes</span> in muscled.<o:p></o:p></p>\r
-  </td>\r
-  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal>Catch exceptions and give an error message if possible.</p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:18;height:6.25pt'>\r
-  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'>phyi</span></span><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal>no<o:p></o:p></p>\r
-  </td>\r
-  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal>Write output in <span class=SpellE>Phylip</span>\r
-  interleaved format.</p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:19;height:6.25pt'>\r
-  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>phys<o:p></o:p></span></p>\r
-  </td>\r
-  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal>no</p>\r
-  </td>\r
-  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal>Write output in <span class=SpellE>Phylip</span>\r
-  sequential format.</p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:20;height:6.25pt'>\r
-  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>profile<o:p></o:p></span></p>\r
-  </td>\r
-  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal>no<o:p></o:p></p>\r
-  </td>\r
-  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal>Compute profile-profile alignment. Input alignments must\r
-  be given using \96<i>in1</i> and \96<i>in2</i> options.</p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:21;height:6.25pt'>\r
-  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>quiet<o:p></o:p></span></p>\r
-  </td>\r
-  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal>no<o:p></o:p></p>\r
-  </td>\r
-  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal>Do not display progress messages.</p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:22;height:6.25pt'>\r
-  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>refine<o:p></o:p></span></p>\r
-  </td>\r
-  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal>no<o:p></o:p></p>\r
-  </td>\r
-  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal>Input file is already aligned, skip first two iterations\r
-  and begin tree dependent refinement.</p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:23;height:6.25pt'>\r
-  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'>refinew</span></span><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal>no<o:p></o:p></p>\r
-  </td>\r
-  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal>Refine an alignment by dividing it into non-overlapping\r
-  windows and re-aligning each window. Typically used for whole-genome\r
-  nucleotide alignments.</p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:24;height:6.25pt'>\r
-  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
-  8.0pt;font-family:"Courier New"'>sp<o:p></o:p></span></p>\r
-  </td>\r
-  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal>no<o:p></o:p></p>\r
-  </td>\r
-  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal>Use sum-of-pairs protein profile score (PAM200). Default\r
-  is \96<i>le.<o:p></o:p></i></p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:25;height:6.25pt'>\r
-  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'>spscore</span></span><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal>no</p>\r
-  </td>\r
-  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal>Compute alignment score of profile-profile alignment.\r
-  Input alignments must be given using \96<i>in1</i> and \96<i>in2</i> options.\r
-  These must be pre-aligned with gapped columns as needed, i.e. must be of the\r
-  same length (have same number of columns).</p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:26;height:6.25pt'>\r
-  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'>spn</span></span><span\r
-  style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal>maybe</p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
-  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal>Use sum-of-pairs nucleotide profile score. This is the\r
-  only option for nucleotides, and is therefore the default. The substitution\r
-  scores and gap penalty scores are &quot;borrowed&quot; from BLASTZ.</p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:27;height:6.25pt'>\r
-  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
-  8.0pt;font-family:"Courier New"'>stable<o:p></o:p></span></p>\r
-  </td>\r
-  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal>no<o:p></o:p></p>\r
-  </td>\r
-  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal>Preserve input order of sequences in output file. Default\r
-  is to group sequences by similarity (\96<i>group</i>).</p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:28;height:6.25pt'>\r
-  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'>sv</span></span><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal>no<o:p></o:p></p>\r
-  </td>\r
-  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal>Use sum-of-pairs profile score (VTML240). Default is \96<i>le.</i></p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:29;height:6.25pt'>\r
-  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>termgaps4<o:p></o:p></span></p>\r
-  </td>\r
-  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal>yes<o:p></o:p></p>\r
-  </td>\r
-  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal>Use 4-way test for treatment of terminal gaps. (Cannot be\r
-  disabled in this version).</p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:30;height:6.25pt'>\r
-  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'>termgapsfull</span></span><span style='font-size:\r
-  8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal>no<o:p></o:p></p>\r
-  </td>\r
-  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal>Terminal gaps penalized with full penalty.</p>\r
-  <p class=MsoNormal>[1] Not fully supported in this version.</p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:31;height:6.25pt'>\r
-  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
-  font-family:"Courier New"'>termgapshalf</span></span><span style='font-size:\r
-  8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal>yes<o:p></o:p></p>\r
-  </td>\r
-  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
-  <p class=MsoNormal>Terminal gaps penalized with half penalty.</p>\r
-  <p class=MsoNormal>[1] Not fully supported in this version.</p>\r
-  <p class=MsoNormal><o:p>&nbsp;</o:p></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:32;height:6.25pt'>\r
-  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
-  height:6.25pt'>\r
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diff --git a/binaries/help/muscle3.7.txt b/binaries/help/muscle3.7.txt
deleted file mode 100644 (file)
index 7f23ee4..0000000
--- a/binaries/help/muscle3.7.txt
+++ /dev/null
@@ -1,32 +0,0 @@
-MUSCLE v3.7 by Robert C. Edgar\r
-\r
-http://www.drive5.com/muscle\r
-This software is donated to the public domain.\r
-Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97.\r
-\r
-\r
-Basic usage\r
-\r
-    muscle -in <inputfile> -out <outputfile>\r
-\r
-Common options (for a complete list please see the User Guide):\r
-\r
-    -in <inputfile>    Input file in FASTA format (default stdin)\r
-    -out <outputfile>  Output alignment in FASTA format (default stdout)\r
-    -diags             Find diagonals (faster for similar sequences)\r
-    -maxiters <n>      Maximum number of iterations (integer, default 16)\r
-    -maxhours <h>      Maximum time to iterate in hours (default no limit)\r
-    -maxmb <m>         Maximum memory to allocate in Mb (default 80% of RAM)\r
-    -html              Write output in HTML format (default FASTA)\r
-    -msf               Write output in GCG MSF format (default FASTA)\r
-    -clw               Write output in CLUSTALW format (default FASTA)\r
-    -clwstrict         As -clw, with 'CLUSTAL W (1.81)' header\r
-    -log[a] <logfile>  Log to file (append if -loga, overwrite if -log)\r
-    -quiet             Do not write progress messages to stderr\r
-    -stable            Output sequences in input order (default is -group)\r
-    -group             Group sequences by similarity (this is the default)\r
-    -version           Display version information and exit\r
-\r
-Without refinement (very fast, avg accuracy similar to T-Coffee): -maxiters 2\r
-Fastest possible (amino acids): -maxiters 1 -diags -sv -distance1 kbit20_3\r
-Fastest possible (nucleotides): -maxiters 1 -diags\r

diff --git a/binaries/help/probcons.pdf b/binaries/help/probcons.pdf
deleted file mode 100644 (file)
index 74dd22b..0000000
Binary files a/binaries/help/probcons.pdf and /dev/null differ

diff --git a/binaries/help/t_coffee.htm b/binaries/help/t_coffee.htm
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-p.MsoFooter, li.MsoFooter, div.MsoFooter\r
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-       {mso-style-parent:List;\r
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-       {mso-style-parent:"List Bullet";\r
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-p.MsoListNumber2, li.MsoListNumber2, div.MsoListNumber2\r
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-p.MsoTitle, li.MsoTitle, div.MsoTitle\r
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-p.MsoBodyText, li.MsoBodyText, div.MsoBodyText\r
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-p.MsoListContinue, li.MsoListContinue, div.MsoListContinue\r
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-p.MsoListContinue2, li.MsoListContinue2, div.MsoListContinue2\r
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-       mso-pagination:widow-orphan;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       letter-spacing:-.25pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.MsoListContinue3, li.MsoListContinue3, div.MsoListContinue3\r
-       {mso-style-parent:"List Continue";\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:8.0pt;\r
-       margin-left:72.0pt;\r
-       text-align:justify;\r
-       mso-pagination:widow-orphan;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       letter-spacing:-.25pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.MsoListContinue4, li.MsoListContinue4, div.MsoListContinue4\r
-       {mso-style-parent:"List Continue";\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:8.0pt;\r
-       margin-left:90.0pt;\r
-       text-align:justify;\r
-       mso-pagination:widow-orphan;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       letter-spacing:-.25pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.MsoListContinue5, li.MsoListContinue5, div.MsoListContinue5\r
-       {mso-style-parent:"List Continue";\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:8.0pt;\r
-       margin-left:108.0pt;\r
-       text-align:justify;\r
-       mso-pagination:widow-orphan;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       letter-spacing:-.25pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.MsoSubtitle, li.MsoSubtitle, div.MsoSubtitle\r
-       {mso-style-parent:Title;\r
-       mso-style-next:"Body Text";\r
-       margin-top:97.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:0mm;\r
-       margin-bottom:.0001pt;\r
-       text-align:center;\r
-       line-height:10.0pt;\r
-       mso-pagination:widow-orphan;\r
-       page-break-after:avoid;\r
-       border:none;\r
-       mso-border-bottom-alt:solid gray .75pt;\r
-       padding:0mm;\r
-       mso-padding-alt:0mm 0mm 14.0pt 0mm;\r
-       font-size:9.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       color:gray;\r
-       text-transform:uppercase;\r
-       letter-spacing:1.5pt;\r
-       mso-font-kerning:14.0pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       mso-bidi-font-weight:bold;}\r
-p.MsoDate, li.MsoDate, div.MsoDate\r
-       {mso-style-parent:"Body Text";\r
-       margin-top:24.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:8.0pt;\r
-       margin-left:0mm;\r
-       text-align:center;\r
-       mso-pagination:widow-orphan;\r
-       font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-a:link, span.MsoHyperlink\r
-       {color:blue;\r
-       text-decoration:underline;\r
-       text-underline:single;}\r
-a:visited, span.MsoHyperlinkFollowed\r
-       {color:purple;\r
-       text-decoration:underline;\r
-       text-underline:single;}\r
-em\r
-       {mso-style-parent:"";\r
-       mso-ansi-font-size:9.0pt;\r
-       font-family:"Arial Black";\r
-       mso-ascii-font-family:"Arial Black";\r
-       mso-hansi-font-family:"Arial Black";\r
-       font-style:normal;}\r
-p.MsoPlainText, li.MsoPlainText, div.MsoPlainText\r
-       {margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-pagination:widow-orphan;\r
-       font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-fareast-language:FR;}\r
-code\r
-       {font-family:"Courier New";\r
-       mso-ascii-font-family:"Courier New";\r
-       mso-fareast-font-family:"MS Mincho";\r
-       mso-hansi-font-family:"Courier New";\r
-       mso-bidi-font-family:"Courier New";}\r
-span.Heading1Char\r
-       {mso-style-name:"Heading 1 Char";\r
-       mso-style-locked:yes;\r
-       mso-style-link:"Heading 1";\r
-       mso-ansi-font-size:16.0pt;\r
-       font-family:"Arial Black";\r
-       mso-ascii-font-family:"Arial Black";\r
-       mso-hansi-font-family:"Arial Black";\r
-       color:gray;\r
-       letter-spacing:-1.25pt;\r
-       mso-font-kerning:14.0pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       mso-bidi-language:AR-SA;}\r
-p.MyNormal, li.MyNormal, div.MyNormal\r
-       {mso-style-name:MyNormal;\r
-       mso-style-update:auto;\r
-       mso-style-link:"MyNormal Char";\r
-       margin-top:2.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:6.0pt;\r
-       margin-left:42.55pt;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:11.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Courier New";\r
-       mso-ansi-language:AF;\r
-       mso-fareast-language:EN-US;}\r
-span.MyNormalChar\r
-       {mso-style-name:"MyNormal Char";\r
-       mso-style-locked:yes;\r
-       mso-style-parent:"example Char";\r
-       mso-style-link:MyNormal;\r
-       mso-ansi-font-size:11.0pt;\r
-       mso-bidi-font-size:11.0pt;\r
-       font-family:"Courier New";\r
-       mso-bidi-font-family:"Courier New";\r
-       mso-ansi-language:AF;\r
-       mso-fareast-language:EN-US;\r
-       mso-bidi-language:AR-SA;}\r
-span.exampleChar\r
-       {mso-style-name:"example Char";\r
-       mso-style-locked:yes;\r
-       mso-style-link:example;\r
-       mso-ansi-font-size:8.0pt;\r
-       font-family:"Courier New";\r
-       mso-ascii-font-family:"Courier New";\r
-       mso-hansi-font-family:"Courier New";\r
-       mso-bidi-font-family:"Courier New";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       mso-bidi-language:AR-SA;}\r
-p.example, li.example, div.example\r
-       {mso-style-name:example;\r
-       mso-style-update:auto;\r
-       mso-style-link:"example Char";\r
-       margin-top:6.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:6.0pt;\r
-       margin-left:0mm;\r
-       text-indent:36.0pt;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:8.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.FAQ, li.FAQ, div.FAQ\r
-       {mso-style-name:FAQ;\r
-       mso-style-update:auto;\r
-       mso-style-parent:"Heading 3";\r
-       margin-top:12.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:6.0pt;\r
-       margin-left:10.0mm;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       page-break-after:avoid;\r
-       mso-outline-level:3;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:14.0pt;\r
-       font-family:"Comic Sans MS";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-GB;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-span.ListChar\r
-       {mso-style-name:"List Char";\r
-       mso-style-locked:yes;\r
-       mso-style-parent:"Text body Char";\r
-       mso-style-link:List;\r
-       mso-ansi-font-size:12.0pt;\r
-       font-family:Garamond;\r
-       mso-ascii-font-family:Garamond;\r
-       mso-hansi-font-family:Garamond;\r
-       letter-spacing:-.25pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       mso-bidi-language:AR-SA;}\r
-span.TextbodyChar\r
-       {mso-style-name:"Text body Char";\r
-       mso-style-locked:yes;\r
-       mso-style-link:"Text body";\r
-       mso-ansi-font-size:12.0pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       mso-bidi-language:AR-SA;}\r
-p.Textbody, li.Textbody, div.Textbody\r
-       {mso-style-name:"Text body";\r
-       mso-style-link:"Text body Char";\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.HeadingBase, li.HeadingBase, div.HeadingBase\r
-       {mso-style-name:"Heading Base";\r
-       mso-style-next:"Body Text";\r
-       margin-top:12.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:6.0pt;\r
-       margin-left:0mm;\r
-       mso-pagination:widow-orphan;\r
-       page-break-after:avoid;\r
-       font-size:18.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Arial;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       mso-font-kerning:14.0pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.BlockQuotation, li.BlockQuotation, div.BlockQuotation\r
-       {mso-style-name:"Block Quotation";\r
-       mso-style-next:"Body Text";\r
-       margin-top:0mm;\r
-       margin-right:30.0pt;\r
-       margin-bottom:12.0pt;\r
-       margin-left:30.0pt;\r
-       text-align:justify;\r
-       mso-pagination:widow-orphan;\r
-       background:#F9F9F9;\r
-       mso-shading:windowtext;\r
-       mso-pattern:gray-10 gray;\r
-       border:none;\r
-       mso-border-alt:solid white .75pt;\r
-       padding:0mm;\r
-       mso-padding-alt:12.0pt 12.0pt 12.0pt 12.0pt;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       letter-spacing:-.25pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.BlockQuotationFirst, li.BlockQuotationFirst, div.BlockQuotationFirst\r
-       {mso-style-name:"Block Quotation First";\r
-       mso-style-next:"Block Quotation";\r
-       margin-top:0mm;\r
-       margin-right:24.0pt;\r
-       margin-bottom:0mm;\r
-       margin-left:24.0pt;\r
-       margin-bottom:.0001pt;\r
-       text-indent:3.0pt;\r
-       mso-pagination:widow-orphan lines-together;\r
-       background:#E5E5E5;\r
-       mso-shading:windowtext;\r
-       mso-pattern:gray-10 auto;\r
-       border:none;\r
-       mso-border-top-alt:solid white .75pt;\r
-       mso-border-left-alt:solid white .75pt;\r
-       mso-border-right-alt:solid white .75pt;\r
-       padding:0mm;\r
-       mso-padding-alt:6.0pt 6.0pt 0mm 6.0pt;\r
-       font-size:10.5pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Arial Black";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       letter-spacing:-.5pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.BlockQuotationLast, li.BlockQuotationLast, div.BlockQuotationLast\r
-       {mso-style-name:"Block Quotation Last";\r
-       mso-style-parent:"Block Quotation";\r
-       mso-style-next:"Body Text";\r
-       margin-top:0mm;\r
-       margin-right:36.0pt;\r
-       margin-bottom:12.0pt;\r
-       margin-left:36.0pt;\r
-       mso-pagination:widow-orphan lines-together;\r
-       font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-style:italic;\r
-       mso-bidi-font-style:normal;}\r
-p.BodyTextKeep, li.BodyTextKeep, div.BodyTextKeep\r
-       {mso-style-name:"Body Text Keep";\r
-       mso-style-parent:"Body Text";\r
-       mso-style-next:"Body Text";\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:12.0pt;\r
-       margin-left:0mm;\r
-       text-align:justify;\r
-       mso-pagination:widow-orphan;\r
-       page-break-after:avoid;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       letter-spacing:-.25pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.ChapterLabel, li.ChapterLabel, div.ChapterLabel\r
-       {mso-style-name:"Chapter Label";\r
-       mso-style-next:"Body Text";\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:12.0pt;\r
-       margin-left:0mm;\r
-       mso-pagination:widow-orphan;\r
-       page-break-after:avoid;\r
-       border:none;\r
-       mso-border-bottom-alt:solid windowtext .75pt;\r
-       padding:0mm;\r
-       mso-padding-alt:0mm 0mm 3.0pt 0mm;\r
-       font-size:7.5pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Arial Black";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       text-transform:uppercase;\r
-       letter-spacing:3.5pt;\r
-       mso-font-kerning:14.0pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.ChapterSubtitle, li.ChapterSubtitle, div.ChapterSubtitle\r
-       {mso-style-name:"Chapter Subtitle";\r
-       mso-style-next:"Body Text";\r
-       margin-top:0mm;\r
-       margin-right:90.0pt;\r
-       margin-bottom:18.0pt;\r
-       margin-left:0mm;\r
-       mso-line-height-alt:12.0pt;\r
-       mso-pagination:widow-orphan lines-together;\r
-       page-break-after:avoid;\r
-       font-size:14.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       letter-spacing:-1.0pt;\r
-       mso-font-kerning:14.0pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-style:italic;\r
-       mso-bidi-font-style:normal;}\r
-p.ChapterTitle, li.ChapterTitle, div.ChapterTitle\r
-       {mso-style-name:"Chapter Title";\r
-       mso-style-update:auto;\r
-       mso-style-link:"Chapter Title Char";\r
-       mso-style-next:"Chapter Subtitle";\r
-       margin-top:30.0pt;\r
-       margin-right:4.25pt;\r
-       margin-bottom:102.0pt;\r
-       margin-left:0mm;\r
-       text-align:center;\r
-       mso-line-height-alt:22.0pt;\r
-       page-break-before:always;\r
-       mso-pagination:widow-orphan lines-together;\r
-       page-break-after:avoid;\r
-       background:#CCCCCC;\r
-       border:none;\r
-       mso-border-alt:solid windowtext 3.0pt;\r
-       padding:0mm;\r
-       mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;\r
-       font-size:36.0pt;\r
-       mso-bidi-font-size:48.0pt;\r
-       font-family:"Arial Black";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       color:white;\r
-       letter-spacing:-1.75pt;\r
-       mso-font-kerning:14.0pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-span.ChapterTitleChar\r
-       {mso-style-name:"Chapter Title Char";\r
-       mso-style-locked:yes;\r
-       mso-style-link:"Chapter Title";\r
-       mso-ansi-font-size:36.0pt;\r
-       mso-bidi-font-size:48.0pt;\r
-       font-family:"Arial Black";\r
-       mso-ascii-font-family:"Arial Black";\r
-       mso-hansi-font-family:"Arial Black";\r
-       color:white;\r
-       letter-spacing:-1.75pt;\r
-       mso-font-kerning:14.0pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       mso-bidi-language:AR-SA;}\r
-p.CompanyName, li.CompanyName, div.CompanyName\r
-       {mso-style-name:"Company Name";\r
-       mso-style-next:Normal;\r
-       margin-top:21.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:3.0pt;\r
-       margin-left:0mm;\r
-       line-height:16.0pt;\r
-       mso-line-height-rule:exactly;\r
-       mso-pagination:widow-orphan;\r
-       font-size:19.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       text-transform:uppercase;\r
-       mso-font-kerning:18.0pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.DocumentLabel, li.DocumentLabel, div.DocumentLabel\r
-       {mso-style-name:"Document Label";\r
-       margin-top:12.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:18.0pt;\r
-       margin-left:0mm;\r
-       mso-pagination:widow-orphan;\r
-       page-break-after:avoid;\r
-       font-size:18.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       mso-font-kerning:14.0pt;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.FooterEven, li.FooterEven, div.FooterEven\r
-       {mso-style-name:"Footer Even";\r
-       mso-style-parent:Footer;\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       text-align:center;\r
-       mso-pagination:widow-orphan lines-together;\r
-       tab-stops:center 216.0pt right 432.0pt;\r
-       border:none;\r
-       mso-border-top-alt:solid windowtext .75pt;\r
-       padding:0mm;\r
-       mso-padding-alt:3.0pt 0mm 0mm 0mm;\r
-       font-size:8.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Arial Black";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
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-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.FAQexampleCxSpFirst, li.FAQexampleCxSpFirst, div.FAQexampleCxSpFirst\r
-       {mso-style-name:FAQ_exampleCxSpFirst;\r
-       mso-style-parent:example;\r
-       mso-style-type:export-only;\r
-       margin-top:12.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:10.0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-add-space:auto;\r
-       line-height:200%;\r
-       mso-pagination:widow-orphan lines-together;\r
-       page-break-after:avoid;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.FAQexampleCxSpMiddle, li.FAQexampleCxSpMiddle, div.FAQexampleCxSpMiddle\r
-       {mso-style-name:FAQ_exampleCxSpMiddle;\r
-       mso-style-parent:example;\r
-       mso-style-type:export-only;\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:10.0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-add-space:auto;\r
-       line-height:200%;\r
-       mso-pagination:widow-orphan lines-together;\r
-       page-break-after:avoid;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.FAQexampleCxSpLast, li.FAQexampleCxSpLast, div.FAQexampleCxSpLast\r
-       {mso-style-name:FAQ_exampleCxSpLast;\r
-       mso-style-parent:example;\r
-       mso-style-type:export-only;\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:12.0pt;\r
-       margin-left:10.0mm;\r
-       mso-add-space:auto;\r
-       line-height:200%;\r
-       mso-pagination:widow-orphan lines-together;\r
-       page-break-after:avoid;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.Firstlineindent, li.Firstlineindent, div.Firstlineindent\r
-       {mso-style-name:"First line indent";\r
-       mso-style-parent:"Text body";\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       text-align:justify;\r
-       text-indent:14.15pt;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.Hangingindent, li.Hangingindent, div.Hangingindent\r
-       {mso-style-name:"Hanging indent";\r
-       mso-style-parent:"Text body";\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:10.0mm;\r
-       margin-bottom:.0001pt;\r
-       text-align:justify;\r
-       text-indent:-14.15pt;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       tab-stops:10.0mm;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.Numbering3, li.Numbering3, div.Numbering3\r
-       {mso-style-name:"Numbering 3";\r
-       mso-style-parent:List;\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:6.0pt;\r
-       margin-left:42.45pt;\r
-       text-align:justify;\r
-       text-indent:-14.15pt;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.TableContents, li.TableContents, div.TableContents\r
-       {mso-style-name:"Table Contents";\r
-       mso-style-parent:"Text body";\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.TableHeading, li.TableHeading, div.TableHeading\r
-       {mso-style-name:"Table Heading";\r
-       mso-style-parent:"Table Contents";\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       text-align:center;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;\r
-       font-style:italic;\r
-       mso-bidi-font-style:normal;}\r
-p.author, li.author, div.author\r
-       {mso-style-name:author;\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.numberedlist, li.numberedlist, div.numberedlist\r
-       {mso-style-name:"numbered list";\r
-       mso-style-update:auto;\r
-       mso-style-parent:"Heading 4";\r
-       margin-top:3.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:3.0pt;\r
-       margin-left:0mm;\r
-       mso-pagination:none;\r
-       page-break-after:avoid;\r
-       mso-outline-level:4;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       mso-bidi-font-size:12.0pt;\r
-       font-family:"Arial Black";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Courier New";\r
-       letter-spacing:1.0pt;\r
-       mso-ansi-language:AF;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;\r
-       font-style:italic;\r
-       mso-bidi-font-style:normal;}\r
-p.Noteboxtitle, li.Noteboxtitle, div.Noteboxtitle\r
-       {mso-style-name:"Notebox\.title";\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       text-align:center;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:18.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Arial;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;}\r
-p.noteboxexample, li.noteboxexample, div.noteboxexample\r
-       {mso-style-name:"notebox\.example";\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       text-indent:36.0pt;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;}\r
-p.noteboxbody, li.noteboxbody, div.noteboxbody\r
-       {mso-style-name:"notebox\.body";\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-style:italic;}\r
-p.Note, li.Note, div.Note\r
-       {mso-style-name:Note;\r
-       mso-style-update:auto;\r
-       mso-style-link:"Note Char";\r
-       margin-top:6.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:12.0pt;\r
-       margin-left:42.55pt;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       tab-stops:10.0mm;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       mso-bidi-font-size:8.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-GB;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-span.NoteChar\r
-       {mso-style-name:"Note Char";\r
-       mso-style-locked:yes;\r
-       mso-style-link:Note;\r
-       mso-bidi-font-size:8.0pt;\r
-       mso-ansi-language:EN-GB;\r
-       mso-fareast-language:EN-US;\r
-       mso-bidi-language:AR-SA;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.Table, li.Table, div.Table\r
-       {mso-style-name:Table;\r
-       mso-style-parent:Index;\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.flag, li.flag, div.flag\r
-       {mso-style-name:flag;\r
-       mso-style-parent:"Heading 4";\r
-       margin-top:12.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:3.0pt;\r
-       margin-left:10.0mm;\r
-       mso-pagination:none;\r
-       page-break-after:avoid;\r
-       mso-outline-level:4;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:12.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Courier New";\r
-       letter-spacing:1.0pt;\r
-       mso-ansi-language:AF;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;\r
-       font-style:italic;\r
-       mso-bidi-font-style:normal;}\r
-p.flagusage, li.flagusage, div.flagusage\r
-       {mso-style-name:"flag usage";\r
-       mso-style-update:auto;\r
-       mso-style-parent:"Heading 5";\r
-       margin-top:3.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:3.0pt;\r
-       margin-left:42.55pt;\r
-       mso-pagination:none;\r
-       mso-outline-level:5;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:13.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.flagdefault, li.flagdefault, div.flagdefault\r
-       {mso-style-name:"flag default";\r
-       mso-style-parent:"Heading 5";\r
-       margin-top:3.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:3.0pt;\r
-       margin-left:18.0pt;\r
-       mso-pagination:none;\r
-       mso-outline-level:5;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:13.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;}\r
-p.flagdescription, li.flagdescription, div.flagdescription\r
-       {mso-style-name:"flag description";\r
-       mso-style-update:auto;\r
-       mso-style-link:"flag description Char";\r
-       margin-top:6.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:42.55pt;\r
-       margin-bottom:.0001pt;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-span.flagdescriptionChar\r
-       {mso-style-name:"flag description Char";\r
-       mso-style-locked:yes;\r
-       mso-style-link:"flag description";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       mso-bidi-language:AR-SA;}\r
-p.flagNote, li.flagNote, div.flagNote\r
-       {mso-style-name:"flag Note";\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       text-align:justify;\r
-       text-indent:.05pt;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;}\r
-p.flagdescriptionid1, li.flagdescriptionid1, div.flagdescriptionid1\r
-       {mso-style-name:"flag description id1";\r
-       mso-style-parent:"flag description";\r
-       margin-top:6.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:70.9pt;\r
-       margin-bottom:.0001pt;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.output, li.output, div.output\r
-       {mso-style-name:output;\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:18.0pt;\r
-       margin-bottom:.0001pt;\r
-       text-align:justify;\r
-       text-indent:.05pt;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:8.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Courier;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.instruction, li.instruction, div.instruction\r
-       {mso-style-name:instruction;\r
-       mso-style-update:auto;\r
-       mso-style-parent:example;\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:42.55pt;\r
-       margin-bottom:.0001pt;\r
-       line-height:200%;\r
-       mso-pagination:widow-orphan lines-together;\r
-       page-break-after:avoid;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.Format, li.Format, div.Format\r
-       {mso-style-name:Format;\r
-       mso-style-parent:example;\r
-       margin-top:12.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:12.0pt;\r
-       margin-left:10.0mm;\r
-       mso-add-space:auto;\r
-       line-height:200%;\r
-       mso-pagination:widow-orphan lines-together;\r
-       page-break-after:avoid;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-GB;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.FormatCxSpFirst, li.FormatCxSpFirst, div.FormatCxSpFirst\r
-       {mso-style-name:FormatCxSpFirst;\r
-       mso-style-parent:example;\r
-       mso-style-type:export-only;\r
-       margin-top:12.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:10.0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-add-space:auto;\r
-       line-height:200%;\r
-       mso-pagination:widow-orphan lines-together;\r
-       page-break-after:avoid;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-GB;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.FormatCxSpMiddle, li.FormatCxSpMiddle, div.FormatCxSpMiddle\r
-       {mso-style-name:FormatCxSpMiddle;\r
-       mso-style-parent:example;\r
-       mso-style-type:export-only;\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:10.0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-add-space:auto;\r
-       line-height:200%;\r
-       mso-pagination:widow-orphan lines-together;\r
-       page-break-after:avoid;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-GB;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.FormatCxSpLast, li.FormatCxSpLast, div.FormatCxSpLast\r
-       {mso-style-name:FormatCxSpLast;\r
-       mso-style-parent:example;\r
-       mso-style-type:export-only;\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:12.0pt;\r
-       margin-left:10.0mm;\r
-       mso-add-space:auto;\r
-       line-height:200%;\r
-       mso-pagination:widow-orphan lines-together;\r
-       page-break-after:avoid;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-GB;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.ListinFlag, li.ListinFlag, div.ListinFlag\r
-       {mso-style-name:"List in Flag";\r
-       mso-style-parent:List;\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.example2, li.example2, div.example2\r
-       {mso-style-name:example2;\r
-       mso-style-parent:example;\r
-       margin-top:12.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:12.0pt;\r
-       margin-left:20.0mm;\r
-       mso-add-space:auto;\r
-       line-height:200%;\r
-       mso-pagination:widow-orphan lines-together;\r
-       page-break-after:avoid;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.example2CxSpFirst, li.example2CxSpFirst, div.example2CxSpFirst\r
-       {mso-style-name:example2CxSpFirst;\r
-       mso-style-parent:example;\r
-       mso-style-type:export-only;\r
-       margin-top:12.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:20.0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-add-space:auto;\r
-       line-height:200%;\r
-       mso-pagination:widow-orphan lines-together;\r
-       page-break-after:avoid;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.example2CxSpMiddle, li.example2CxSpMiddle, div.example2CxSpMiddle\r
-       {mso-style-name:example2CxSpMiddle;\r
-       mso-style-parent:example;\r
-       mso-style-type:export-only;\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:20.0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-add-space:auto;\r
-       line-height:200%;\r
-       mso-pagination:widow-orphan lines-together;\r
-       page-break-after:avoid;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.example2CxSpLast, li.example2CxSpLast, div.example2CxSpLast\r
-       {mso-style-name:example2CxSpLast;\r
-       mso-style-parent:example;\r
-       mso-style-type:export-only;\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:12.0pt;\r
-       margin-left:20.0mm;\r
-       mso-add-space:auto;\r
-       line-height:200%;\r
-       mso-pagination:widow-orphan lines-together;\r
-       page-break-after:avoid;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.StyleNote, li.StyleNote, div.StyleNote\r
-       {mso-style-name:"Style Note";\r
-       mso-style-parent:Note;\r
-       margin-top:6.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:12.0pt;\r
-       margin-left:-35.45pt;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       tab-stops:10.0mm;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       mso-bidi-font-size:8.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-GB;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;}\r
-p.examplefile, li.examplefile, div.examplefile\r
-       {mso-style-name:example_file;\r
-       mso-style-update:auto;\r
-       margin-top:6.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:6.0pt;\r
-       margin-left:0mm;\r
-       mso-add-space:auto;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       background:#E6E6E6;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       border:none;\r
-       mso-border-alt:solid windowtext .5pt;\r
-       padding:0mm;\r
-       mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;\r
-       font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.examplefileCxSpFirst, li.examplefileCxSpFirst, div.examplefileCxSpFirst\r
-       {mso-style-name:example_fileCxSpFirst;\r
-       mso-style-update:auto;\r
-       mso-style-type:export-only;\r
-       margin-top:6.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-add-space:auto;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       background:#E6E6E6;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       border:none;\r
-       mso-border-alt:solid windowtext .5pt;\r
-       padding:0mm;\r
-       mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;\r
-       font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.examplefileCxSpMiddle, li.examplefileCxSpMiddle, div.examplefileCxSpMiddle\r
-       {mso-style-name:example_fileCxSpMiddle;\r
-       mso-style-update:auto;\r
-       mso-style-type:export-only;\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-add-space:auto;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       background:#E6E6E6;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       border:none;\r
-       mso-border-alt:solid windowtext .5pt;\r
-       padding:0mm;\r
-       mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;\r
-       font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.examplefileCxSpLast, li.examplefileCxSpLast, div.examplefileCxSpLast\r
-       {mso-style-name:example_fileCxSpLast;\r
-       mso-style-update:auto;\r
-       mso-style-type:export-only;\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:6.0pt;\r
-       margin-left:0mm;\r
-       mso-add-space:auto;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       background:#E6E6E6;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       border:none;\r
-       mso-border-alt:solid windowtext .5pt;\r
-       padding:0mm;\r
-       mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;\r
-       font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.Warning, li.Warning, div.Warning\r
-       {mso-style-name:Warning;\r
-       mso-style-update:auto;\r
-       mso-style-link:"Warning Char";\r
-       mso-margin-top-alt:auto;\r
-       margin-right:0mm;\r
-       mso-margin-bottom-alt:auto;\r
-       margin-left:0mm;\r
-       mso-pagination:widow-orphan;\r
-       background:#F7CBB7;\r
-       border:none;\r
-       mso-border-alt:solid windowtext 1.5pt;\r
-       padding:0mm;\r
-       mso-padding-alt:0mm 0mm 0mm 0mm;\r
-       font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-span.WarningChar\r
-       {mso-style-name:"Warning Char";\r
-       mso-style-locked:yes;\r
-       mso-style-parent:"Note Char";\r
-       mso-style-link:Warning;\r
-       mso-bidi-font-size:8.0pt;\r
-       font-family:Garamond;\r
-       mso-ascii-font-family:Garamond;\r
-       mso-hansi-font-family:Garamond;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       mso-bidi-language:AR-SA;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.Heaing3, li.Heaing3, div.Heaing3\r
-       {mso-style-name:"Heaing 3";\r
-       mso-style-parent:Note;\r
-       margin-top:6.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:12.0pt;\r
-       margin-left:42.55pt;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       tab-stops:10.0mm;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       mso-bidi-font-size:8.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-GB;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.NormalJustified, li.NormalJustified, div.NormalJustified\r
-       {mso-style-name:"Normal + Justified";\r
-       mso-style-link:"Normal + Justified Char";\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-GB;\r
-       mso-fareast-language:EN-US;}\r
-span.NormalJustifiedChar\r
-       {mso-style-name:"Normal + Justified Char";\r
-       mso-style-locked:yes;\r
-       mso-style-link:"Normal + Justified";\r
-       mso-ansi-font-size:12.0pt;\r
-       mso-ansi-language:EN-GB;\r
-       mso-fareast-language:EN-US;\r
-       mso-bidi-language:AR-SA;}\r
-p.MyNormalID, li.MyNormalID, div.MyNormalID\r
-       {mso-style-name:MyNormalID;\r
-       mso-style-update:auto;\r
-       mso-style-parent:"List Bullet";\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:31.2pt;\r
-       margin-bottom:.0001pt;\r
-       text-indent:0mm;\r
-       mso-pagination:none;\r
-       mso-list:l8 level1 lfo7;\r
-       mso-hyphenate:none;\r
-       tab-stops:list 18.0pt;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.MyExample, li.MyExample, div.MyExample\r
-       {mso-style-name:MyExample;\r
-       mso-style-update:auto;\r
-       mso-margin-top-alt:auto;\r
-       margin-right:0mm;\r
-       mso-margin-bottom-alt:auto;\r
-       margin-left:20.0mm;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       background:#FFFFCC;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       border:none;\r
-       mso-border-top-alt:solid black .25pt;\r
-       mso-border-bottom-alt:solid black .25pt;\r
-       padding:0mm;\r
-       mso-padding-alt:10.0pt 0mm 10.0pt 0mm;\r
-       font-size:9.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.Style1, li.Style1, div.Style1\r
-       {mso-style-name:Style1;\r
-       mso-style-update:auto;\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-pagination:widow-orphan;\r
-       font-size:8.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-GB;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.StyleHeading6Bold, li.StyleHeading6Bold, div.StyleHeading6Bold\r
-       {mso-style-name:"Style Heading 6 + Bold";\r
-       mso-style-update:auto;\r
-       mso-style-link:"Style Heading 6 + Bold Char";\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-pagination:widow-orphan;\r
-       font-size:8.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:Garamond;\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;}\r
-span.StyleHeading6BoldChar\r
-       {mso-style-name:"Style Heading 6 + Bold Char";\r
-       mso-style-locked:yes;\r
-       mso-style-link:"Style Heading 6 + Bold";\r
-       mso-ansi-font-size:8.0pt;\r
-       font-family:Garamond;\r
-       mso-ascii-font-family:Garamond;\r
-       mso-hansi-font-family:Garamond;\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       mso-bidi-language:AR-SA;\r
-       font-weight:bold;}\r
-p.MyNormaBoldl, li.MyNormaBoldl, div.MyNormaBoldl\r
-       {mso-style-name:MyNormaBoldl;\r
-       mso-style-parent:MyNormal;\r
-       mso-style-link:"MyNormaBoldl Char";\r
-       margin-top:2.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:6.0pt;\r
-       margin-left:42.55pt;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:11.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Courier New";\r
-       mso-ansi-language:AF;\r
-       mso-fareast-language:EN-US;}\r
-p.Mylist, li.Mylist, div.Mylist\r
-       {mso-style-name:Mylist;\r
-       mso-style-parent:MyNormal;\r
-       margin-top:2.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:6.0pt;\r
-       margin-left:128.7pt;\r
-       text-align:justify;\r
-       text-indent:-72.0pt;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:11.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Courier New";\r
-       mso-ansi-language:AF;\r
-       mso-fareast-language:EN-US;\r
-       font-style:italic;\r
-       mso-bidi-font-style:normal;}\r
-p.MyNormalBold, li.MyNormalBold, div.MyNormalBold\r
-       {mso-style-name:MyNormalBold;\r
-       mso-style-parent:MyNormalID;\r
-       margin-top:6.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:12.0pt;\r
-       margin-left:31.2pt;\r
-       text-indent:0mm;\r
-       mso-pagination:lines-together;\r
-       mso-list:l8 level1 lfo7;\r
-       tab-stops:list 18.0pt;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.StyleflagdescriptionBoldItalic, li.StyleflagdescriptionBoldItalic, div.StyleflagdescriptionBoldItalic\r
-       {mso-style-name:"Style flag description + Bold Italic";\r
-       mso-style-update:auto;\r
-       mso-style-parent:"flag description";\r
-       mso-style-link:"Style flag description + Bold Italic Char";\r
-       margin-top:3.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:3.0pt;\r
-       margin-left:42.55pt;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       font-style:italic;}\r
-span.StyleflagdescriptionBoldItalicChar\r
-       {mso-style-name:"Style flag description + Bold Italic Char";\r
-       mso-style-locked:yes;\r
-       mso-style-parent:"flag description Char";\r
-       mso-style-link:"Style flag description + Bold Italic";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       mso-bidi-language:AR-SA;\r
-       font-weight:bold;\r
-       font-style:italic;}\r
-p.Formula, li.Formula, div.Formula\r
-       {mso-style-name:Formula;\r
-       mso-style-parent:"flag description";\r
-       margin-top:6.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:42.55pt;\r
-       margin-bottom:.0001pt;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.examplefilesmall, li.examplefilesmall, div.examplefilesmall\r
-       {mso-style-name:example_file_small;\r
-       mso-style-parent:example_file;\r
-       margin-top:6.0pt;\r
-       margin-right:10.0mm;\r
-       margin-bottom:6.0pt;\r
-       margin-left:0mm;\r
-       mso-add-space:auto;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       background:#E6E6E6;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       border:none;\r
-       mso-border-alt:solid windowtext .5pt;\r
-       padding:0mm;\r
-       mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;\r
-       font-size:8.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.examplefilesmallCxSpFirst, li.examplefilesmallCxSpFirst, div.examplefilesmallCxSpFirst\r
-       {mso-style-name:example_file_smallCxSpFirst;\r
-       mso-style-parent:example_file;\r
-       mso-style-type:export-only;\r
-       margin-top:6.0pt;\r
-       margin-right:10.0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-add-space:auto;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       background:#E6E6E6;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       border:none;\r
-       mso-border-alt:solid windowtext .5pt;\r
-       padding:0mm;\r
-       mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;\r
-       font-size:8.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.examplefilesmallCxSpMiddle, li.examplefilesmallCxSpMiddle, div.examplefilesmallCxSpMiddle\r
-       {mso-style-name:example_file_smallCxSpMiddle;\r
-       mso-style-parent:example_file;\r
-       mso-style-type:export-only;\r
-       margin-top:0mm;\r
-       margin-right:10.0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-add-space:auto;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       background:#E6E6E6;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       border:none;\r
-       mso-border-alt:solid windowtext .5pt;\r
-       padding:0mm;\r
-       mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;\r
-       font-size:8.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.examplefilesmallCxSpLast, li.examplefilesmallCxSpLast, div.examplefilesmallCxSpLast\r
-       {mso-style-name:example_file_smallCxSpLast;\r
-       mso-style-parent:example_file;\r
-       mso-style-type:export-only;\r
-       margin-top:0mm;\r
-       margin-right:10.0mm;\r
-       margin-bottom:6.0pt;\r
-       margin-left:0mm;\r
-       mso-add-space:auto;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       background:#E6E6E6;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       border:none;\r
-       mso-border-alt:solid windowtext .5pt;\r
-       padding:0mm;\r
-       mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;\r
-       font-size:8.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut, li.StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut, div.StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut\r
-       {mso-style-name:"Style notebox\.body + Bold Not Italic Box\: \(Single solid line Aut\.\.\.";\r
-       mso-style-parent:"notebox\.body";\r
-       margin:0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       background:#FFFF89;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       border:none;\r
-       mso-border-alt:solid windowtext 1.5pt;\r
-       padding:0mm;\r
-       mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;\r
-       font-size:12.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;}\r
-p.MyNormalJustified, li.MyNormalJustified, div.MyNormalJustified\r
-       {mso-style-name:MyNormalJustified;\r
-       mso-style-parent:MyNormal;\r
-       margin-top:2.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:6.0pt;\r
-       margin-left:42.55pt;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:11.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Courier New";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;}\r
-p.flagheading2, li.flagheading2, div.flagheading2\r
-       {mso-style-name:"flag heading 2";\r
-       mso-style-update:auto;\r
-       mso-style-parent:"flag description";\r
-       margin-top:6.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:45.0pt;\r
-       margin-bottom:.0001pt;\r
-       text-align:justify;\r
-       mso-pagination:none;\r
-       mso-hyphenate:none;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       font-family:"Times New Roman";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;\r
-       font-style:italic;\r
-       mso-bidi-font-style:normal;\r
-       text-decoration:underline;\r
-       text-underline:single;}\r
-p.example1, li.example1, div.example1\r
-       {mso-style-name:example1;\r
-       mso-style-parent:example2;\r
-       margin-top:12.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:12.0pt;\r
-       margin-left:20.0mm;\r
-       mso-add-space:auto;\r
-       line-height:200%;\r
-       mso-pagination:widow-orphan lines-together;\r
-       page-break-after:avoid;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.example1CxSpFirst, li.example1CxSpFirst, div.example1CxSpFirst\r
-       {mso-style-name:example1CxSpFirst;\r
-       mso-style-parent:example2;\r
-       mso-style-type:export-only;\r
-       margin-top:12.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:20.0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-add-space:auto;\r
-       line-height:200%;\r
-       mso-pagination:widow-orphan lines-together;\r
-       page-break-after:avoid;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.example1CxSpMiddle, li.example1CxSpMiddle, div.example1CxSpMiddle\r
-       {mso-style-name:example1CxSpMiddle;\r
-       mso-style-parent:example2;\r
-       mso-style-type:export-only;\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:0mm;\r
-       margin-left:20.0mm;\r
-       margin-bottom:.0001pt;\r
-       mso-add-space:auto;\r
-       line-height:200%;\r
-       mso-pagination:widow-orphan lines-together;\r
-       page-break-after:avoid;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-p.example1CxSpLast, li.example1CxSpLast, div.example1CxSpLast\r
-       {mso-style-name:example1CxSpLast;\r
-       mso-style-parent:example2;\r
-       mso-style-type:export-only;\r
-       margin-top:0mm;\r
-       margin-right:0mm;\r
-       margin-bottom:12.0pt;\r
-       margin-left:20.0mm;\r
-       mso-add-space:auto;\r
-       line-height:200%;\r
-       mso-pagination:widow-orphan lines-together;\r
-       page-break-after:avoid;\r
-       mso-layout-grid-align:none;\r
-       punctuation-wrap:simple;\r
-       text-autospace:none;\r
-       font-size:10.0pt;\r
-       font-family:"Courier New";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-ansi-language:EN-US;\r
-       mso-fareast-language:EN-US;\r
-       font-weight:bold;\r
-       mso-bidi-font-weight:normal;}\r
-span.MyNormaBoldlChar\r
-       {mso-style-name:"MyNormaBoldl Char";\r
-       mso-style-locked:yes;\r
-       mso-style-parent:"MyNormal Char";\r
-       mso-style-link:MyNormaBoldl;\r
-       mso-ansi-font-size:11.0pt;\r
-       mso-bidi-font-size:11.0pt;\r
-       font-family:"Courier New";\r
-       mso-bidi-font-family:"Courier New";\r
-       mso-ansi-language:AF;\r
-       mso-fareast-language:EN-US;\r
-       mso-bidi-language:AR-SA;}\r
-p.MyNormall, li.MyNormall, div.MyNormall\r
-       {mso-style-name:MyNormall;\r
-       mso-style-parent:"Heading 2";\r
-       margin-top:12.0pt;\r
-       margin-right:0mm;\r
-       margin-bottom:6.0pt;\r
-       margin-left:0mm;\r
-       mso-line-height-alt:12.0pt;\r
-       mso-pagination:widow-orphan;\r
-       page-break-after:avoid;\r
-       mso-outline-level:2;\r
-       font-size:16.0pt;\r
-       mso-bidi-font-size:10.0pt;\r
-       font-family:"Arial Black";\r
-       mso-fareast-font-family:"Times New Roman";\r
-       mso-bidi-font-family:"Times New Roman";\r
-       color:gray;\r
-       letter-spacing:-.5pt;\r
-       mso-font-kerning:14.0pt;\r
-       mso-ansi-language:AF;\r
-       mso-fareast-language:EN-US;}\r
-ins\r
-       {mso-style-type:export-only;\r
-       text-decoration:none;}\r
-span.msoDel\r
-       {mso-style-type:export-only;\r
-       mso-style-name:"";\r
-       text-decoration:line-through;\r
-       display:none;\r
-       color:red;}\r
- /* Page Definitions */\r
- @page\r
-       {mso-footnote-separator:url("t_coffee_technical_files/header.htm") fs;\r
-       mso-footnote-continuation-separator:url("t_coffee_technical_files/header.htm") fcs;\r
-       mso-endnote-separator:url("t_coffee_technical_files/header.htm") es;\r
-       mso-endnote-continuation-separator:url("t_coffee_technical_files/header.htm") ecs;}\r
-@page Section1\r
-       {size:210.0mm 842.0pt;\r
-       margin:48.0pt 48.0pt 48.0pt 48.0pt;\r
-       mso-header-margin:0mm;\r
-       mso-footer-margin:0mm;\r
-       mso-page-numbers:0;\r
-       mso-title-page:yes;\r
-       mso-footer:url("t_coffee_technical_files/header.htm") f1;\r
-       mso-paper-source:0;}\r
-div.Section1\r
-       {page:Section1;}\r
-@page Section2\r
-       {size:210.0mm 842.0pt;\r
-       margin:90.0pt 60.0pt 90.0pt 60.0pt;\r
-       mso-header-margin:48.0pt;\r
-       mso-footer-margin:48.0pt;\r
-       mso-page-numbers:roman-lower 1;\r
-       mso-title-page:yes;\r
-       mso-footer:url("t_coffee_technical_files/header.htm") f1;\r
-       mso-first-footer:url("t_coffee_technical_files/header.htm") ff2;\r
-       mso-paper-source:0;}\r
-div.Section2\r
-       {page:Section2;}\r
-@page Section3\r
-       {size:210.0mm 842.0pt;\r
-       margin:90.0pt 60.0pt 90.0pt 60.0pt;\r
-       mso-header-margin:48.0pt;\r
-       mso-footer-margin:48.0pt;\r
-       mso-page-numbers:1;\r
-       mso-header:url("t_coffee_technical_files/header.htm") h3;\r
-       mso-footer:url("t_coffee_technical_files/header.htm") f3;\r
-       mso-first-header:url("t_coffee_technical_files/header.htm") fh3;\r
-       mso-first-footer:url("t_coffee_technical_files/header.htm") ff3;\r
-       mso-paper-source:0;}\r
-div.Section3\r
-       {page:Section3;}\r
-@page Section4\r
-       {size:210.0mm 842.0pt;\r
-       margin:72.0pt 90.0pt 72.0pt 90.0pt;\r
-       mso-header-margin:36.0pt;\r
-       mso-footer-margin:36.0pt;\r
-       mso-header:url("t_coffee_technical_files/header.htm") h4;\r
-       mso-footer:url("t_coffee_technical_files/header.htm") f4;\r
-       mso-first-header:url("t_coffee_technical_files/header.htm") fh4;\r
-       mso-first-footer:url("t_coffee_technical_files/header.htm") ff3;\r
-       mso-paper-source:0;}\r
-div.Section4\r
-       {page:Section4;}\r
- /* List Definitions */\r
- @list l0\r
-       {mso-list-id:-132;\r
-       mso-list-type:simple;\r
-       mso-list-template-ids:243462170;}\r
-@list l0:level1\r
-       {mso-level-style-link:"List Number 3";\r
-       mso-level-tab-stop:90.0pt;\r
-       mso-level-number-position:left;\r
-       margin-left:90.0pt;\r
-       text-indent:-18.0pt;}\r
-@list l1\r
-       {mso-list-id:-131;\r
-       mso-list-type:simple;\r
-       mso-list-template-ids:579796312;}\r
-@list l1:level1\r
-       {mso-level-style-link:"List Number 2";\r
-       mso-level-tab-stop:72.0pt;\r
-       mso-level-number-position:left;\r
-       margin-left:72.0pt;\r
-       text-indent:-18.0pt;}\r
-@list l2\r
-       {mso-list-id:-130;\r
-       mso-list-type:simple;\r
-       mso-list-template-ids:-525153058;}\r
-@list l2:level1\r
-       {mso-level-style-link:"List Bullet 5";\r
-       mso-level-tab-stop:54.0pt;\r
-       mso-level-number-position:left;\r
-       margin-left:54.0pt;\r
-       text-indent:-18.0pt;}\r
-@list l3\r
-       {mso-list-id:-129;\r
-       mso-list-type:simple;\r
-       mso-list-template-ids:1970563230;}\r
-@list l3:level1\r
-       {mso-level-style-link:"List Bullet 4";\r
-       mso-level-tab-stop:36.0pt;\r
-       mso-level-number-position:left;\r
-       text-indent:-18.0pt;}\r
-@list l4\r
-       {mso-list-id:-128;\r
-       mso-list-type:simple;\r
-       mso-list-template-ids:-118980482;}\r
-@list l4:level1\r
-       {mso-level-number-format:bullet;\r
-       mso-level-style-link:"List Bullet 3";\r
-       mso-level-text:\F0B7;\r
-       mso-level-tab-stop:90.0pt;\r
-       mso-level-number-position:left;\r
-       margin-left:90.0pt;\r
-       text-indent:-18.0pt;\r
-       font-family:Symbol;}\r
-@list l5\r
-       {mso-list-id:-127;\r
-       mso-list-type:simple;\r
-       mso-list-template-ids:-1465100272;}\r
-@list l5:level1\r
-       {mso-level-number-format:bullet;\r
-       mso-level-style-link:"List Bullet 2";\r
-       mso-level-text:\F0B7;\r
-       mso-level-tab-stop:72.0pt;\r
-       mso-level-number-position:left;\r
-       margin-left:72.0pt;\r
-       text-indent:-18.0pt;\r
-       font-family:Symbol;}\r
-@list l6\r
-       {mso-list-id:-126;\r
-       mso-list-type:simple;\r
-       mso-list-template-ids:-368430812;}\r
-@list l6:level1\r
-       {mso-level-number-format:bullet;\r
-       mso-level-style-link:"List 5";\r
-       mso-level-text:\F0B7;\r
-       mso-level-tab-stop:54.0pt;\r
-       mso-level-number-position:left;\r
-       margin-left:54.0pt;\r
-       text-indent:-18.0pt;\r
-       font-family:Symbol;}\r
-@list l7\r
-       {mso-list-id:-125;\r
-       mso-list-type:simple;\r
-       mso-list-template-ids:-706941758;}\r
-@list l7:level1\r
-       {mso-level-number-format:bullet;\r
-       mso-level-style-link:"List 4";\r
-       mso-level-text:\F0B7;\r
-       mso-level-tab-stop:36.0pt;\r
-       mso-level-number-position:left;\r
-       text-indent:-18.0pt;\r
-       font-family:Symbol;}\r
-@list l8\r
-       {mso-list-id:-120;\r
-       mso-list-type:simple;\r
-       mso-list-template-ids:1576020400;}\r
-@list l8:level1\r
-       {mso-level-style-link:"Plain Text";\r
-       mso-level-tab-stop:18.0pt;\r
-       mso-level-number-position:left;\r
-       margin-left:18.0pt;\r
-       text-indent:-18.0pt;}\r
-@list l9\r
-       {mso-list-id:-119;\r
-       mso-list-type:simple;\r
-       mso-list-template-ids:96769246;}\r
-@list l9:level1\r
-       {mso-level-number-format:bullet;\r
-       mso-level-style-link:"Text body Char";\r
-       mso-level-text:\F0B7;\r
-       mso-level-tab-stop:18.0pt;\r
-       mso-level-number-position:left;\r
-       margin-left:18.0pt;\r
-       text-indent:-18.0pt;\r
-       font-family:Symbol;}\r
-@list l10\r
-       {mso-list-id:-5;\r
-       mso-list-template-ids:-1557078836;}\r
-@list l10:level1\r
-       {mso-level-number-format:none;\r
-       mso-level-suffix:none;\r
-       mso-level-text:"";\r
-       mso-level-tab-stop:none;\r
-       mso-level-number-position:left;\r
-       margin-left:0mm;\r
-       text-indent:0mm;}\r
-@list l10:level2\r
-       {mso-level-number-format:none;\r
-       mso-level-text:"";\r
-       mso-level-tab-stop:none;\r
-       mso-level-number-position:left;\r
-       mso-level-legacy:yes;\r
-       mso-level-legacy-indent:0mm;\r
-       mso-level-legacy-space:0mm;\r
-       margin-left:0mm;\r
-       text-indent:0mm;}\r
-@list l10:level3\r
-       {mso-level-number-format:none;\r
-       mso-level-text:"";\r
-       mso-level-tab-stop:none;\r
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-<![endif]>\r
-\r
-<p class=CompanyName><span lang=EN-US style='font-size:14.0pt'>Centre National\r
-De LA Recherche scientifique (France)<br>\r
-CeNTRO De REGULACIO GENOMICA (<st1:place w:st="on"><st1:country-region w:st="on">SPAIN</st1:country-region></st1:place>)<o:p></o:p></span></p>\r
-\r
-<div style='mso-element:para-border-div;border:none;border-top:solid windowtext 1.0pt;\r
-mso-border-top-alt:solid windowtext .75pt;padding:1.0pt 0mm 0mm 0mm'>\r
-\r
-<p class=SubtitleCover><span lang=EN-US>Cédric Notredame<br>\r
-www.tcoffee.org</span></p>\r
-\r
-</div>\r
-\r
-<div style='mso-element:para-border-div;border:solid white 1.0pt;mso-border-alt:\r
-solid white .75pt;padding:31.0pt 31.0pt 31.0pt 31.0pt;background:#E5E5E5;\r
-mso-shading:windowtext;mso-pattern:gray-10 auto'>\r
-\r
-<p class=TitleCover style='margin:0mm;margin-bottom:.0001pt;background:#E5E5E5;\r
-mso-shading:windowtext;mso-pattern:gray-10 auto'><span lang=EN-US>T-Coffee:<br>\r
-Technical Documentation</span></p>\r
-\r
-</div>\r
-\r
-<div style='mso-element:para-border-div;border:none;border-top:solid windowtext 1.0pt;\r
-mso-border-top-alt:solid windowtext .75pt;padding:1.0pt 0mm 0mm 0mm'>\r
-\r
-<p class=SubtitleCover><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-</div>\r
-\r
-</div>\r
-\r
-<span lang=EN-US style='font-size:72.0pt;mso-bidi-font-size:10.0pt;font-family:\r
-Garamond;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman";\r
-letter-spacing:-3.5pt;mso-font-kerning:14.0pt;mso-ansi-language:EN-US;\r
-mso-fareast-language:EN-US;mso-bidi-language:AR-SA'><br clear=all\r
-style='page-break-before:always;mso-break-type:section-break'>\r
-</span>\r
-\r
-<div class=Section2>\r
-\r
-<div style='mso-element:para-border-div;border:none;border-bottom:solid gray 1.0pt;\r
-mso-border-bottom-alt:solid gray .75pt;padding:0mm 0mm 14.0pt 0mm'>\r
-\r
-<p class=MsoTitle><span lang=EN-US>T-Coffee Technical Documentation<br>\r
-(Version 8.01, July 2009)<br>\r
-www.tcoffee.org<br>\r
-<br>\r
-T-Coffee, seq_reformat<br>\r
-<span style='mso-spacerun:yes'> </span>PSI-Coffee, 3D-Coffee, M-Coffee, R-Coffee,\r
-APDB, iRMSD, T-RMSD</span></p>\r
-\r
-</div>\r
-\r
-<p class=ReturnAddress><span lang=EN-US style='font-family:Symbol;mso-ascii-font-family:\r
-Garamond;mso-hansi-font-family:Garamond;mso-char-type:symbol;mso-symbol-font-family:\r
-Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:Symbol'>ã</span></span><span\r
-lang=EN-US> Cédric Notredame, Centro de Regulacio Genomica, Centre National de\r
-la Recherche <st1:place w:st="on"><st1:City w:st="on">Scientifique</st1:City>, <st1:country-region\r
- w:st="on">France</st1:country-region></st1:place></span><span lang=EN-US\r
-style='letter-spacing:0pt'><o:p></o:p></span></p>\r
-\r
-</div>\r
-\r
-<span lang=EN-US style='font-size:8.0pt;mso-bidi-font-size:10.0pt;font-family:\r
-Garamond;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman";\r
-mso-ansi-language:EN-US;mso-fareast-language:EN-US;mso-bidi-language:AR-SA'><br\r
-clear=all style='page-break-before:always;mso-break-type:section-break'>\r
-</span>\r
-\r
-<div class=Section3>\r
-\r
-<p class=MsoToc1 style='tab-stops:right dotted 474.85pt'><!--[if supportFields]><i\r
-style='mso-bidi-font-style:normal'><span lang=EN-US style='font-size:11.0pt;\r
-font-family:"Times New Roman"'><span style='mso-element:field-begin'></span><span\r
-style='mso-spacerun:yes'> </span>TOC \h \z \t &quot;Heading 1;2;Heading\r
-2;3;Heading 3;4;Chapter Title;1;flag;4;FAQ;4&quot; <span style='mso-element:\r
-field-separator'></span></span></i><![endif]--><span class=MsoHyperlink><span\r
-lang=EN-US style='mso-no-proof:yes'><a href="#_Toc235958452">License and Terms\r
-of Use<span style='color:black;display:none;mso-hide:screen;text-decoration:\r
-none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958452 \h </span><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>6</span><span style='color:black;display:none;mso-hide:\r
-screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400350032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:\r
-"MS Mincho";color:windowtext;mso-ansi-language:FR;mso-fareast-language:JA;\r
-font-weight:normal;mso-bidi-font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958453">T-Coffee is distributed under the Gnu Public License<span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958453 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>6</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400350033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958454">T-Coffee code can be re-used freely<span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958454 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>6</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400350034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958455">T-Coffee can be incorporated in most pipelines:\r
-Plug-in/Plug-out\85<span style='color:windowtext;display:none;mso-hide:screen;\r
-text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>... </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958455 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>6</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400350035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc1 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958456">Addresses and Contacts<span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958456 \h </span><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>7</span><span style='color:black;display:none;mso-hide:\r
-screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400350036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:\r
-"MS Mincho";color:windowtext;mso-ansi-language:FR;mso-fareast-language:JA;\r
-font-weight:normal;mso-bidi-font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958457">Contributors<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958457 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>7</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400350037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958458">Addresses<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958458 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>7</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400350038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc1 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958459">Citations<span style='color:black;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958459 \h </span><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>8</span><span style='color:black;display:none;mso-hide:\r
-screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400350039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:\r
-"MS Mincho";color:windowtext;mso-ansi-language:FR;mso-fareast-language:JA;\r
-font-weight:normal;mso-bidi-font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958460">T-Coffee<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958460 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>8</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400360030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958461">Mocca<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958461 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>9</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400360031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958462">CORE<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958462 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>10</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400360032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958463">Other Contributions<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958463 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>10</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400360033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958464">Bug Reports and Feedback<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958464 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>10</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400360034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc1 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958465">Installation of The T-Coffee Packages<span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958465 \h </span><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>11</span><span style='color:black;display:none;mso-hide:\r
-screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400360035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:\r
-"MS Mincho";color:windowtext;mso-ansi-language:FR;mso-fareast-language:JA;\r
-font-weight:normal;mso-bidi-font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958466">Third Party Packages and On Demand Installations<span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958466 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>11</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400360036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958467">Standard Installation of T-Coffee<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958467 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>11</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400360037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958468">Unix<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958468 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>11</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400360038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958469">Microsoft Windows/Cygwin<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958469 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>13</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400360039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958470">MAC osX, Linux<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958470 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>13</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400370030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958471">CLUSTER Installation<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958471 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>13</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400370031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958472">If you have PDB installed:<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958472 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>13</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400370032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958473">Installing BLAST for T-Coffee<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958473 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>14</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400370033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958474">Why Do I need BLAST with T-Coffee?<span style='color:\r
-windowtext;display:none;mso-hide:screen;text-decoration:none;text-underline:\r
-none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958474 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>14</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400370034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958475">Using the EBI BLAST Client<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958475 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>14</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400370035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958476">Using the NCBI BLAST Client<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958476 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>15</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400370036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958477">Using another Client<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958477 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>15</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400370037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958478">Using a BLAST local version on UNIX<span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958478 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>16</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400370038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958479">Using a BLAST local version on Windows/cygwin<span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958479 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>16</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400370039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958480">Installing Other Companion Packages<span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958480 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>17</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400380030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958481">Installation of PSI-Coffee and Expresso<span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958481 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>18</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400380031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958482">Installation of M-Coffee<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958482 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>19</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400380032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958483">Automated Installation<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958483 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>19</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400380033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958484">Manual Installation<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958484 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>20</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400380034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958485">Installation of APDB and iRMSD<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958485 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>21</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400380035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958486">Installation of tRMSD<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958486 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>21</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400380036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958487">Installation of seq_reformat<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958487 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>22</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400380037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958488">Installation of extract_from_pdb<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958488 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>22</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400380038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958489">Installation of 3D-Coffee/Expresso<span style='color:\r
-windowtext;display:none;mso-hide:screen;text-decoration:none;text-underline:\r
-none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958489 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>22</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400380039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958490">Automated Installation<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958490 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>22</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400390030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958491">Manual Installation<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958491 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>23</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400390031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958492">Installing Fugue for T-Coffee<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958492 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>23</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400390032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958493">Installation of R-Coffee<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958493 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>23</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400390033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958494">Automated Installation<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958494 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>24</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400390034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958495">Manual Installation<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958495 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>24</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400390035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958496">Installing ProbbonsRNA for R-Coffee<span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958496 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>24</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400390036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958497">Installing Consan for R-Coffee<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958497 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>24</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400390037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc1 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958498">Quick Start<span style='color:black;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958498 \h </span><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>25</span><span style='color:black;display:none;mso-hide:\r
-screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400390038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:\r
-"MS Mincho";color:windowtext;mso-ansi-language:FR;mso-fareast-language:JA;\r
-font-weight:normal;mso-bidi-font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958499">T-COFFEE<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958499 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>25</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400390039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958500">M-Coffee<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958500 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>25</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500300030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958501">Expresso<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958501 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>26</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500300031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958502">R-Coffee<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958502 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>26</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500300032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958503">iRMSD and APDB<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958503 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>27</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500300033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958504">tRMSD<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958504 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>27</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500300034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958505">MOCCA<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958505 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>28</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500300035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc1 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958506">Recent Modifications<span style='color:black;display:\r
-none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958506 \h </span><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>29</span><span style='color:black;display:none;mso-hide:\r
-screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500300036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:\r
-"MS Mincho";color:windowtext;mso-ansi-language:FR;mso-fareast-language:JA;\r
-font-weight:normal;mso-bidi-font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc1 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958507">Reference Manual<span style='color:black;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958507 \h </span><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>30</span><span style='color:black;display:none;mso-hide:\r
-screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500300037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:\r
-"MS Mincho";color:windowtext;mso-ansi-language:FR;mso-fareast-language:JA;\r
-font-weight:normal;mso-bidi-font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958508">Environment Variables<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958508 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>30</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500300038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958509">http_proxy_4_TCOFFEE<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958509 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>30</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500300039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958510">email_4_TCOFFEE<span style='color:windowtext;display:\r
-none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958510 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>31</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500310030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958511">DIR_4_TCOFFEE<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958511 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>31</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500310031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958512">TMP_4_TCOFFEE<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958512 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>31</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500310032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958513">CACHE_4_TCOFFEE<span style='color:windowtext;display:\r
-none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958513 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>31</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500310033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958514">NO_ERROR_REPORT_4_TCOFFEE<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958514 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>31</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500310034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958515">PDB_DIR<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958515 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>31</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500310035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958516">NO_WARNING_4_TCOFFEE<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958516 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>31</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500310036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958517">Setting up the T-Coffee environment variables<span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958517 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>31</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500310037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958518">Well Behaved Parameters<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958518 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>32</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500310038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958519">Separation<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958519 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>32</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500310039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958520">Posix<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958520 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>32</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500320030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958521">Entering the right parameters<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958521 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>32</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500320031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958522">Parameters Syntax<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958522 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>32</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500320032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958523">No Flag<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958523 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>32</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500320033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958524">-parameters<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958524 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>33</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500320034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958525">-t_coffee_defaults<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958525 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>33</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500320035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958526">-mode<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958526 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>33</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500320036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958527">-score [Deprecated]<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958527 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>34</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500320037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958528">-evaluate<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958528 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>34</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500320038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958529">-convert [cw]<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958529 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>34</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500320039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958530">-do_align [cw]<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958530 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>34</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500330030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958531">Special Parameters<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958531 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>35</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500330031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958532">-version<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958532 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>35</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500330032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958533">-proxy<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958533 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>35</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500330033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958534">-email<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958534 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>35</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500330034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958535">-check_configuration<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958535 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>35</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500330035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958536">-cache<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958536 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>35</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500330036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958537">-update<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958537 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>35</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500330037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958538">-full_log<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958538 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>35</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500330038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958539">-other_pg<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958539 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>36</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500330039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958540">Input<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958540 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>36</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500340030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958541">Sequence Input<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958541 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>36</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500340031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958542">-infile [cw]<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958542 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>36</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500340032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958543">-in (Cf \96in from the Method and Library Input section)<span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958543 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>36</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500340033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958544">-get_type<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958544 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>36</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500340034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958545">-type [cw]<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958545 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>36</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500340035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958546">-seq<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958546 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>37</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500340036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958547">-seq_source<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958547 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>37</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500340037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958548">Structure Input<span style='color:windowtext;display:\r
-none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958548 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>37</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500340038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958549">-pdb<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958549 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>37</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500340039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958550">Tree Input<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958550 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>37</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500350030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958551">-usetree<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958551 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>37</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500350031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958552">Structures, Sequences Methods and Library Input via the\r
-&#61590;in Flag<span style='color:windowtext;display:none;mso-hide:screen;\r
-text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958552 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>38</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500350032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958553">-in<span style='color:windowtext;display:none;mso-hide:\r
-screen;text-decoration:none;text-underline:none'><span style='mso-tab-count:\r
-1 dotted'>. </span></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-begin'></span></span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'> PAGEREF\r
-_Toc235958553 \h </span><span style='color:windowtext;display:none;mso-hide:\r
-screen;text-decoration:none;text-underline:none'><span style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>38</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500350033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958554">Profile Input<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958554 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>40</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500350034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958555">-profile<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958555 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>40</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500350035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958556">-profile1 [cw]<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958556 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>40</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500350036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958557">-profile2 [cw]<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958557 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>40</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500350037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958558">Alignment Computation<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958558 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>40</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500350038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958559">Library Computation: Methods<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958559 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>40</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500350039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958560">-lalign_n_top<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958560 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>40</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500360030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958561">-align_pdb_param_file<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958561 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>41</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500360031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958562">-align_pdb_hasch_mode<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958562 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>41</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500360032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958563">Library Computation: Extension<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958563 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>41</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500360033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958564">-lib_list [Unsupported]<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958564 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>41</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500360034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958565">-do_normalise<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958565 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>41</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500360035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958566">-extend<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958566 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>41</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500360036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958567">-extend_mode<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958567 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>41</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500360037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958568">-max_n_pair<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958568 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>42</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500360038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958569">-seq_name_for_quadruplet<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958569 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>42</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500360039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958570">-compact<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958570 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>42</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500370030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958571">-clean<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958571 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>42</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500370031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958572">-maximise<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958572 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>42</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500370032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958573">-do_self<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958573 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>42</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500370033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958574">-seq_name_for_quadruplet<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958574 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>42</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500370034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958575">-weight<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958575 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>43</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500370035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958576">Tree Computation<span style='color:windowtext;display:\r
-none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958576 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>43</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500370036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958577">-distance_matrix_mode<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958577 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>43</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500370037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958578">-quicktree [CW]<span style='color:windowtext;display:\r
-none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958578 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>44</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500370038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958579">Pair-wise Alignment Computation<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958579 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>44</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500370039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958580">-dp_mode<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958580 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>44</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500380030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958581">-ktuple<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958581 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>45</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500380031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958582">-ndiag<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958582 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>45</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500380032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958583">-diag_mode<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958583 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>45</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500380033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958584">-diag_threshold<span style='color:windowtext;display:\r
-none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958584 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>46</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500380034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958585">-sim_matrix<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958585 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>46</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500380035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958586">-matrix [CW]<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958586 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>46</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500380036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958587">-nomatch<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958587 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>46</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500380037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958588">-gapopen<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958588 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>46</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500380038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958589">-gapext<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958589 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>47</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500380039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958590">-fgapopen<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958590 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>47</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500390030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958591">-fgapext<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958591 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>47</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500390031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958592">-cosmetic_penalty<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958592 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>47</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500390032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958593">-tg_mode<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958593 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>47</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500390033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958594">Weighting Schemes<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958594 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>47</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500390034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958595">-seq_weight<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958595 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>47</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500390035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958596">Multiple Alignment Computation<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958596 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>48</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500390036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958597">-msa_mode<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958597 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>48</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500390037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958598">-one2all<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958598 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>48</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500390038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958599">-profile_comparison<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958599 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>48</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500390039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958600">-profile_mode<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958600 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>49</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600300030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958601">Alignment Post-Processing<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958601 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>49</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600300031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958602">-clean_aln<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958602 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>49</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600300032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958603">-clean_threshold<span style='color:windowtext;display:\r
-none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958603 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>49</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600300033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958604">-clean_iteration<span style='color:windowtext;display:\r
-none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958604 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>49</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600300034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958605">-clean_evaluation_mode<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958605 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>49</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600300035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958606">-iterate<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958606 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>49</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600300036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958607">CPU Control<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958607 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>50</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600300037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958608">Multithreading<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958608 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>50</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600300038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958609">-multi_thread [NOT Supported]<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958609 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>50</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600300039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958610">Limits<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958610 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>50</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600310030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958611">-mem_mode<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958611 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>50</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600310031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958612">-ulimit<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958612 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>50</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600310032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958613">-maxlen<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958613 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>50</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600310033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958614">Aligning more than 100 sequences with DPA<span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958614 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>50</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600310034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958615">-maxnseq<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958615 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>50</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600310035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958616">-dpa_master_aln<span style='color:windowtext;display:\r
-none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958616 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>50</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600310036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958617">-dpa_maxnseq<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958617 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>51</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600310037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958618">-dpa_min_score1<span style='color:windowtext;display:\r
-none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958618 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>51</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600310038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958619">-dpa_min_score2<span style='color:windowtext;display:\r
-none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958619 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>51</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600310039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958620">-dap_tree [NOT IMPLEMENTED]<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958620 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>51</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600320030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958621">Using Structures<span style='color:windowtext;display:\r
-none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958621 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>51</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600320031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958622">Generic<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958622 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>51</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600320032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958623">-mode<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958623 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>51</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600320033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958624">-check_pdb_status<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958624 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>52</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600320034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958625">3D Coffee: Using SAP<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958625 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>52</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600320035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958626">Using/finding PDB templates for the Sequences<span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958626 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>52</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600320036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958627">-template_file<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958627 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>52</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600320037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958628">-struc_to_use<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958628 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>54</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600320038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958629">Multiple Local Alignments<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958629 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>54</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600320039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958630">-domain/-mocca<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958630 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>55</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600330030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958631">-start<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958631 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>55</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600330031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958632">-len<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958632 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>55</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600330032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958633">-scale<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958633 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>55</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600330033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958634">-domain_interactive [Examples]<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958634 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>56</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600330034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958635">Output Control<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958635 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>57</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600330035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958636">Generic<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958636 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>57</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600330036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958637">Conventions Regarding Filenames<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958637 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>57</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600330037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958638">Identifying the Output files automatically<span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958638 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>57</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600330038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958639">-no_warning<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958639 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>57</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600330039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958640">Alignments<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958640 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>57</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600340030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958641">-outfile<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958641 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>57</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600340031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958642">-output<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958642 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>57</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600340032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958643">-outseqweight<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958643 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>58</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600340033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958644">-case<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958644 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>58</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600340034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958645">-cpu<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958645 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>58</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600340035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958646">-outseqweight<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958646 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>58</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600340036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958647">-outorder [cw]<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958647 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>59</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600340037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958648">-inorder [cw]<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958648 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>59</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600340038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958649">-seqnos<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958649 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>59</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600340039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958650">Libraries<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958650 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>59</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600350030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958651">-out_lib<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958651 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>59</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600350031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958652">-lib_only<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958652 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>59</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600350032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958653">Trees<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958653 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>60</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600350033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958654">-newtree<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958654 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>60</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600350034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958655">Reliability Estimation<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958655 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>60</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600350035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958656">CORE Computation<span style='color:windowtext;display:\r
-none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958656 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>60</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600350036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958657">-evaluate_mode<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958657 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>60</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600350037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958658">Generic Output<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958658 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>61</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600350038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958659">-run_name<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958659 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>61</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600350039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958660">-quiet<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958660 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>61</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600360030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958661">-align [CW]<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958661 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>61</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600360031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958662">APDB, iRMSD and tRMSD Parameters<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958662 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>61</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600360032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958663">-quiet [Same as T-Coffee]<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958663 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>61</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600360033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958664">-run_name [Same as T-Coffee]<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958664 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>61</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600360034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958665">-aln<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958665 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>61</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600360035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958666">-n_excluded_nb<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958666 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>62</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600360036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958667">-maximum_distance<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958667 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>62</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600360037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958668">-similarity_threshold<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958668 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>62</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600360038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958669">-local_mode<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958669 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>62</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600360039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958670">-filter<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958670 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>62</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600370030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958671">-print_rapdb [Unsupported]<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958671 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>63</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600370031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958672">-outfile [Same as T-Coffee]<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958672 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>63</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600370032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958673">-color_mode<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958673 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>63</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600370033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc1 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958674">Building a Server<span style='color:black;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958674 \h </span><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>64</span><span style='color:black;display:none;mso-hide:\r
-screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600370034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:\r
-"MS Mincho";color:windowtext;mso-ansi-language:FR;mso-fareast-language:JA;\r
-font-weight:normal;mso-bidi-font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958675">Environment Variables<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958675 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>64</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600370035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958676">Output of the .dnd file.<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958676 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>65</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600370036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958677">Permissions<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958677 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>65</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600370037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958678">Other Programs<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958678 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>65</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600370038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc1 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958679">Formats<span style='color:black;display:none;mso-hide:\r
-screen;text-decoration:none;text-underline:none'><span style='mso-tab-count:\r
-1 dotted'>. </span></span><!--[if supportFields]><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-begin'></span></span><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'> PAGEREF\r
-_Toc235958679 \h </span><span style='color:black;display:none;mso-hide:screen;\r
-text-decoration:none;text-underline:none'><span style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>66</span><span style='color:black;display:none;mso-hide:\r
-screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600370039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:\r
-"MS Mincho";color:windowtext;mso-ansi-language:FR;mso-fareast-language:JA;\r
-font-weight:normal;mso-bidi-font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958680">Parameter files<span style='color:windowtext;display:\r
-none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958680 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>66</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600380030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958681">Sequence Name Handling<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958681 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>66</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600380031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958682">Automatic Format Recognition<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958682 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>67</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600380032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958683">Structures<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958683 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>67</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600380033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958684">RNA Structures<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958684 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>67</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600380034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958685">Sequences<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958685 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>67</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600380035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958686">Alignments<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958686 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>67</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600380036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958687">Libraries<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958687 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>68</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600380037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958688">T-COFFEE_LIB_FORMAT_01<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958688 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>68</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600380038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958689">T-COFFEE_LIB_FORMAT_02<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958689 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>69</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600380039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958690">Library List<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958690 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>69</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600390030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958691">Substitution matrices.<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958691 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>69</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600390031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958692">ClustalW Style [Deprecated]<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958692 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>69</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600390032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958693">BLAST Format [Recommended]<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958693 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>70</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600390033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958694">Sequences Weights<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958694 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>70</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600390034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc1 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958695">Known Problems<span style='color:black;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958695 \h </span><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>71</span><span style='color:black;display:none;mso-hide:\r
-screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600390035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:\r
-"MS Mincho";color:windowtext;mso-ansi-language:FR;mso-fareast-language:JA;\r
-font-weight:normal;mso-bidi-font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc1 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958696">Technical Notes<span style='color:black;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958696 \h </span><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>72</span><span style='color:black;display:none;mso-hide:\r
-screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600390036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:\r
-"MS Mincho";color:windowtext;mso-ansi-language:FR;mso-fareast-language:JA;\r
-font-weight:normal;mso-bidi-font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958697">Development<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958697 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>72</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600390037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958698">Command Line List<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc235958698 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>72</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600390038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:\r
-FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc1 style='tab-stops:right dotted 474.85pt'><span\r
-class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a\r
-href="#_Toc235958699">To Do\85<span style='color:black;display:none;mso-hide:\r
-screen;text-decoration:none;text-underline:none'><span style='mso-tab-count:\r
-1 dotted'>.. </span></span><!--[if supportFields]><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-begin'></span></span><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'> PAGEREF\r
-_Toc235958699 \h </span><span style='color:black;display:none;mso-hide:screen;\r
-text-decoration:none;text-underline:none'><span style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:black;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>74</span><span style='color:black;display:none;mso-hide:\r
-screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600390039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:black;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:\r
-"MS Mincho";color:windowtext;mso-ansi-language:FR;mso-fareast-language:JA;\r
-font-weight:normal;mso-bidi-font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoNormal><!--[if supportFields]><i><span lang=EN-US style='font-size:\r
-11.0pt;font-family:"Times New Roman"'><span style='mso-element:field-end'></span></span></i><![endif]--></p>\r
-\r
-</div>\r
-\r
-<span lang=EN-US style='font-size:8.0pt;mso-bidi-font-size:10.0pt;font-family:\r
-Garamond;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman";\r
-mso-ansi-language:EN-US;mso-fareast-language:EN-US;mso-bidi-language:AR-SA'><br\r
-clear=all style='page-break-before:auto;mso-break-type:section-break'>\r
-</span>\r
-\r
-<div class=Section4>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 3.0pt;\r
-padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0mm;margin-right:\r
-4.25pt'>\r
-\r
-<p class=ChapterTitle><a name="_Toc235958452"></a><a name="_Toc102494650"></a><a\r
-name="_Toc101065185"><span style='mso-bookmark:_Toc102494650'><span\r
-style='mso-bookmark:_Toc235958452'><span lang=EN-US>License and Terms of Use</span></span></span></a></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<h2><a name="_Toc235958453"></a><a name="_Toc102494651"></a><a\r
-name="_Toc102494275"><span style='mso-bookmark:_Toc102494651'><span\r
-style='mso-bookmark:_Toc235958453'><span lang=EN-US>T-Coffee is distributed\r
-under the Gnu Public License</span></span></span></a></h2>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MyNormal><span lang=AF>Please make sure you have agreed with the terms\r
-of the license attached to the package before using the T-Coffee package or its\r
-documentation. T-Coffee is a freeware open source distributed under a GPL license.\r
-This means that there are very little restrictions to its use, either in an\r
-academic or a non academic environment.</span></p>\r
-\r
-<h2><a name="_Toc235958454"></a><a name="_Toc102494652"></a><a\r
-name="_Toc102494276"><span style='mso-bookmark:_Toc102494652'><span\r
-style='mso-bookmark:_Toc235958454'><span lang=EN-US>T-Coffee code can be\r
-re-used freely</span></span></span></a></h2>\r
-\r
-<p class=MyNormal><span lang=AF>Our philosophy is that code is meant to be re-used,\r
-including ours. No permission is needed for the cut and paste of a few\r
-functions, although we are always happy to receive pieces of improved code.</span></p>\r
-\r
-<h2><a name="_Toc102494653"></a><a name="_Toc101065186"></a><a\r
-name="_Toc235958455"><span style='mso-bookmark:_Toc101065186'><span\r
-style='mso-bookmark:_Toc102494653'><span lang=EN-US>T-Coffee can be\r
-incorporated in most pipelines: Plug-in/Plug-out\85</span></span></span></a><span\r
-style='mso-bookmark:_Toc101065186'><span style='mso-bookmark:_Toc102494653'></span></span></h2>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065186'><span\r
-style='mso-bookmark:_Toc102494653'><span lang=AF>Our philosophy is to insure\r
-that as many methods as possible can be used as plug-ins within T-Coffee.\r
-Likewise, we will give as much support as possible to anyone wishing to turn\r
-T-Coffee into a plug-in for another method. For more details on how to do this,\r
-see the plug-in and the plug-out sections of the Tutorial Manual.</span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065186'><span\r
-style='mso-bookmark:_Toc102494653'><span lang=AF>Again, you do not need our\r
-permission to either use T-Coffee (or your method as a plug-in/out) but if you\r
-let us know, we will insure the stability of T-Coffee within your system\r
-through future releases. </span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065186'><span\r
-style='mso-bookmark:_Toc102494653'><span lang=AF>The current license only\r
-allows for the incorporation of T-Coffee in non-commercial pipelines (i.e.\r
-where you do not sell the pipeline, or access to it). If your pipeline is\r
-commercial, please get in touch with us. </span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065186'><span\r
-style='mso-bookmark:_Toc102494653'><span lang=AF><o:p>&nbsp;</o:p></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 3.0pt;\r
-padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0mm;margin-right:\r
-4.25pt'>\r
-\r
-<p class=ChapterTitle><span style='mso-bookmark:_Toc101065186'><span\r
-style='mso-bookmark:_Toc102494653'><a name="_Toc235958456"><span lang=EN-US>Addresses\r
-and Contacts</span></a></span></span><span style='mso-bookmark:_Toc235958456'></span><span\r
-style='mso-bookmark:_Toc102494653'></span><span style='mso-bookmark:_Toc101065186'></span><span\r
-lang=EN-US style='font-size:98.0pt;mso-bidi-font-size:48.0pt'><o:p></o:p></span></p>\r
-\r
-</div>\r
-\r
-<h2><a name="_Toc235958457"><span lang=EN-US>Contributors</span></a></h2>\r
-\r
-<p class=MsoBodyText><span lang=EN-US>T-coffee is developed, maintained,\r
-monitored, used and debugged by a dedicated team that include or have included:</span></p>\r
-\r
-<p class=MsoBodyText><span lang=EN-US><span style='mso-tab-count:1'>            </span>Cédric\r
-Notredame, Fabrice Armougom, Des Higgins, Sebastien Moretti, Orla O\92Sullivan. Eamon\r
-O\92Toole, Olivier Poirot, Karsten Suhre, Iain Wallace, Andreas Wilm</span></p>\r
-\r
-<h2><a name="_Toc235958458"><span lang=EN-US>Addresses</span></a></h2>\r
-\r
-<p class=MyNormal><span lang=AF>We are always very eager to get some user\r
-feedback. Please do not hesitate to drop us a line<span\r
-style='mso-spacerun:yes'>  </span>at: <a\r
-href="mailto:cedric.notredame@europe.com"><span lang=EN-US style='mso-ansi-language:\r
-EN-US'>cedric.notredame@europe.com</span></a> The latest updates of T-Coffee\r
-are always available<span style='mso-spacerun:yes'>  </span>on: www.tcoffee.org\r
-. On this address you will also find a link to some of the online T-Coffee\r
-servers, including Tcoffee@igs </span></p>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MyNormal><span lang=AF>T-Coffee can be used to automatically check if\r
-an updated version is available, however the program will not update\r
-automatically, as this can cause endless reproducibility problems.</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee \96update</span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 3.0pt;\r
-padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0mm;margin-right:\r
-4.25pt'>\r
-\r
-<p class=ChapterTitle><a name="_Toc235958459"></a><a name="_Toc102494654"></a><a\r
-name="_Toc101065187"><span style='mso-bookmark:_Toc102494654'><span\r
-style='mso-bookmark:_Toc235958459'><span lang=EN-US>Citations</span></span></span></a></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF>It is important that you cite T-Coffee when you\r
-use it. Citing us is (almost) like giving us money: it helps us convincing our\r
-institutions that what we do is useful and that they should keep paying our\r
-salaries and deliver Donuts to our offices from time to time (Not that they\r
-ever did it, but it would be nice anyway). </span></p>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MyNormal><span lang=AF>Cite the server if you used it, otherwise, cite\r
-the original paper from 2000 (No, it was never named &quot;T-Coffee 2000&quot;).</span></p>\r
-\r
-<table class=MsoNormalTable border=0 cellspacing=5 cellpadding=0 width="81%"\r
- style='width:81.78%;mso-cellspacing:3.7pt;mso-padding-alt:0mm 0mm 0mm 0mm'>\r
- <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>\r
-  <td width="53%" style='width:53.48%;padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US><a\r
-  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=10964570">Notredame\r
-  C, Higgins DG, Heringa J.</a></span><span lang=EN-US style='mso-bidi-font-size:\r
-  12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width="43%" nowrap valign=top style='width:43.3%;padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US><a\r
-  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Display&amp;dopt=pubmed_pubmed&amp;from_uid=10964570"><span\r
-  style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <script language="JavaScript1.2">\r
-<!--
-var PopUpMenu2_LocalConfig_jsmenu3Config = [
-  ["ShowCloseIcon","yes"],
-  ["Help","window.open('/entrez/query/static/popup.html','Links_Help','resizable=no,scrollbars=yes,toolbar=no,location=no,directories=no,status=no,menubar=no,copyhistory=no,alwaysRaised=no,depend=no,width=400,height=500');"],
-  ["TitleText"," Links "]
-]
-//-->\r
-  </script><script language="JavaScript1.2">\r
-<!--
-var Menu10964570 = [
-  ["UseLocalConfig","jsmenu3Config","",""],
-  ["Cited in PMC","window.top.location='http://www.pubmedcentral.gov/tocrender.fcgi?action=cited&tool=pubmed&pubmedid=10964570'","",""],
-  ["Cited in Books","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Display&dopt=pubmed_books_refs&from_uid=10964570'","",""],
-  ["Books","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=10964570&dopt=Books'","",""],
-  ["LinkOut","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=10964570&dopt=ExternalLink'","",""]
-]
-//-->\r
-  </script><a href="javascript:PopUpMenu2_Set(Menu10964570);" target="_self"><span\r
-  style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></a> </span><span\r
-  lang=EN-US style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>\r
-  <td width="97%" colspan=2 style='width:97.86%;padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US>T-Coffee: A novel method for fast\r
-  and accurate multiple sequence alignment.<br>\r
-  J Mol Biol. 2000 Sep 8;302(1):205-17. <br>\r
-  PMID: 10964570 [PubMed - indexed for MEDLINE]</span><span lang=EN-US\r
-  style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
- </tr>\r
-</table>\r
-\r
-<p class=MyNormal><span lang=AF>Other useful publications include:</span></p>\r
-\r
-<h2><a name="_Toc235958460"></a><a name="_Toc102494655"></a><a\r
-name="_Toc102494277"></a><a name="_Toc101065188"><span style='mso-bookmark:\r
-_Toc102494277'><span style='mso-bookmark:_Toc102494655'><span style='mso-bookmark:\r
-_Toc235958460'><span lang=EN-US>T-Coffee</span></span></span></span></a></h2>\r
-\r
-<table class=MsoNormalTable border=0 cellspacing=5 cellpadding=0 width="81%"\r
- style='width:81.78%;mso-cellspacing:3.7pt;mso-padding-alt:0mm 0mm 0mm 0mm'>\r
- <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>\r
-  <td width="53%" style='width:53.48%;padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US><a\r
-  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=15215460">Claude\r
-  JB, Suhre K, Notredame C, Claverie JM, Abergel C.</a></span><span lang=EN-US\r
-  style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
-  <td width="43%" nowrap valign=top style='width:43.3%;padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US><a\r
-  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Display&amp;dopt=pubmed_pubmed&amp;from_uid=15215460"><span\r
-  style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <script language="JavaScript1.2">\r
-<!--
-var PopUpMenu2_LocalConfig_jsmenu3Config = [
-  ["ShowCloseIcon","yes"],
-  ["Help","window.open('/entrez/query/static/popup.html','Links_Help','resizable=no,scrollbars=yes,toolbar=no,location=no,directories=no,status=no,menubar=no,copyhistory=no,alwaysRaised=no,depend=no,width=400,height=500');"],
-  ["TitleText"," Links "]
-]
-//-->\r
-  </script><script language="JavaScript1.2">\r
-<!--
-var Menu15215460 = [
-  ["UseLocalConfig","jsmenu3Config","",""],
-  ["Free in PMC","window.top.location='http://www.pubmedcentral.gov/articlerender.fcgi?tool=pubmed&pubmedid=15215460'","",""],
-  ["Books","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=15215460&dopt=Books'","",""],
-  ["LinkOut","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=15215460&dopt=ExternalLink'","",""]
-]
-//-->\r
-  </script><a href="javascript:PopUpMenu2_Set(Menu15215460);" target="_self"><span\r
-  style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></a> </span><span\r
-  lang=EN-US style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>\r
-  <td width="97%" colspan=2 style='width:97.86%;padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US>CaspR: a web server for automated\r
-  molecular replacement using homology modelling.<br>\r
-  Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W606-9. <br>\r
-  PMID: 15215460 [PubMed - indexed for MEDLINE]</span><span lang=EN-US\r
-  style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
- </tr>\r
-</table>\r
-\r
-<p class=MyNormalJustified><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<table class=MsoNormalTable border=0 cellspacing=5 cellpadding=0 width="81%"\r
- style='width:81.98%;mso-cellspacing:3.7pt;mso-padding-alt:0mm 0mm 0mm 0mm'>\r
- <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>\r
-  <td width="53%" style='width:53.5%;padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US><a\r
-  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=15215345">Poirot\r
-  O, Suhre K, Abergel C, O'Toole E, Notredame C.</a></span><span lang=EN-US\r
-  style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
-  <td nowrap valign=top style='padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US><a\r
-  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Display&amp;dopt=pubmed_pubmed&amp;from_uid=15215345"><span\r
-  style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <script language="JavaScript1.2">\r
-<!--
-var Menu15215345 = [
-  ["UseLocalConfig","jsmenu3Config","",""],
-  ["Free in PMC","window.top.location='http://www.pubmedcentral.gov/articlerender.fcgi?tool=pubmed&pubmedid=15215345'","",""],
-  ["Cited in PMC","window.top.location='http://www.pubmedcentral.gov/tocrender.fcgi?action=cited&tool=pubmed&pubmedid=15215345'","",""],
-  ["Books","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=15215345&dopt=Books'","",""],
-  ["LinkOut","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=15215345&dopt=ExternalLink'","",""]
-]
-//-->\r
-  </script><a href="javascript:PopUpMenu2_Set(Menu15215345);" target="_self"><span\r
-  style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></a> </span><span\r
-  lang=EN-US style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>\r
-  <td colspan=2 style='padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US>3DCoffee@igs: a web server for\r
-  combining sequences and structures into a multiple sequence alignment.<br>\r
-  Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W37-40. <br>\r
-  PMID: 15215345 [PubMed - indexed for MEDLINE]</span><span lang=EN-US\r
-  style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
- </tr>\r
-</table>\r
-\r
-<p class=MyNormalJustified><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<table class=MsoNormalTable border=0 cellspacing=5 cellpadding=0 width="81%"\r
- style='width:81.98%;mso-cellspacing:3.7pt;mso-padding-alt:0mm 0mm 0mm 0mm'>\r
- <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>\r
-  <td width="53%" style='width:53.5%;padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US><a\r
-  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=15201059">O'Sullivan\r
-  O, Suhre K, Abergel C, Higgins DG, Notredame C.</a></span><span lang=EN-US\r
-  style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
-  <td nowrap valign=top style='padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US><a\r
-  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Display&amp;dopt=pubmed_pubmed&amp;from_uid=15201059"><span\r
-  style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <script language="JavaScript1.2">\r
-<!--
-var Menu15201059 = [
-  ["UseLocalConfig","jsmenu3Config","",""],
-  ["Cited in PMC","window.top.location='http://www.pubmedcentral.gov/tocrender.fcgi?action=cited&tool=pubmed&pubmedid=15201059'","",""],
-  ["Books","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=15201059&dopt=Books'","",""],
-  ["LinkOut","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=15201059&dopt=ExternalLink'","",""]
-]
-//-->\r
-  </script><a href="javascript:PopUpMenu2_Set(Menu15201059);" target="_self"><span\r
-  style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></a> </span><span\r
-  lang=EN-US style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>\r
-  <td colspan=2 style='padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US>3DCoffee: combining protein\r
-  sequences and structures within multiple sequence alignments.<br>\r
-  J Mol Biol. 2004 Jul 2;340(2):385-95. <br>\r
-  PMID: 15201059 [PubMed - indexed for MEDLINE]</span><span lang=EN-US\r
-  style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
- </tr>\r
-</table>\r
-\r
-<p class=MyNormalJustified><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<table class=MsoNormalTable border=0 cellspacing=5 cellpadding=0 width="81%"\r
- style='width:81.98%;mso-cellspacing:3.7pt;mso-padding-alt:0mm 0mm 0mm 0mm'>\r
- <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>\r
-  <td width="53%" style='width:53.5%;padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US><a\r
-  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=12824354">Poirot\r
-  O, O'Toole E, Notredame C.</a></span><span lang=EN-US style='mso-bidi-font-size:\r
-  12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
-  <td nowrap valign=top style='padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US><a\r
-  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Display&amp;dopt=pubmed_pubmed&amp;from_uid=12824354"><span\r
-  style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <script language="JavaScript1.2">\r
-<!--
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-  ["Books","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=12824354&dopt=Books'","",""],
-  ["LinkOut","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=12824354&dopt=ExternalLink'","",""]
-]
-//-->\r
-  </script><a href="javascript:PopUpMenu2_Set(Menu12824354);" target="_self"><span\r
-  style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></a> </span><span\r
-  lang=EN-US style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>\r
-  <td colspan=2 style='padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US>Tcoffee@igs: A web server for\r
-  computing, evaluating and combining multiple sequence alignments.<br>\r
-  Nucleic Acids Res. 2003 Jul 1;31(13):3503-6. <br>\r
-  PMID: 12824354 [PubMed - indexed for MEDLINE]</span><span lang=EN-US\r
-  style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
- </tr>\r
-</table>\r
-\r
-<p class=MyNormalJustified><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<table class=MsoNormalTable border=0 cellspacing=5 cellpadding=0 width="81%"\r
- style='width:81.98%;mso-cellspacing:3.7pt;mso-padding-alt:0mm 0mm 0mm 0mm'>\r
- <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>\r
-  <td width="53%" style='width:53.5%;padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US><a\r
-  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=11301309">Notredame\r
-  C.</a></span><span lang=EN-US style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
-  <td nowrap valign=top style='padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US><a\r
-  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Display&amp;dopt=pubmed_pubmed&amp;from_uid=11301309"><span\r
-  style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <script language="JavaScript1.2">\r
-<!--
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-]
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-  </script><a href="javascript:PopUpMenu2_Set(Menu11301309);" target="_self"><span\r
-  style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></a> </span><span\r
-  lang=EN-US style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>\r
-  <td colspan=2 style='padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US>Mocca: semi-automatic method for\r
-  domain hunting.<br>\r
-  Bioinformatics. 2001 Apr;17(4):373-4. <br>\r
-  PMID: 11301309 [PubMed - indexed for MEDLINE]</span><span lang=EN-US\r
-  style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
- </tr>\r
-</table>\r
-\r
-<p class=MyNormalJustified><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<table class=MsoNormalTable border=0 cellspacing=5 cellpadding=0 width="81%"\r
- style='width:81.98%;mso-cellspacing:3.7pt;mso-padding-alt:0mm 0mm 0mm 0mm'>\r
- <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>\r
-  <td width="53%" style='width:53.5%;padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US><a\r
-  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=10964570">Notredame\r
-  C, Higgins DG, Heringa J.</a></span><span lang=EN-US style='mso-bidi-font-size:\r
-  12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
-  <td nowrap valign=top style='padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US><a\r
-  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Display&amp;dopt=pubmed_pubmed&amp;from_uid=10964570"><span\r
-  style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <script language="JavaScript1.2">\r
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-  ["LinkOut","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=10964570&dopt=ExternalLink'","",""]
-]
-//-->\r
-  </script><a href="javascript:PopUpMenu2_Set(Menu10964570);" target="_self"><span\r
-  style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></a> </span><span\r
-  lang=EN-US style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>\r
-  <td colspan=2 style='padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US>T-Coffee: A novel method for fast\r
-  and accurate multiple sequence alignment.<br>\r
-  J Mol Biol. 2000 Sep 8;302(1):205-17. <br>\r
-  PMID: 10964570 [PubMed - indexed for MEDLINE]</span><span lang=EN-US\r
-  style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
- </tr>\r
-</table>\r
-\r
-<p class=MyNormalJustified><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<table class=MsoNormalTable border=0 cellspacing=5 cellpadding=0 width="81%"\r
- style='width:81.98%;mso-cellspacing:3.7pt;mso-padding-alt:0mm 0mm 0mm 0mm'>\r
- <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>\r
-  <td width="53%" style='width:53.5%;padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US><a\r
-  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=9682054">Notredame\r
-  C, Holm L, Higgins DG.</a></span><span lang=EN-US style='mso-bidi-font-size:\r
-  12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
-  <td nowrap valign=top style='padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormalJustified><span lang=EN-US><a\r
-  href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Display&amp;dopt=pubmed_pubmed&amp;from_uid=9682054"><span\r
-  style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <script language="JavaScript1.2">\r
-<!--
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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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-  ["Books","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=11301309&dopt=Books'","",""],
-  ["LinkOut","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=11301309&dopt=ExternalLink'","",""]
-]
-//-->\r
-  </script><a href="javascript:PopUpMenu2_Set(Menu11301309);" target="_self"><span\r
-  lang=EN-US style='mso-bidi-font-size:9.0pt;color:#336699;mso-ansi-language:\r
-  EN-US'>Links</span></a> </span><span lang=AF style='mso-bidi-font-size:12.0pt;\r
-  color:black'><o:p></o:p></span></p>\r
-  </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>\r
-  <td colspan=2 style='padding:0mm 0mm 0mm 0mm'>\r
-  <p class=MyNormal><span lang=AF>Mocca: semi-automatic method for domain\r
-  hunting.<br>\r
-  Bioinformatics. 2001 Apr;17(4):373-4. <br>\r
-  PMID: 11301309 [PubMed - indexed for MEDLINE]</span><span lang=AF\r
-  style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>\r
-  </td>\r
- </tr>\r
-</table>\r
-\r
-<h2><a name="_Toc235958462"></a><a name="_Toc102494657"></a><a\r
-name="_Toc102494279"><span style='mso-bookmark:_Toc102494657'><span\r
-style='mso-bookmark:_Toc235958462'><span lang=EN-US>CORE</span></span></span></a></h2>\r
-\r
-<p class=MyNormal><span lang=AF><a\r
-href="http://www.tcoffee.org/Publications/Pdf/core.pp.pdf"><span lang=EN-US\r
-style='mso-ansi-language:EN-US'>http://www.tcoffee.org/Publications/Pdf/core.pp.pdf<o:p></o:p></span></a></span></p>\r
-\r
-<h2><a name="_Toc102494658"></a><a name="_Toc102494280"></a><a\r
-name="_Toc101065367"><span style='mso-bookmark:_Toc102494280'><span\r
-style='mso-bookmark:_Toc102494658'></span></span></a><a name="_Toc235958463"><span\r
-style='mso-bookmark:_Toc102494658'><span style='mso-bookmark:_Toc102494280'><span\r
-style='mso-bookmark:_Toc101065367'><span lang=EN-US>Other Contributions</span></span></span></span></a></h2>\r
-\r
-<p class=MyNormal><span lang=AF>We do not mean to steal code, but we will always\r
-try to re-use pre-existing code whenever that code exists, free of copyright,\r
-just like we expect people to do with our code. However, whenever this happens,\r
-we make a point at properly citing the source of the original contribution. If\r
-ever you recognize a piece of your code improperly cited, please drop us a note\r
-and we will be happy to correct that.</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>In the mean time, here are some important pieces\r
-of code from other packages that have been incorporated within the T-Coffee\r
-package. These include: </span></p>\r
-\r
-<p class=MyNormal><span lang=AF><span style='mso-tab-count:1'>         </span>-The\r
-Sim algorithm of Huang and Miller that given two sequences computes the N best\r
-scoring local alignments.</span></p>\r
-\r
-<p class=MyNormal><span lang=AF><span style='mso-tab-count:1'>         </span>-The\r
-tree reading/computing routines are taken from the ClustalW Package, courtesy\r
-of Julie Thompson, Des Higgins and Toby Gibson (Thompson, Higgins, Gibson,\r
-1994, 4673-4680,vol. 22, Nucleic Acid Research).</span></p>\r
-\r
-<p class=MyNormal><span lang=AF><span style='mso-tab-count:1'>         </span>-The\r
-implementation of the algorithm for aligning two sequences in linear space was\r
-adapted from Myers and Miller, in CABIOS, 1988, 11-17, vol. 1)</span></p>\r
-\r
-<p class=MyNormal><span lang=AF><span style='mso-spacerun:yes'> </span><span\r
-style='mso-tab-count:1'>        </span>-Various techniques and algorithms have\r
-been implemented. Whenever relevant, the source of the code/algorithm/idea is\r
-indicated in the corresponding function.</span></p>\r
-\r
-<p class=MyNormal><span lang=AF><span style='mso-tab-count:1'>         </span>-64\r
-Bits compliance was implemented by Benjamin Sohn, Performance Computing Center\r
-Stuttgart (HLRS), <st1:place w:st="on"><st1:country-region w:st="on">Germany</st1:country-region></st1:place></span></p>\r
-\r
-<p class=MyNormal><span lang=AF><span style='mso-tab-count:1'>         </span>-David\r
-Mathog (Caltech) provided many fixes and useful feedback for improving the code\r
-and making the whole soft behaving more rationally</span></p>\r
-\r
-<h2><a name="_Toc235958464"><span lang=EN-US>Bug Reports and Feedback</span></a></h2>\r
-\r
-<p class=MyNormal><span lang=AF><span style='mso-tab-count:1'>         </span>-Prof\r
-David Jones (UCL) reported and corrected the PDB1K bug (now t_coffee/sap can\r
-align PDB sequences longer than 1000 AA).</span></p>\r
-\r
-<p class=MyNormal><span lang=AF><span style='mso-tab-count:1'>         </span>-Johan\r
-Leckner reported several bugs related to the treatment of PDB structures,\r
-insuring a consistent behavior between version 1.37 and current ones.</span></p>\r
-\r
-<p class=MyNormal><span lang=AF><span style='mso-spacerun:yes'> </span></span></p>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 3.0pt;\r
-padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0mm;margin-right:\r
-4.25pt'>\r
-\r
-<p class=ChapterTitle><a name="_Toc235958465"></a><a name="_Toc102494673"></a><a\r
-name="_Toc101065204"><span style='mso-bookmark:_Toc102494673'><span\r
-style='mso-bookmark:_Toc235958465'><span lang=EN-US>I</span></span></span></a><span\r
-style='mso-bookmark:_Toc235958465'><span lang=EN-US>nstallation of The T-Coffee\r
-Packages</span></span></p>\r
-\r
-</div>\r
-\r
-<h2><a name="_Toc102494674"></a><a name="_Toc102494294"></a><a\r
-name="_Toc101065205"></a><a name="_Toc235958466"><span style='mso-bookmark:\r
-_Toc101065205'><span style='mso-bookmark:_Toc102494294'><span style='mso-bookmark:\r
-_Toc102494674'><span lang=EN-US>Third Party Packages and On Demand\r
-Installations</span></span></span></span></a><span style='mso-bookmark:_Toc101065205'><span\r
-style='mso-bookmark:_Toc102494294'><span style='mso-bookmark:_Toc102494674'></span></span></span></h2>\r
-\r
-<p class=MyNormaBoldl><span style='mso-bookmark:_Toc101065205'><span\r
-style='mso-bookmark:_Toc102494294'><span style='mso-bookmark:_Toc102494674'><span\r
-lang=AF>T-Coffee is a complex package that interacts with many other third part\r
-software. If you only want a standalone version of T-Coffee, you may install\r
-that package on its own. If you want to use a most sophisticated flavor\r
-(3dcoffee, expresso, rcofeee, etc...), the installer will try to install all\r
-the third paparty packages required.</span></span></span></span></p>\r
-\r
-<p class=MyNormaBoldl><span style='mso-bookmark:_Toc101065205'><span\r
-style='mso-bookmark:_Toc102494294'><span style='mso-bookmark:_Toc102494674'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<p class=MyNormaBoldl><span style='mso-bookmark:_Toc101065205'><span\r
-style='mso-bookmark:_Toc102494294'><span style='mso-bookmark:_Toc102494674'><span\r
-lang=AF>Note that since version 7.56, T-Coffee will use 'on demand'\r
-installation and install the third party packages it needs *when* it needs\r
-them. This only works for packages not requiring specific licenses and that can\r
-be installed by the regular installer. Please let us know if you would like\r
-another third party package to be included. </span></span></span></span></p>\r
-\r
-<p class=MyNormaBoldl><span style='mso-bookmark:_Toc101065205'><span\r
-style='mso-bookmark:_Toc102494294'><span style='mso-bookmark:_Toc102494674'><span\r
-lang=AF>Whenver on-demand installation or automated installation fails because\r
-of unforessen system specificities, users should install the third party\r
-package manually. In this documentation gives some tips we have found useful,\r
-but users are encouraged to check the original documentation.</span></span></span></span></p>\r
-\r
-<h2><span style='mso-bookmark:_Toc101065205'><span style='mso-bookmark:_Toc102494294'><span\r
-style='mso-bookmark:_Toc102494674'><a name="_Toc235958467"><span lang=EN-US>Standard\r
-Installation</span></a></span></span></span><span style='mso-bookmark:_Toc235958467'><span\r
-lang=EN-US> of T-Coffee</span></span></h2>\r
-\r
-<h3><a name="_Toc235958468"><span lang=EN-US>Unix</span></a></h3>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>You need to have: gcc, g77, CPAN and an internet\r
-connection and your root password (to install SOAP). If you cannot log as root,\r
-ask (kindly) your system manager to install <a\r
-href="http://search.cpan.org/%7Ebyrne/SOAP-Lite-0.60a/"><span lang=EN-US\r
-style='mso-ansi-language:EN-US'>SOAP::Lite</span></a> for you. You may do this\r
-before or after the installation of T-Coffee. Even without SOAP you will still\r
-be able to use the basic functions of T-Coffee (simplest usage).</span></p>\r
-\r
-<p class=MsoNormal style='margin-left:72.0pt'><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;\r
-margin-left:72.0pt;text-indent:-18.0pt;mso-list:l24 level2 lfo39;tab-stops:\r
-list 72.0pt'><![if !supportLists]><span lang=EN-US style='font-family:Arial;\r
-mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>1.<span\r
-style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;\r
-</span></span></span><![endif]><span dir=LTR><code><span lang=EN-US\r
-style='font-size:10.0pt'>gunzip t_coffee.tar.gz</span></code></span><span\r
-lang=EN-US style='font-family:Arial'><o:p></o:p></span></p>\r
-\r
-<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;\r
-margin-left:72.0pt;text-indent:-18.0pt;mso-list:l24 level2 lfo39;tab-stops:\r
-list 72.0pt'><![if !supportLists]><span lang=EN-US style='font-family:Arial;\r
-mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2.<span\r
-style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;\r
-</span></span></span><![endif]><span dir=LTR><code><span lang=EN-US\r
-style='font-size:10.0pt'>tar -xvf t_coffee.tar</span></code></span><span\r
-lang=EN-US style='font-family:Arial'><o:p></o:p></span></p>\r
-\r
-<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;\r
-margin-left:72.0pt;text-indent:-18.0pt;mso-list:l24 level2 lfo39;tab-stops:\r
-list 72.0pt'><![if !supportLists]><span lang=EN-US style='font-family:Arial;\r
-mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>3.<span\r
-style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;\r
-</span></span></span><![endif]><span dir=LTR><code><span lang=EN-US\r
-style='font-size:10.0pt'>cd t_coffee</span></code></span><span lang=EN-US\r
-style='font-family:Arial'><o:p></o:p></span></p>\r
-\r
-<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;\r
-margin-left:72.0pt;text-indent:-18.0pt;mso-list:l24 level2 lfo39;tab-stops:\r
-list 72.0pt'><![if !supportLists]><span lang=EN-US style='font-family:Arial;\r
-mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>4.<span\r
-style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;\r
-</span></span></span><![endif]><span dir=LTR><code><span lang=EN-US\r
-style='font-size:10.0pt'>./install t_coffee</span></code></span><span\r
-lang=EN-US style='font-family:Arial'><o:p></o:p></span></p>\r
-\r
-<p class=MyNormal><span lang=AF>This installation will try to install EVERY\r
-flavor of T-Coffee along with the packages it requires. It will not re-install\r
-the packages that are already on your computer.</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>If you want a more specific installation, you\r
-can try:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US><span\r
-style='mso-tab-count:1'>   </span>./install t_coffee</span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US><span\r
-style='mso-tab-count:1'>   </span>./install mcoffee</span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US><span\r
-style='mso-tab-count:1'>   </span>./install 3dcoffee</span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US><span\r
-style='mso-tab-count:1'>   </span>./install rcoffee</span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US><span\r
-style='mso-tab-count:1'>   </span>./install psicoffee</span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MyNormal><span lang=AF>Or even</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US><span\r
-style='mso-tab-count:1'>   </span>./install all</span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MyNormal><span lang=AF>-All the corresponding executables will be\r
-downloaded automatically and installed in</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US><span\r
-style='mso-tab-count:1'>   </span>$HOME/.t_coffee/plugins</span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MyNormal><span lang=AF>-if you executables are in a different\r
-location, give it to T-Coffee using the -plugins flag.</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>-If the installation of any of the companion\r
-package fails, you should install it yourself using the provided link (see\r
-below) and following the authors instructions.<span style='mso-tab-count:1'>      </span></span></p>\r
-\r
-<p class=MyNormal><span lang=AF>-If you have not managed to install SOAP::Lite,\r
-you can re-install it later (from anywhere) following steps 1-2.</span></p>\r
-\r
-<p class=MsoNormal style='margin-left:72.0pt'><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>-This procedure attempts 3 things:\r
-installing and Compiling T-Coffee (C program), Installing and compiling <a\r
-href="http://zhang.bioinformatics.ku.edu/TM-align/"><span lang=EN-US\r
-style='mso-ansi-language:EN-US'>TMalign</span></a> (Fortran), Installing and\r
-compiling <a href="http://search.cpan.org/%7Ebyrne/SOAP-Lite-0.60a/"><span\r
-lang=EN-US style='mso-ansi-language:EN-US'>SOAP::Lite</span></a>(Perl Module).</span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>-If you have never installed SOAP::Lite,\r
-CPAN will ask you many questions: say Yes to all </span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>-If everything went well, the procedure has\r
-created in the <b>bin</b> directory two executables: t_coffee and TMalign (<b>Make\r
-sure these executables are on your $PATH!</b>)</span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<h3><a name="_Toc235958469"><span lang=EN-US>Microsoft Windows/Cygwin</span></a></h3>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>Install <a href="http://www.cygwin.com"><span\r
-lang=EN-US style='color:windowtext;mso-ansi-language:EN-US;text-decoration:\r
-none;text-underline:none'>Cygwin</span></a></span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>Download The Installer (NOT Cygwin/X)</span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>Click on view to list ALL the packages</span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>Select: gcc-core, make, wget</span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>Optional: ssh, xemacs, nano</span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>Run mkpasswd in Cywin (as requested when\r
-you start cygwin)</span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>Install T-Coffee within Cygwin using the\r
-Unix procedure</span></p>\r
-\r
-<h3><a name="_Toc235958470"><span lang=EN-US>MAC osX, Linux</span></a></h3>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>Make sure you have the Developer's kit installed\r
-(compilers and makefile)</span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>Follow the Unix Procedure</span></p>\r
-\r
-<p class=Mylist><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<h3><a name="_Toc235958471"><span lang=EN-US>CLUSTER Installation</span></a></h3>\r
-\r
-<p class=MyNormal><span lang=AF>In order to run, T-Coffee must have a value for\r
-the http_proxy and for the E-mail. In order to do so you can either:</span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>export the following values:</span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>export\r
-http_proxy_4_TCOFFEE=&quot;proxy&quot; or &quot;&quot; if no proxy</span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>export EMAIL_4_TCOFFEE=&quot;your\r
-email&quot;</span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>OR </span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>modify the file ~/.t_coffee/t_coffee_env</span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>OR</span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>add to your command line: t_coffee \85.\r
--proxy=&lt;proxy&gt; -email=&lt;email</span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>if you have no proxy: t_coffee \85 -proxy\r
--email=&lt;email&gt;</span></p>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<h3><a name="_Toc235958472"><span lang=EN-US>If you have PDB installed:</span></a></h3>\r
-\r
-<p class=MyNormal><span lang=AF>Assuming you have a standard PDB installation\r
-in your file system</span></p>\r
-\r
-<p class=example2CxSpFirst><span lang=EN-US>setenv (or export)<span\r
-style='mso-spacerun:yes'>  </span>PDB_DIR &lt;abs path&gt;/data/structures/all/pdb/</span></p>\r
-\r
-<p class=example2CxSpMiddle><span lang=EN-US>OR</span></p>\r
-\r
-<p class=example2CxSpLast><span lang=EN-US>setenv (or export)<span\r
-style='mso-spacerun:yes'>  </span>PDB_DIR &lt;abs\r
-path&gt;/structures/divided/pdb/</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>If you do not have PDB installed, don't worry,\r
-t_coffee will go and fetch any structure it needs directly from the PDB\r
-repository. It will simply be a bit slower than if you had PDB locally. </span></p>\r
-\r
-<h2><a name="_Toc102494675"></a><a name="_Toc102494295"></a><a\r
-name="_Toc101065206"></a><a name="_Toc235958473"><span style='mso-bookmark:\r
-_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:\r
-_Toc102494675'><span lang=EN-US>Installing BLAST for T-Coffee</span></span></span></span></a><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'></span></span></span></h2>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>BLAST is a program that search sequence databases for homologues of a\r
-query sequence. It works for proteins and Nucleic Acids. In theory BLAST is\r
-just a package like any, but in practice things are a bit more complex. To run\r
-well, BLST requires up to date databases (that can be fairly large, like NR or\r
-UNIPROT) and a powerful computer.</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>Fortunately, an increasing number of institutes or companies are now providing\r
-BLAST clients that run over the net. It means that all you need is a small\r
-program that send your query to the big server and gets the results back. This\r
-prevents you from the hassle of installing and maintaining BLAST, but of course\r
-it is less private and you rely on the network and the current load of these\r
-busy servers.</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>Thanks to its interaction with BLAST, T-Coffee can gather structures\r
-and protein profiles and deliver an alignment significantly more accurate than\r
-the default you would get with T-Coffee or any similar method.</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>Let us go through the various modes available for T-Coffee</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><a name="_Toc235958474"><span lang=EN-US>Why\r
-Do I need BLAST with T-Coffee?</span></a></span></span></span></h3>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>The most accurate modes of T-Coffe scan the databases for templates\r
-that they use to align the sequences. There are currently two types of templates\r
-for proteins:</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>structures (PDB) that can be found by a blastp against the PDB database\r
-and profiles that can be constructed with eiether a blastp or a psiblast\r
-against nr or uniprot.</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>These templates are automatically built if you use:</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:\r
-1'>   </span>t_coffee &lt;yourseq&gt; -mode expresso</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><span style='mso-tab-count:1'>         </span>that fetches aand uses\r
-pdb templates, or</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:\r
-1'>   </span><span style='mso-tab-count:1'>       </span>t_coffee &lt;your\r
-seq&gt; -mode psicoffee</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><span style='mso-tab-count:1'>         </span>that fetches and uses\r
-profile templates, or</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:\r
-1'>   </span><span style='mso-tab-count:1'>       </span>t_coffee &lt;your\r
-seq&gt; -mode accurate</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><span style='mso-tab-count:1'>         </span>that does everything and\r
-tries to use the best template. Now that you see why it is useful let's see how\r
-to get BLAST up and running, from the easy solution to tailor made ones.</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><a name="_Toc235958475"><span lang=EN-US>Using\r
-the EBI BLAST Client</span></a></span></span></span></h3>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>This is by far the easiest (and the default mode). The perl clients are\r
-already incorporated in T-Coffeem and all you need is the SOAP::Lite perl\r
-library. In theory, T-Coffee should have already installed this library during\r
-the standard installation. Yet, this requires having toot access. If you did\r
-not have it at the time of the installation, or if you need your system administrator\r
-to install SOAP::Lite, simply follow the instruction provided on the website:</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:\r
-1'>   </span>http://search.cpan.org/~byrne/SOAP-Lite-0.60a</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>It really is worth the effort, since the EBI is providing one of the\r
-best webservice available around, and most notably, the only public psiblast\r
-via a web service.</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><span style='mso-spacerun:yes'> </span></span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>Another important point is that the EBI requires your E-mail address to\r
-process your queries. Normally, T-Coffee should have asked you to provide this\r
-address. If you have not, or if you have provided a phony address, you should\r
-correct this by directly editing the file</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:\r
-1'>   </span>~/.t_coffee/email.txt</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><b><span\r
-lang=AF>Be Careful! </span></b><span lang=AF>If you provide a fake E-mail, the\r
-EBI may suspend the service for all machines associated with your IP address\r
-(that could mean your entire lab, or entire institute, or even the entire\r
-country or, but I doubt it, the whole universe).</span></span></span></span></p>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><a name="_Toc235958476"><span lang=EN-US>Using\r
-the NCBI BLAST Client</span></a></span></span></span></h3>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>The NCBI is the next best alternative. In my hand it was always a bit\r
-slower and most of all, it does not incorporate PSI-BLAST (as a web sevice). A\r
-big miss. The NCBI web blast client is a small executable that you should\r
-install on your system following the instructions given on this link</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US>ftp://ftp.ncbi.nih.gov/blast/executables/LATEST</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>Simply go for <b>netbl,</b> download the executable that corresponds to\r
-your architecture (cygwin users should go for the win executable). Despite all\r
-the files that come along the executable blastcl3 is a stand alone executable\r
-that you can safely move to your $BIN.</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>All you will then need to do is to make sure that T-Coffee uses the\r
-right client, when you run it.</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US>-blast_server=NCBI</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>No need for any E-mail here, but you don't get psiblast, and whenever\r
-T-Coffee wants to use it, blastp will be used instead.</span></span></span></span></p>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><a name="_Toc235958477"><span lang=EN-US>Using\r
-another Client</span></a></span></span></span></h3>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>You may have your own client (lucky you). If that is so, all you need\r
-is to make sure that this client is complient with the blast command line. If\r
-your client is named foo.pl, all you need to to is run T-Coffee with</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US>-blast_server=CLIENT_foo.pl</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>Foo will be called as if it were blastpgp, and it is your responsability\r
-to make sure it can handle the following command line:</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US>foo.pl -p &lt;method&gt; -d\r
-&lt;db&gt; -i &lt;infile&gt; -o &lt;outfile&gt; -m 7</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>method can either be blastp or psiblast.</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>infile is a FASTA file</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>-m7 triggers the XML output. T-Coffee is able to parse both the EBI XML\r
-output and the NCBI XML output.</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>If foo.pl behaves differently, the easiest will probably be to write a\r
-wrapper around it so that wrapped_foo.pl behaves like blastpgp</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><a name="_Toc235958478"><span lang=EN-US>Using\r
-a BLAST local version on UNIX</span></a></span></span></span></h3>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>If you have blastpgp installed, you can run it instead of the remote\r
-clients by using:</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US>-blast_server=LOCAL</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><span style='mso-spacerun:yes'> </span>The documnentation for blastpgp\r
-can be found on:</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US>www.ncbi.nlm.nih.gov/staff/tao/URLAPI/blastpgp.html</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>and the package is part of the standard BLAST distribution</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US>ftp://ftp.ncbi.nih.gov/blast/executables/LATEST</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>Depending on your system, your own skills, your requirements and on\r
-more parameters than I have fingers to count, installing a BLAST server suited\r
-for your needs can range from a 10 minutes job to an achivement spread over\r
-several generations. So at this point, you should roam the NCBI website for\r
-suitable information.</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>If you want to have your own BLAST server to run your own databases,\r
-you should know that it is possible to control both the database and the\r
-program used by BLAST:</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>-prot_db: will specify the database used by all the psi-blast modes</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpLast><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>-pdb_db: will specify the database used by the pdb modes</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><a name="_Toc235958479"><span lang=EN-US>Using\r
-a BLAST local version on Windows/cygwin</span></a></span></span></span></h3>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>For those of you using cygwin, be careful. While cygwin behaves like a\r
-UNIX system, the BLAST executable required for cygwin (win32) is expecting\r
-WINDOWS path and not UNIX path. This has three important consequences:</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>1- the ncbi file declaring the Data directory must be:</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><span style='mso-tab-count:1'>         </span>C:WINDOWS//ncbi.init<span\r
-style='mso-spacerun:yes'>  </span>[at the root of your WINDOWS]</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>2- the address mentionned with this file must be WINDOWS formated, for\r
-instance, on my system:</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>Data=C:\cygwin\home\notredame\blast\data</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>3- When you pass database addresses to BLAST, these must be in Windows\r
-format:</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><span style='mso-tab-count:1'>         </span>-protein_db=&quot;c:/somewhere/somewhereelse/database&quot;</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>(using the slash (/) or the andtislash (\) does not matter on new\r
-systems but I would reommand against incorporating white spaces.</span></span></span></span></p>\r
-\r
-<h2><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><a name="_Toc235958480"><span lang=EN-US>Installing\r
-Other Companion Packages</span></a></span></span></span></h2>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>T-Coffee is meant to interact with as many packages as possible, either\r
-for aligning or using predictions. If you type </span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:\r
-1'>   </span>t_coffee</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>You will receive a list of supported packages that looks like the next\r
-table. In theory, most of these packages can be installed by T-Coffee</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>****** Pairwise Sequence Alignment Methods:</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>--------------------------------------------</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>fast_pair <span style='mso-spacerun:yes'>         </span>built_in</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>exon3_pair<span style='mso-spacerun:yes'>         </span>built_in</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>exon2_pair<span style='mso-spacerun:yes'>         </span>built_in</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>exon_pair<span style='mso-spacerun:yes'>          </span>built_in</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>slow_pair<span style='mso-spacerun:yes'>          </span>built_in</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>proba_pair<span style='mso-spacerun:yes'>         </span>built_in</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>lalign_id_pair<span style='mso-spacerun:yes'>     </span>built_in</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>seq_pair<span style='mso-spacerun:yes'>           </span>built_in</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>externprofile_pair built_in</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>hh_pair<span style='mso-spacerun:yes'>       </span><span\r
-style='mso-spacerun:yes'>     </span>built_in</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>profile_pair<span style='mso-spacerun:yes'>       </span>built_in</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>cdna_fast_pair<span style='mso-spacerun:yes'>     </span>built_in</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>cdna_cfast_pair<span style='mso-spacerun:yes'>    </span>built_in</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>clustalw_pair<span style='mso-spacerun:yes'>     \r
-</span>ftp://www.ebi.ac.uk/pub/clustalw</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>mafft_pair<span style='mso-spacerun:yes'>        \r
-</span>http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>mafftjtt_pair<span style='mso-spacerun:yes'>      </span>http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>mafftgins_pair<span style='mso-spacerun:yes'>    \r
-</span>http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>dialigntx_pair<span style='mso-spacerun:yes'>    \r
-</span>http://dialign-tx.gobics.de/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>dialignt_pair<span style='mso-spacerun:yes'>     \r
-</span>http://dialign-t.gobics.de/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>poa_pair<span style='mso-spacerun:yes'>           </span>http://www.bioinformatics.ucla.edu/poa/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>probcons_pair<span style='mso-spacerun:yes'>     \r
-</span>http://probcons.stanford.edu/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>muscle_pair<span style='mso-spacerun:yes'>       \r
-</span>http://www.drive5.com/muscle/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>t_coffee_pair<span style='mso-spacerun:yes'>     \r
-</span>http://www.tcoffee.org</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>pcma_pair<span style='mso-spacerun:yes'>         \r
-</span>ftp://iole.swmed.edu/pub/PCMA/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>kalign_pair<span style='mso-spacerun:yes'>       \r
-</span>http://msa.cgb.ki.se</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>amap_pair<span style='mso-spacerun:yes'>         \r
-</span>http://bio.math.berkeley.edu/amap/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>proda_pair<span style='mso-spacerun:yes'>        \r
-</span>http://bio.math.berkeley.edu/proda/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>prank_pair<span style='mso-spacerun:yes'>        \r
-</span>http://www.ebi.ac.uk/goldman-srv/prank/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>consan_pair<span style='mso-spacerun:yes'>       \r
-</span>http://selab.janelia.org/software/consan/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>****** Pairwise Structural Alignment Methods:</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>--------------------------------------------</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>align_pdbpair<span style='mso-spacerun:yes'>      </span>built_in</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>lalign_pdbpair<span style='mso-spacerun:yes'>     </span>built_in</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>extern_pdbpair<span style='mso-spacerun:yes'>     </span>built_in</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>thread_pair<span style='mso-spacerun:yes'>        </span>built_in</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>fugue_pair<span style='mso-spacerun:yes'>        \r
-</span>http://www-cryst.bioc.cam.ac.uk/fugue/download.html</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>pdb_pair<span style='mso-spacerun:yes'>           </span>built_in</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>sap_pair<span style='mso-spacerun:yes'>          \r
-</span>http://www-cryst.bioc.cam.ac.uk/fugue/download.html</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>mustang_pair<span style='mso-spacerun:yes'>      \r
-</span>http://www.cs.mu.oz.au/~arun/mustang/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>tmalign_pair<span style='mso-spacerun:yes'>      \r
-</span>http://zhang.bioinformatics.ku.edu/TM-align/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>****** Multiple Sequence Alignment Methods:</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>--------------------------------------------</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>clustalw_msa<span style='mso-spacerun:yes'>      \r
-</span>ftp://www.ebi.ac.uk/pub/clustalw</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>mafft_msa<span style='mso-spacerun:yes'>         \r
-</span>http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>mafftjtt_msa<span style='mso-spacerun:yes'>      \r
-</span>http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>mafftgins_msa<span style='mso-spacerun:yes'>     \r
-</span>http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>dialigntx_msa<span style='mso-spacerun:yes'>     \r
-</span>http://dialign-tx.gobics.de/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>dialignt_msa<span style='mso-spacerun:yes'>      \r
-</span>http://dialign-t.gobics.de/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>poa_msa<span style='mso-spacerun:yes'>           \r
-</span>http://www.bioinformatics.ucla.edu/poa/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>probcons_msa<span style='mso-spacerun:yes'>      \r
-</span>http://probcons.stanford.edu/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>muscle_msa<span style='mso-spacerun:yes'>        \r
-</span>http://www.drive5.com/muscle/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>t_coffee_msa<span style='mso-spacerun:yes'>      \r
-</span>http://www.tcoffee.org</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>pcma_msa<span style='mso-spacerun:yes'>          \r
-</span>ftp://iole.swmed.edu/pub/PCMA/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>kalign_msa<span style='mso-spacerun:yes'>        \r
-</span>http://msa.cgb.ki.se</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>amap_msa<span style='mso-spacerun:yes'>          \r
-</span>http://bio.math.berkeley.edu/amap/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>proda_msa<span style='mso-spacerun:yes'>         \r
-</span>http://bio.math.berkeley.edu/proda/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>prank_msa<span style='mso-spacerun:yes'>         \r
-</span>http://www.ebi.ac.uk/goldman-srv/prank/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>#######<span style='mso-spacerun:yes'>   </span>Prediction Methods\r
-available to generate Templates</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>-------------------------------------------------------------</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>RNAplfold<span style='mso-spacerun:yes'>         \r
-</span>http://www.tbi.univie.ac.at/~ivo/RNA/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>HMMtop<span style='mso-spacerun:yes'>            \r
-</span>www.enzim.hu/hmmtop/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>GOR4<span style='mso-spacerun:yes'>              \r
-</span>http://mig.jouy.inra.fr/logiciels/gorIV/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>wublast_client<span style='mso-spacerun:yes'>    \r
-</span>http://www.ebi.ac.uk/Tools/webservices/services/wublast</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>blastpgp_client<span style='mso-spacerun:yes'>    </span>http://www.ebi.ac.uk/Tools/webservices/services/blastpgp<span\r
-style='mso-spacerun:yes'>            </span></span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpLast><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>==========================================================</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<h2><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><a name="_Toc235958481"><span lang=EN-US>Installation\r
-of PSI-Coffee and Expresso</span></a></span></span></span></h2>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>PSI-Coffee is a mode of T-Coffee that runs a a Psi-BLAST on each of\r
-your sequences and makes a multiple profile alignment. If you do not have any\r
-structural information, it is by far the most accurate mode of T-Coffee. To use\r
-it, you must have SOAP installed so that the EBI BLAST client can run on your\r
-system.</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>It is a bit slow, but really worth it if your sequences are hard to\r
-align and if the accuracy of your alignment is important. <span\r
-style='mso-spacerun:yes'> </span></span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>To use this mode, try:</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:\r
-1'>   </span>t_coffee &lt;yoursequence&gt; -mode psicoffee</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>Note that because PSI-BLAST is time consuming, T-Coffee stores the runs\r
-in its cache (./tcoffee/cache) so that it does not need to be re-run. It means\r
-that if you re-align your sequences (or add a few extra sequences), things will\r
-be considerably faster.</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>If your installation procedure has managed to compile TMalign, and if\r
-T-Coffee has access to the EBI BLAST server (or any other server) you can also\r
-do the following:</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:\r
-1'>   </span>t_coffee &lt;yoursequence&gt; -mode expresso</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>That will look for structural templates. And if both these modes are\r
-running fine, then you are ready for the best, the &quot;crème de la\r
-crème&quot;:</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:\r
-1'>   </span>t_coffee &lt;yoursequence&gt; -mode accurate</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<h2><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><a name="_Toc235958482"><span lang=EN-US>Installation\r
-of M-Coffee</span></a></span></span></span></h2>\r
-\r
-<p class=MsoNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>M-Coffee is a special mode of T-Coffee that makes it possible to\r
-combine the output of many multiple sequence alignment packages. </span></span></span></span><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US style='mso-ansi-language:\r
-EN-US'><o:p></o:p></span></span></span></span></p>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><a name="_Toc235958483"><span lang=EN-US>Automated\r
-Installation</span></a></span></span></span></h3>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>In the T-Coffee distribution, type:</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US>./install mcoffee</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MsoNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>In theory, this command should download and install every required\r
-package. If, however, it fails, you should switch to the manual installation\r
-(see next).</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>By default these packages will be in </span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US>$HOME/.t_coffee/plugins</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>If you want to have these companion packages in a different directory,\r
-you can either set the environement variable </span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US>PLUGINS_4_TCOFFEE=&lt;plugins\r
-dir&gt;</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>Or use the command line flag -plugin (over-rides every other setting)</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US>t_coffee ...\r
--plugins=&lt;plugins dir&gt;</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><a name="_Toc235958484"><span lang=EN-US>Manual\r
-Installation</span></a></span></span></span></h3>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>M-Coffee requires a standard T-Coffee installation (c.f. previous\r
-section) and the following packages to be installed on your system:</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><span style='mso-tab-count:1'>         </span></span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>Package<span style='mso-tab-count:2'>           </span>Where From</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>==========================================================</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>ClustalW<span style='mso-tab-count:2'>          </span>can interact\r
-with t_coffee</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>----------------------------------------------------------</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>Poa<span style='mso-tab-count:3'>               </span>http://www.bioinformatics.ucla.edu/poa/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>----------------------------------------------------------</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>Muscle<span style='mso-tab-count:2'>            </span>http://www.drive5.com</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US><span style='mso-spacerun:yes'> </span>----------------------------------------------------------</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>ProbCons<span style='mso-tab-count:2'>          </span>http://probcons.stanford.edu/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>ProbConsRNA<span style='mso-tab-count:2'>       </span>http://probcons.stanford.edu/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>----------------------------------------------------------</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>MAFFT<span style='mso-tab-count:1'> </span></span></span></span></span><a\r
-href="http://www.biophys.kyoto-/"><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>http://www.biophys.kyoto-</span></span></span></span><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'></span></span></span></a><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US>u.ac.jp/~katoh/programs/align/mafft/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>----------------------------------------------------------</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>Dialign-T<span style='mso-tab-count:2'>         </span></span></span></span></span><a\r
-href="http://dialign-t.gobics.de/"><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>http://dialign-t.gobics.de/</span></span></span></span><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'></span></span></span></a><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>Dialign-TX<span style='mso-tab-count:2'>        </span></span></span></span></span><a\r
-href="http://dialign-t.gobics.de/"><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>http://dialign-tx.gobics.de/</span></span></span></span><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'></span></span></span></a><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>----------------------------------------------------------</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>PCMA<span style='mso-tab-count:3'>              </span></span></span></span></span><a\r
-href="ftp://iole.swmed.edu/pub/PCMA/"><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>ftp://iole.swmed.edu/pub/PCMA/</span></span></span></span><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'></span></span></span></a><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>----------------------------------------------------------</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>kalign<span style='mso-spacerun:yes'>           \r
-</span>http://msa.cgb.ki.se</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>----------------------------------------------------------</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>amap<span style='mso-spacerun:yes'>             \r
-</span>http://bio.math.berkeley.edu/amap/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>-----------------------------------------------------------</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>proda_msa<span style='mso-spacerun:yes'>       \r
-</span>http://bio.math.berkeley.edu/proda/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>-----------------------------------------------------------</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>prank_msa<span style='mso-spacerun:yes'>        </span>http://www.ebi.ac.uk/goldman-srv/prank/</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpLast><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>In our hands all these packages where very straightforward to compile\r
-and install on a standard cygwin or Linux configuration. Just make sure you\r
-have gcc, the C compiler, properly installed.</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>Once the package is compiled and ready to use, make sure that the\r
-executable is on your path, so that t_coffee can find it automatically. Our\r
-favorite procedure is to create a bin directory in the home. If you do so, make\r
-sure this bin is in your path and fill it with all your executables (this is a\r
-standard Unix practice).</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>If for some reason, you do not want this directory to be on your path,\r
-or you want to specify a precise directory containing the executables, you can\r
-use:</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:\r
-1'>   </span>export PLUGINS_4_TCOFFEE=&lt;dir&gt;</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>By default this directory is set to $HOME/.t_coffee/plugins/$OS, but\r
-you can over-ride it with the environement variable or using the flag:</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:\r
-1'>   </span>t_coffee ...-plugins=&lt;dir&gt;</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>If you cannot, or do not want to use a single bin directory, you can\r
-set the following environment variables to the absolute path values of the\r
-executable you want to use. Whenever they are set, these variables will supersede\r
-any other declaration. This is a convenient way to experiment with multiple\r
-package versions.</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:70.2pt;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US>POA_4_TCOOFFEE<br>\r
-CLUSTALW_4_TCOFFEE<br>\r
-POA_4_TCOFFEE<br>\r
-TCOFFEE_4_TCOFFEE<br>\r
-MAFFT_4_TCOFFEE<br>\r
-MUSCLE_4_TCOFFEE<br>\r
-DIALIGNT_4_TCOFFEE<br>\r
-PRANK_4_TCOFFEE<br>\r
-DIALIGNTX_4_TCOFFEE<br>\r
-<span style='mso-spacerun:yes'> </span></span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>For three of these packages, you will need to copy some of the files in\r
-a special T-Coffee directory.</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:\r
-1'>   </span>cp POA_DIR/* ~/.t_coffee/mcoffee/</span></span></span></span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:\r
-1'>   </span>cp DIALIGN-T/conf/*<span style='mso-spacerun:yes'>  </span>~/.t_coffee/mcoffee</span></span></span></span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:\r
-1'>   </span>cp DIALIGN-TX/conf/*<span style='mso-spacerun:yes'> \r
-</span>~/.t_coffee/mcoffee</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>Note that the following files are enough for default usage:</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US>BLOSUM.diag_prob_t10<span\r
-style='mso-spacerun:yes'>   </span>BLOSUM75.scr<span style='mso-spacerun:yes'> \r
-</span>blosum80_trunc.mat<span style='mso-spacerun:yes'>           </span></span></span></span></span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US>dna_diag_prob_100_exp_330000<span\r
-style='mso-spacerun:yes'>  </span>dna_diag_prob_200_exp_110000</span></span></span></span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US>BLOSUM.scr<span\r
-style='mso-spacerun:yes'>             </span>BLOSUM90.scr<span\r
-style='mso-spacerun:yes'>  </span>dna_diag_prob_100_exp_110000</span></span></span></span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US>dna_diag_prob_100_exp_550000<span\r
-style='mso-spacerun:yes'>  </span>dna_diag_prob_250_exp_110000</span></span></span></span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US>BLOSUM75.diag_prob_t2<span\r
-style='mso-spacerun:yes'>  </span>blosum80.mat<span style='mso-spacerun:yes'> \r
-</span>dna_diag_prob_100_exp_220000<span style='mso-spacerun:yes'>  </span></span></span></span></span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US>dna_diag_prob_150_exp_110000<span\r
-style='mso-spacerun:yes'>  </span>dna_matrix.scr</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF>If you would rather have the mcoffee directory in some other location,\r
-set the MCOFFEE_4_TCOFFEE environement variable to the propoer directory:</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:\r
-1'>   </span>setenv MCOFFEE_4_TCOFFEE &lt;directory containing mcoffee\r
-files&gt;</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<h2><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><a name="_Toc235958485"><span lang=EN-US>Installation\r
-of APDB and iRMSD</span></a></span></span></span></h2>\r
-\r
-<p class=MsoBodyText><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>APDB and iRMSD are incorporated in T-Coffee. Once t_coffee is\r
-installed, you can invoque these programs by typing:</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:\r
-1'>   </span>t_coffee \96other_pg apdb<br>\r
-<span style='mso-tab-count:1'>   </span>t_coffee \96other_pg irmsd</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<h2><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><a name="_Toc235958486"><span lang=EN-US>Installation\r
-of tRMSD</span></a></span></span></span></h2>\r
-\r
-<p class=MsoBodyText><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>tRMSD comes along with t_coffee but it also requires the package\r
-phylip in order to be functional. Phylip can be obtained from:</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=AF><span style='mso-tab-count:1'>         </span></span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>Package<span style='mso-tab-count:2'>           </span>Function</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>===================================================</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>---------------------------------------------------</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>Phylip<span style='mso-tab-count:2'>            </span>Phylogenetic\r
-tree computation</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US><span style='mso-tab-count:3'>                  </span>evolution.genetics.washington.edu/phylip.html</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpLast><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>---------------------------------------------------</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;text-indent:14.1pt;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US>t_coffee \96other_pg trmsd</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<h2><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US><o:p>&nbsp;</o:p></span></span></span></span></h2>\r
-\r
-<h2><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><a name="_Toc235958487"><span lang=EN-US>Installation\r
-of seq_reformat</span></a></span></span></span></h2>\r
-\r
-<p class=MsoBodyText><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>Seq_reformat is a reformatting package that is part of t_coffee. To\r
-use it (and see the available options), type:</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:\r
-1'>   </span>t_coffee \96other_pg seq_reformat</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<h2><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><a name="_Toc235958488"><span lang=EN-US>Installation\r
-of extract_from_pdb</span></a></span></span></span></h2>\r
-\r
-<p class=MsoBodyText><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>Extract_from_pdb is a PDB reformatting package that is part of\r
-t_coffee. To use it (and see the available options), type.</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span\r
-style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:\r
-1'>   </span>t_coffee \96other_pg apdb \96h</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MsoBodyText><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US>Extract_from_pdb requires wget in order to automatically fetch PDB\r
-structures.</span></span></span></span></p>\r
-\r
-<p class=MsoBodyText><span style='mso-bookmark:_Toc101065206'><span\r
-style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span\r
-lang=EN-US><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<span style='mso-bookmark:_Toc102494675'></span><span style='mso-bookmark:_Toc102494295'></span><span\r
-style='mso-bookmark:_Toc101065206'></span>\r
-\r
-<h2><a name="_Toc235958489"><span lang=EN-US>Installation of 3D-Coffee/Expresso</span></a></h2>\r
-\r
-<p class=MyNormal><span lang=AF>3D-Coffee/Expresso is a special mode of\r
-T-Coffee that makes it possible to combine sequences and structures. The main\r
-difference between Expresso and 3D-Coffee is that Expresso fetches the\r
-structures itself. </span><span lang=EN-US style='mso-ansi-language:EN-US'><o:p></o:p></span></p>\r
-\r
-<h3><a name="_Toc235958490"><span lang=EN-US>Automated Installation</span></a></h3>\r
-\r
-<p class=MyNormal><span lang=AF>In the T-Coffee distribution, type:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>./install\r
-expresso</span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>OR</span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>./install\r
-3dcoffee</span></p>\r
-\r
-</div>\r
-\r
-<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MyNormal><span lang=AF>In theory, this command should download and\r
-install every required package (<b>except fugue</b>). If, however, it fails,\r
-you should switch to the manual installation (see next).</span></p>\r
-\r
-<h3><a name="_Toc235958491"><span lang=EN-US>Manual Installation</span></a></h3>\r
-\r
-<p class=MyNormal><span lang=AF>In order to make the most out of T-Coffee, you\r
-will need to install the following packages (make sure the executable is named\r
-as indicated below):</span></p>\r
-\r
-<p class=MyNormal><span lang=AF><span style='mso-tab-count:1'>         </span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span lang=EN-US>Package<span style='mso-tab-count:\r
-2'>           </span>Function</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>===================================================</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>---------------------------------------------------</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>wget<span style='mso-tab-count:\r
-2'>        </span><span style='mso-tab-count:1'>      </span>3DCoffee </span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US><span style='mso-tab-count:\r
-3'>                  </span>Automatic Downloading of Structures</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>---------------------------------------------------</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>sap<span style='mso-tab-count:\r
-1'>   </span><span style='mso-tab-count:1'>      </span><span style='mso-tab-count:\r
-1'>      </span>structure/structure comparisons </span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>(obtain it from <st1:place\r
-w:st="on">W. Taylor</st1:place>, NIMR-MRC).</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>---------------------------------------------------</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>TMalign<span style='mso-tab-count:\r
-2'>           </span>zhang.bioinformatics.ku.edu/TM-align/</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>---------------------------------------------------</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>mustang<span style='mso-tab-count:\r
-2'>           </span>www.cs.mu.oz.au/~arun/mustang/</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>---------------------------------------------------</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>wublastclient<span\r
-style='mso-spacerun:yes'>     </span>www.ebi.ac.uk/Tools/webservices/clients/wublast</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>---------------------------------------------------</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>Blast<span style='mso-tab-count:\r
-2'>       </span><span style='mso-tab-count:1'>      </span><a\r
-href="http://www.ncbi.nih.nlm.gov/">www.ncbi.nih.nlm.gov</a></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>---------------------------------------------------</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>Fugue*<span style='mso-tab-count:\r
-2'>            </span>protein to structure alignment program</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US><span style='mso-tab-count:\r
-3'>                  </span>http://www-cryst.bioc.cam.ac.uk/fugue/download.html</span></p>\r
-\r
-<p class=examplefileCxSpLast><span lang=EN-US><span style='mso-tab-count:3'>                  </span>***NOT\r
-COMPULSORY***</span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MyNormal><span lang=AF>Once the package is installed, make sure make\r
-sure that the executable is on your path, so that t_coffee can find it\r
-automatically.</span></p>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MyNormal><span lang=AF>The wublast client makes it possible to run\r
-BLAST at the EBI without having to install any database locally. It is an ideal\r
-solution if you are only using expresso occasionally.</span></p>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<h3><a name="_Toc235958492"><span lang=EN-US>Installing Fugue for T-Coffee</span></a></h3>\r
-\r
-<p class=MyNormal><span lang=AF>Uses a standard fugue installation. You only\r
-need to install the following packages:</span></p>\r
-\r
-<p class=MyNormal><span lang=AF><span style='mso-spacerun:yes'> </span>joy,\r
-melody, fugueali, sstruc, hbond</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>If you have root privileges, you can install\r
-the common data in: </span></p>\r
-\r
-<p class=MyNormal><span lang=AF>cp fugue/classdef.dat<span style='mso-tab-count:\r
-1'>           </span>/data/fugue/SUBST/classdef.dat</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>otherwise</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>Setenv MELODY_CLASSDEF=&lt;location&gt;</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>Setenv MELODY_SUBST=fugue/allmat.dat</span></p>\r
-\r
-<p class=MyNormal><span lang=AF><span style='mso-spacerun:yes'> </span></span></p>\r
-\r
-<p class=MyNormal><span lang=AF>All the other configuration files must be in\r
-the right location. </span></p>\r
-\r
-<h2><a name="_Toc235958493"><span lang=EN-US>Installation of R-Coffee</span></a></h2>\r
-\r
-<p class=MyNormal><span lang=AF>R-Coffee is a special mode able to align RNA\r
-sequences while taking into account their secondary structure.</span><span\r
-lang=EN-US style='mso-ansi-language:EN-US'><o:p></o:p></span></p>\r
-\r
-<h3><a name="_Toc235958494"><span lang=EN-US>Automated Installation</span></a></h3>\r
-\r
-<p class=MyNormal><span lang=AF>In the T-Coffee distribution, type:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>./install\r
-rcoffee</span></p>\r
-\r
-</div>\r
-\r
-<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MyNormal><span lang=AF>In theory, this command should download and\r
-install every required package (except <b>consan</b>). If, however, it fails,\r
-you should switch to the manual installation (see next).</span></p>\r
-\r
-<h3><a name="_Toc235958495"><span lang=EN-US>Manual Installation</span></a></h3>\r
-\r
-<p class=MyNormal><span lang=AF>R-Coffee only requires the package <st1:place\r
-w:st="on"><st1:City w:st="on">Vienna</st1:City></st1:place> to be installed, in\r
-order to compute multiple sequence alignments. To make the best out of it, you\r
-should also have all the packages required by M-Coffee</span></p>\r
-\r
-<p class=MyNormal><span lang=AF><span style='mso-tab-count:1'>         </span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span lang=EN-US>Package<span style='mso-tab-count:\r
-2'>           </span>Function</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>===================================================</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>---------------------------------------------------</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>consan<span style='mso-tab-count:\r
-2'>            </span>R-Coffee </span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US><span style='mso-tab-count:\r
-3'>                  </span>Computes highly accurate pairwise Alignments</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US><span style='mso-tab-count:\r
-3'>                  </span>***NOT COMPULSORY***</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US><span style='mso-tab-count:\r
-3'>                  </span>selab.janelia.org/software/consan/</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>---------------------------------------------------</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>RNAplfold<span\r
-style='mso-tab-count:2'>         </span>Computes RNA secondary Structures </span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US><span style='mso-tab-count:\r
-3'>                  </span>www.tbi.univie.ac.at/~ivo/RNA/</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>---------------------------------------------------</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>probconsRNA<span\r
-style='mso-tab-count:2'>       </span>probcons.stanford.edu/</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US><span\r
-style='mso-spacerun:yes'>        </span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>---------------------------------------------------</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>M-Coffee<span style='mso-tab-count:\r
-2'>          </span>T-Coffee and the most common MSA Packages</span></p>\r
-\r
-<p class=examplefileCxSpLast><span lang=EN-US><span style='mso-tab-count:3'>                  </span>(cf\r
-M-Coffee in this installation guide)</span></p>\r
-\r
-</div>\r
-\r
-<h3><a name="_Toc235958496"><span lang=EN-US>Installing ProbbonsRNA for R-Coffee</span></a></h3>\r
-\r
-<p class=MyNormal><span lang=AF>Follow the installation procedure, but make\r
-sure you rename the probcons executable into probconsRNA.</span></p>\r
-\r
-<h3><a name="_Toc235958497"><span lang=EN-US>Installing Consan for R-Coffee</span></a></h3>\r
-\r
-<p class=MyNormal><span lang=AF>In order to insure a proper interface beween\r
-consan and R-Coffee, you must make sure that the file mix80.mod is in the\r
-directory ~/.t_coffee/mcoffee or in the mcoffee directory otherwise declared.</span></p>\r
-\r
-<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 3.0pt;\r
-padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0mm;margin-right:\r
-4.25pt'>\r
-\r
-<p class=ChapterTitle><a name="_Toc235958498"></a><a name="_Toc102494676"></a><a\r
-name="_Toc101065207"><span style='mso-bookmark:_Toc102494676'><span\r
-style='mso-bookmark:_Toc235958498'><span lang=EN-US>Q</span></span></span></a><span\r
-style='mso-bookmark:_Toc235958498'><span lang=EN-US>uick Start</span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MsoBodyText><span lang=EN-US>We only give you the very basics here.\r
-Please use the Tutorial for more detailed information on how to use our tools.</span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.5pt;\r
-padding:0mm 0mm 0mm 0mm;background:#F7CBB7'>\r
-\r
-<p class=Warning><a name="_Toc102494677"></a><a name="_Toc102494296"></a><a\r
-name="_Toc101065208"><span style='mso-bookmark:_Toc102494296'><span\r
-style='mso-bookmark:_Toc102494677'><span lang=EN-US>IMPORTANT: All the files\r
-mentionned here (sampe_seq...) can be found in the example directory of the\r
-distribution.</span></span></span></a></p>\r
-\r
-</div>\r
-\r
-<h2><span style='mso-bookmark:_Toc101065208'><span style='mso-bookmark:_Toc102494296'><span\r
-style='mso-bookmark:_Toc102494677'><a name="_Toc235958499"><span lang=EN-US>T-COFFEE</span></a></span></span></span></h2>\r
-\r
-<p class=MyNormal><span lang=AF>Write your sequences in the same file\r
-(Swiss-prot, Fasta or Pir) and type. </span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee sample_seq1.fasta<span style='mso-spacerun:yes'>  </span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF>This will output two files:</span></p>\r
-\r
-<p class=example2CxSpFirst><span lang=EN-US>sample_seq1.aln: your Multiple\r
-Sequence Alignment</span></p>\r
-\r
-<p class=example2CxSpLast><span lang=EN-US>sample_seq1.dnd: The Guide tree\r
-(newick Format)</span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.5pt;\r
-padding:0mm 0mm 0mm 0mm;background:#F7CBB7'>\r
-\r
-<p class=Warning><span lang=EN-US>IMPORTANT: </span></p>\r
-\r
-<p class=Warning><span lang=EN-US>In theory nucleic acids should be\r
-automatically detected and the default methods should be adapted appropriately.\r
-However, sometimes this may fail, either because the sequences are too short or\r
-contain too many ambiguity codes. </span></p>\r
-\r
-<p class=Warning><span lang=EN-US>When this happens, you are advised to\r
-explicitly set the type of your sequences</span></p>\r
-\r
-<p class=Warning><span lang=EN-US>NOTE: the \96mode=dna is not needed or\r
-supported anymore</span></p>\r
-\r
-</div>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee sample_dnaseq1.fasta \96type=dna</span></p>\r
-\r
-</div>\r
-\r
-<h2><a name="_Toc102494678"></a><a name="_Toc102494297"></a><a\r
-name="_Toc101065209"></a><a name="_Toc235958500"><span style='mso-bookmark:\r
-_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:\r
-_Toc102494678'><span lang=EN-US>M-Coffee</span></span></span></span></a><span\r
-style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span\r
-style='mso-bookmark:_Toc102494678'></span></span></span></h2>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF>M-Coffee is a <st1:place w:st="on">Meta</st1:place> version of T-Coffee\r
-that makes it possible to combine the output of at least eight packages\r
-(Muscle, probcons, poa, dialignT, mafft, clustalw, PCMA and T-Coffee).</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF>If all these packages are already installed on your machine. You must:</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF>1-set the following environment variables</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span\r
-style='mso-bookmark:_Toc102494678'><span lang=EN-US><span style='mso-tab-count:\r
-1'>   </span>export POA_DIR=[absolute path of the POA installation dir]</span></span></span></span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span\r
-style='mso-bookmark:_Toc102494678'><span lang=EN-US><span style='mso-tab-count:\r
-1'>   </span>export DIALIGNT_DIR=[Absolute path of the DIALIGN-T/conf</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF>Once this is done, write your sequences in a file and run: same file\r
-(Swiss-prot, Fasta or Pir) and type. </span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span\r
-style='mso-bookmark:_Toc102494678'><span lang=EN-US>PROMPT: t_coffee\r
-sample_seq1.fasta \96mode mcoffee </span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF>If the program starts complaining one package or the other is missing,\r
-this means you will have to go the hard way and install all these packages\r
-yourself... Proceed to the M-Coffee section for more detailed instructions.</span></span></span></span></p>\r
-\r
-<h2><span style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span\r
-style='mso-bookmark:_Toc102494678'><a name="_Toc235958501"><span lang=EN-US>Expresso</span></a></span></span></span></h2>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF>If you have installed the EBI wublast.pl client, Expresso will BLAST\r
-your sequences against PDB, identify the best targets and use these to align\r
-your proteins.</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span\r
-style='mso-bookmark:_Toc102494678'><span lang=EN-US>PROMPT: t_coffee\r
-sample_seq1.fasta \96mode expresso</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF>If you did not manage to install all the required structural packages\r
-for Expresso, like Fugue or Sap, you can still run expresso by selecting\r
-yourself the structural packages you want to use. For instance, if you'd rather\r
-use TM-Align than sap, try: </span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF><span style='mso-tab-count:1'>         </span></span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span\r
-style='mso-bookmark:_Toc102494678'><span lang=EN-US>PROMPT: t_coffee\r
-sample_seq1.fasta \96template_file EXPRESSO -method TMalign_pair</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<h2><span style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span\r
-style='mso-bookmark:_Toc102494678'><a name="_Toc235958502"><span lang=EN-US>R-Coffee</span></a></span></span></span></h2>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF>R-Coffee can be used to align RNA sequences, using their RNApfold\r
-predicted secondary structures. The best results are obtained by using the\r
-consan pairwise method. If you have consan installed:</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span\r
-style='mso-bookmark:_Toc102494678'><span lang=EN-US>t_coffee\r
-sample_rnaseq1.fasta \96special_mode rcoffee_consan </span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF>This will only work if your sequences are short enough (less than 200\r
-nucleotides). A good alternative is the rmcoffee mode that will run Muscle,\r
-Probcons4RNA and MAfft and then use the secondary structures predicted by\r
-RNApfold. </span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span\r
-style='mso-bookmark:_Toc102494678'><span lang=EN-US>PROMPT: t_coffee\r
-sample_rnaseq1.fasta \96mode mrcoffee </span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF>If you want to decide yourself which methods should be combined by\r
-R-Coffee, run:</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span\r
-style='mso-bookmark:_Toc102494678'><span lang=EN-US>PROMPT: t_coffee\r
-sample_rnaseq1.fasta \96mode rcoffee -method lalign_id_pair slow_pair </span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<h2><span style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span\r
-style='mso-bookmark:_Toc102494678'><span lang=EN-US><br>\r
-<a name="_Toc235958503">iRMSD and APDB</a></span></span></span></span></h2>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF>All you need is a file containing the alignment of sequences with a\r
-known structure. These sequences must be named according to their PDB ID,\r
-followed by the chain index ( 1aabA for instance). All the sequences do not\r
-need to have a known structure, but at least two need to have it.</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF>Given the alignment:</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:42.55pt;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span\r
-style='mso-bookmark:_Toc102494678'><span lang=EN-US>PROMPT: t_coffee \96other_pg\r
-irmsd -aln 3d_sample4.aln </span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<h2><span style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span\r
-style='mso-bookmark:_Toc102494678'><a name="_Toc235958504"><span lang=EN-US>tRMSD</span></a></span></span></span></h2>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF>tRMSD is a structure based clustering method using the iRMSD to drive\r
-the clustering. The T-RMSD supports all the parameters supported by iRMSD or\r
-APDB.</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:42.55pt;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span\r
-style='mso-bookmark:_Toc102494678'><span lang=EN-US>PROMPT: t_coffee \96other_pg\r
-trmsd -aln 3d_sample5.aln -template_file 3d_sample5.template_list </span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=EN-US style='mso-ansi-language:EN-US'>3d_sample5.aln is a multiple\r
-alignment in which each sequence has a known structure. The file </span><span\r
-lang=AF>3d_sample5.template_list is a fasta like file declaring the structure\r
-associated with each sequence, in the form: </span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6;margin-left:0mm;margin-right:10.0mm'>\r
-\r
-<p class=examplefilesmall><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=EN-US>&gt; &lt;seq_name&gt; _P_ &lt;PDB structure file or name&gt; </span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=EN-US>******* 3d_sample5.template_list ********<span style='mso-tab-count:\r
-1'>      </span></span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=EN-US>&gt;2UWI-3A _P_ 2UWI-3.pdb</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=EN-US>&gt;2UWI-2A _P_ 2UWI-2.pdb</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=EN-US>&gt;2UWI-1A _P_ 2UWI-1.pdb</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=EN-US>&gt;2HEY-4R _P_ 2HEY-4.pdb</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=EN-US>...</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpLast><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=EN-US>**************************************</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF>The program then outputs a series of files</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=EN-US style='font-size:8.0pt'>Template Type: [3d_sample5.template_list]\r
-Mode Or File: [3d_sample5.template_list] [Start]<o:p></o:p></span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=EN-US style='font-size:8.0pt'><span style='mso-spacerun:yes'>        \r
-</span>[Sample Columns][TOT=<span style='mso-spacerun:yes'>   </span>51][100\r
-%][ELAPSED TIME:<span style='mso-spacerun:yes'>    </span>0 sec.]<o:p></o:p></span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=EN-US style='font-size:8.0pt'><span style='mso-spacerun:yes'>   </span><span\r
-style='mso-spacerun:yes'>      </span>[Tree Cmp][TOT=<span\r
-style='mso-spacerun:yes'>   </span>13][ 92 %][ELAPSED TIME:<span\r
-style='mso-spacerun:yes'>    </span>0 sec.]<o:p></o:p></span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=EN-US style='font-size:8.0pt'><span style='mso-spacerun:yes'> </span>####\r
-File Type=<span style='mso-spacerun:yes'>   </span>TreeList Format=<span\r
-style='mso-spacerun:yes'>     </span>newick Name= 3d_sample5.tot_pos_list<o:p></o:p></span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=EN-US style='font-size:8.0pt'><span style='mso-spacerun:yes'> </span>####\r
-File Type=<span style='mso-spacerun:yes'>       </span>Tree Format=<span\r
-style='mso-spacerun:yes'>     </span>newick Name= 3d_sample5.struc_tree10<o:p></o:p></span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=EN-US style='font-size:8.0pt'><span style='mso-spacerun:yes'> </span>####\r
-File Type=<span style='mso-spacerun:yes'>       </span>Tree Format=<span\r
-style='mso-spacerun:yes'>     </span>newick Name= 3d_sample5.struc_tree50<o:p></o:p></span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=EN-US style='font-size:8.0pt'><span style='mso-spacerun:yes'> </span>####\r
-File Type=<span style='mso-spacerun:yes'>       </span>Tree Format=<span\r
-style='mso-spacerun:yes'>     </span>newick Name= 3d_sample5.struc_tree100<o:p></o:p></span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=EN-US style='font-size:8.0pt'><span style='mso-spacerun:yes'> </span>####\r
-File Type= Colored MSA Format= score_html Name= 3d_sample5.struc_tree.html<o:p></o:p></span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpLast><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=EN-US><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF>3d_sample5.tot_pos_list <span style='mso-tab-count:1'>      </span>is a\r
-list of the tRMSD tree associated with every position. </span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF>3d_sample5.struc_tree100<span style='mso-tab-count:1'>   </span>is a\r
-consensus tree (phylip/consense) of the trees contained in the previous file. <b>This\r
-file is the default output<o:p></o:p></b></span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF>3d_sample5.struc_tree10<span style='mso-tab-count:1'>     </span>is a\r
-consensus tree (phylip/consense) of the 10% trees having the higest average\r
-agreement with the rest</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF>3d_sample5.struc_tree10<span style='mso-tab-count:1'>     </span>is a\r
-consensus tree (phylip/consense) of the 50% trees having the higest average\r
-agreement with the rest</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF>3d_sample5.html<span style='mso-tab-count:1'>      </span>is a colored\r
-version of the output showing in red the positions that give the highest\r
-support to 3d_sample5.struc_tree100</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span\r
-style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<h2><span style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span\r
-style='mso-bookmark:_Toc102494678'><a name="_Toc235958505"><span lang=EN-US>MOCCA</span></a></span></span></span></h2>\r
-\r
-<p class=MyNormal><span lang=AF>Write your sequences in the same file\r
-(Swiss-prot, Fasta or Pir) and type. </span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee \96other_pg mocca sample_seq1.fasta </span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF>This command output one files (&lt;your\r
-sequences&gt;.mocca_lib) and starts an interactive menu. </span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 3.0pt;\r
-padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0mm;margin-right:\r
-4.25pt'>\r
-\r
-<p class=ChapterTitle><a name="_Toc235958506"></a><a name="_Toc102494679"></a><a\r
-name="_Toc101065210"><span style='mso-bookmark:_Toc102494679'><span\r
-style='mso-bookmark:_Toc235958506'><span lang=EN-US>Recent M</span></span></span></a><span\r
-style='mso-bookmark:_Toc235958506'><span lang=EN-US>odifications</span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF>Warning: This log of recent modifications is\r
-not as thorough and accurate as it should be.</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>-5.80 Novel assembly algorithm\r
-(linked_pair_wise) and the primary library is now made of probcons style\r
-pairwise alignments (proba_pair)</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>-4.30 and upward: the FAQ has moved into a new\r
-tutorial document</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>-4.30 and upward: -in has will be deprecated\r
-and replaced by the flags: -profile,-method,-aln,-seq,-pdb</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>-4.02: -mode=dna is still available but not any\r
-more needed or supported. Use type=protein or dna if you need to force things</span></p>\r
-\r
-<p class=MyNormal><b style='mso-bidi-font-weight:normal'><span lang=AF>-</span></b><span\r
-lang=AF>3.28: corrected a bug that prevents short sequences from being\r
-correctly aligned</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>-Use of @ as a separator when specifying\r
-methods parameters</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>-The most notable modifications have to do with\r
-the structure of the input. From version 2.20, all files must be tagged to\r
-indicate their nature (A: alignment, S: Sequence, L: Library\85). We are becoming\r
-stricter, but that\92s for your own good\85 </span></p>\r
-\r
-<p class=MyNormal><span lang=AF>Another important modification has to do with\r
-the flag -matrix: it now controls the matrix being used for the computation </span></p>\r
-\r
-<span lang=AF style='font-size:11.0pt;font-family:"Times New Roman";mso-fareast-font-family:\r
-"Times New Roman";mso-bidi-font-family:"Courier New";mso-ansi-language:AF;\r
-mso-fareast-language:EN-US;mso-bidi-language:AR-SA'><br clear=all\r
-style='page-break-before:always'>\r
-</span>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 3.0pt;\r
-padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0mm;margin-right:\r
-4.25pt'>\r
-\r
-<p class=ChapterTitle><a name="_Toc235958507"><span lang=EN-US>Reference Manual</span></a></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MyNormal><span lang=AF>This reference manual gives a list of all the\r
-flags that can be used to modify the behavior of T-Coffee. For your\r
-convenience, we have grouped them according to their nature. To display a list\r
-of all the flags used in the version of T-Coffee you are using (along with\r
-their default value), type:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee </span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF>Or</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee \96help </span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF>Or</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee \96help \96in</span><span class=MyNormalChar><span lang=EN-US\r
-style='font-size:11.0pt;mso-ansi-language:EN-US'><o:p></o:p></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF>Or any other parameter</span></p>\r
-\r
-<h2><a name="_Toc102494743"></a><a name="_Toc102494358"></a><a\r
-name="_Toc101065212"><span style='mso-bookmark:_Toc102494358'><span\r
-style='mso-bookmark:_Toc102494743'><span lang=EN-US><o:p>&nbsp;</o:p></span></span></span></a></h2>\r
-\r
-<h2><span style='mso-bookmark:_Toc101065212'><span style='mso-bookmark:_Toc102494358'><span\r
-style='mso-bookmark:_Toc102494743'><a name="_Toc235958508"><span lang=EN-US>Environment\r
-Variables</span></a></span></span></span></h2>\r
-\r
-<p class=MsoBodyText><span style='mso-bookmark:_Toc101065212'><span\r
-style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span\r
-lang=EN-US>It is possible to modify T-Coffee\92s behavior by setting any of the\r
-following environement variables. On the bash shell, use export VAR=\94value\94. On\r
-the cshell, use set $VAR=\94xxx\94</span></span></span></span></p>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065212'><span style='mso-bookmark:_Toc102494358'><span\r
-style='mso-bookmark:_Toc102494743'><a name="_Toc235958509"><span lang=EN-US>http_proxy_4_TCOFFEE</span></a></span></span></span></h3>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065212'><span\r
-style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span\r
-lang=AF>Sets the http_proxy and HTTP_proxy values used by T-Coffee. </span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065212'><span\r
-style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span\r
-lang=AF>These values get supersede http_proxy and HTTP_proxy.\r
-http_proxy_4_TCOFFEE gets superseded by the command line values (-proxy and\r
--email)</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065212'><span\r
-style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span\r
-lang=AF>If you have no proxy, just set this value to an empty string.</span></span></span></span></p>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065212'><span style='mso-bookmark:_Toc102494358'><span\r
-style='mso-bookmark:_Toc102494743'><a name="_Toc235958510"><span lang=EN-US>email_4_TCOFFEE</span></a></span></span></span></h3>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065212'><span\r
-style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span\r
-lang=AF>Set the E-mail values provided to web services called upon by T-Coffee.\r
-Can be over-riden by the flag <i>-email.<o:p></o:p></i></span></span></span></span></p>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065212'><span style='mso-bookmark:_Toc102494358'><span\r
-style='mso-bookmark:_Toc102494743'><a name="_Toc235958511"><span lang=EN-US>DIR_4_TCOFFEE</span></a></span></span></span></h3>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065212'><span\r
-style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span\r
-lang=AF>By default this variable is set to $HOME/.t_coffee. This is where\r
-T-Coffee expects to find its cache, tmp dir and possibly any temporary data\r
-stored by the program.</span></span></span></span></p>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065212'><span style='mso-bookmark:_Toc102494358'><span\r
-style='mso-bookmark:_Toc102494743'><a name="_Toc235958512"><span lang=EN-US>TMP_4_TCOFFEE</span></a></span></span></span></h3>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065212'><span\r
-style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span\r
-lang=AF>By default this variable is set to $HOME/.t_coffee/tmp. This is where\r
-T-Coffee stores temporary files.</span></span></span></span></p>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065212'><span style='mso-bookmark:_Toc102494358'><span\r
-style='mso-bookmark:_Toc102494743'><a name="_Toc235958513"><span lang=EN-US>CACHE_4_TCOFFEE</span></a></span></span></span></h3>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065212'><span\r
-style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span\r
-lang=AF>By default this variable is set to $HOME/.t_coffee/cache. This is where\r
-T-Coffee stores any data expensive to obtain: pdb files, sap alignments....</span></span></span></span></p>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065212'><span style='mso-bookmark:_Toc102494358'><span\r
-style='mso-bookmark:_Toc102494743'><span lang=EN-US>PLUGINS_4_TCOFFEE</span></span></span></span></h3>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065212'><span\r
-style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span\r
-lang=AF>By default all the companion packages are searched in the directory\r
-DIR_4_TCOFFEE/plugins/&lt;OS&gt;. This variable overrides the default. This\r
-variable can also be overriden by the <i>-plugins</i> T-Coffee flag</span></span></span></span></p>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065212'><span style='mso-bookmark:_Toc102494358'><span\r
-style='mso-bookmark:_Toc102494743'><a name="_Toc235958514"><span lang=EN-US>NO_ERROR_REPORT_4_TCOFFEE</span></a></span></span></span></h3>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065212'><span\r
-style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span\r
-lang=AF>By default this variable is no set. Set it if you do not want the\r
-program to generate a verbose error output file (useful for running a server).</span></span></span></span></p>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065212'><span style='mso-bookmark:_Toc102494358'><span\r
-style='mso-bookmark:_Toc102494743'><a name="_Toc235958515"><span lang=EN-US>PDB_DIR</span></a></span></span></span></h3>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065212'><span\r
-style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span\r
-lang=AF>Indicate the location of your local PDB installation.</span></span></span></span></p>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065212'><span style='mso-bookmark:_Toc102494358'><span\r
-style='mso-bookmark:_Toc102494743'><a name="_Toc235958516"><span lang=EN-US>NO_WARNING_4_TCOFFEE</span></a></span></span></span></h3>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065212'><span\r
-style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span\r
-lang=AF>Suppresses all the warnings.</span></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065212'><span\r
-style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span\r
-lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<h2><span style='mso-bookmark:_Toc101065212'><span style='mso-bookmark:_Toc102494358'><span\r
-style='mso-bookmark:_Toc102494743'><a name="_Toc235958517"><span lang=EN-US>Setting\r
-up the T-Coffee environment variables</span></a></span></span></span></h2>\r
-\r
-<p class=MsoBodyText><span style='mso-bookmark:_Toc101065212'><span\r
-style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span\r
-lang=EN-US>T-Coffee can have its own environment file. This environment is kept\r
-in a file named $HOME/.t_coffee/t_coffee_env and can be edited. The value of\r
-any legal variable can be modified through that file. For instance, here is an\r
-example of a configuration file when not requiring a proxy.</span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc101065212'><span\r
-style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span\r
-lang=EN-US>http_proxy_4_TCOFFEE=</span></span></span></span></p>\r
-\r
-<p class=examplefileCxSpLast><span style='mso-bookmark:_Toc101065212'><span\r
-style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span\r
-lang=EN-US>EMAIL_4_TCOFFEE=cedric.notredame@europe.com</span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.5pt;\r
-padding:0mm 0mm 0mm 0mm;background:#F7CBB7'>\r
-\r
-<p class=Warning><span style='mso-bookmark:_Toc101065212'><span\r
-style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span\r
-lang=EN-US>IMPORTANT: </span></span></span></span></p>\r
-\r
-<p class=Warning style='text-align:justify;text-indent:35.4pt;background:#F7CBB7'><span\r
-style='mso-bookmark:_Toc101065212'><span style='mso-bookmark:_Toc102494358'><span\r
-style='mso-bookmark:_Toc102494743'><span lang=EN-US>-proxy, -email &gt;&gt;\r
-t_coffee_env &gt;&gt; env</span></span></span></span></p>\r
-\r
-<p class=Warning style='text-align:justify;background:#F7CBB7'><span\r
-style='mso-bookmark:_Toc101065212'><span style='mso-bookmark:_Toc102494358'><span\r
-style='mso-bookmark:_Toc102494743'><span lang=EN-US><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MsoBodyText><span style='mso-bookmark:_Toc101065212'><span\r
-style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span\r
-lang=EN-US><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<p class=MsoBodyText><span style='mso-bookmark:_Toc101065212'><span\r
-style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span\r
-lang=EN-US><o:p>&nbsp;</o:p></span></span></span></span></p>\r
-\r
-<h2><span style='mso-bookmark:_Toc101065212'><span style='mso-bookmark:_Toc102494358'><span\r
-style='mso-bookmark:_Toc102494743'><a name="_Toc235958518"><span lang=EN-US>Well\r
-Behaved Parameters</span></a></span></span></span></h2>\r
-\r
-<h3><a name="_Toc235958519"></a><a name="_Toc102494744"></a><a\r
-name="_Toc102494359"></a><a name="_Toc101065213"><span style='mso-bookmark:\r
-_Toc102494359'><span style='mso-bookmark:_Toc102494744'><span style='mso-bookmark:\r
-_Toc235958519'><span lang=EN-US>Separation</span></span></span></span></a></h3>\r
-\r
-<p class=MyNormal><span lang=AF>You can use any kind of separator you want\r
-(i.e. ,; &lt;space&gt;=). The syntax used in this document is meant to be\r
-consistent with that of ClustalW. However, in order to take advantage of the\r
-automatic filename compleation provided by many shells, you can replace \93=\94 and\r
-\93,\94 with a space.</span></p>\r
-\r
-<h3><a name="_Toc235958520"></a><a name="_Toc102494745"></a><a\r
-name="_Toc102494360"></a><a name="_Toc101065214"><span style='mso-bookmark:\r
-_Toc102494360'><span style='mso-bookmark:_Toc102494745'><span style='mso-bookmark:\r
-_Toc235958520'><span lang=EN-US>Posix</span></span></span></span></a></h3>\r
-\r
-<p class=MyNormal><span lang=AF>T-Coffee is not POSIX compliant.</span></p>\r
-\r
-<h3><a name="_Toc235958521"></a><a name="_Toc102494746"></a><a\r
-name="_Toc102494361"></a><a name="_Toc101065215"><span style='mso-bookmark:\r
-_Toc102494361'><span style='mso-bookmark:_Toc102494746'><span style='mso-bookmark:\r
-_Toc235958521'><span lang=EN-US>Entering the right parameters</span></span></span></span></a></h3>\r
-\r
-<p class=MyNormal><span lang=AF>There are many ways to enter parameters in\r
-T-Coffee, see the -parameter flag in </span></p>\r
-\r
-<p class=Noteboxtitle><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.5pt;\r
-padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#FFFF89'>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut align=center\r
-style='text-align:center;background:#FFFF89'><span lang=EN-US style='font-size:\r
-20.0pt;mso-bidi-font-size:10.0pt'>Parameters Priority<o:p></o:p></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US>In\r
-general you will not need to use these complicated parameters. Yet, if you find\r
-yourself typing long command lines on a regular basis, it may be worth reading\r
-this section.</span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US>One\r
-may easily feel confused with the various manners in which the parameters can\r
-be passed to t_coffee. The reason for these many mechanisms is that they allow\r
-several levels of intervention. For instance, you may install t_coffee for all\r
-the users and decide that the defaults we provide are not the proper ones\85 In\r
-this case, you will need to make your own t_coffee_default file.</span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US>Later\r
-on, a user may find that he/she needs to keep re-using a specific set of\r
-parameters, different from those in t_coffee_default, hence the possibility to\r
-write an extra parameter file: parameters. In summary:</span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US>-parameters\r
-&gt; prompt parameters &gt; -t_coffee_defaults &gt; -mode</span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US>This\r
-means that -<i>parameters</i> supersede all the others, while parameters\r
-provided via -<i>special mode</i> are the weakest.</span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<h2><a name="_Toc235958522"></a><a name="_Toc102494747"></a><a\r
-name="_Toc102494362"></a><a name="_Toc101065216"><span style='mso-bookmark:\r
-_Toc102494362'><span style='mso-bookmark:_Toc102494747'><span style='mso-bookmark:\r
-_Toc235958522'><span lang=EN-US>Parameters Syntax</span></span></span></span></a></h2>\r
-\r
-<p class=flag><a name="_Toc235958523"></a><a name="_Toc102494748"></a><a\r
-name="_Toc101065218"><span style='mso-bookmark:_Toc102494748'><span\r
-style='mso-bookmark:_Toc235958523'><span lang=AF>No Flag</span></span></span></a></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>If no flag is used<b\r
-style='mso-bidi-font-weight:normal'> </b><i style='mso-bidi-font-style:normal'>&lt;your\r
-sequence&gt; </i>must be the first argument. See format for further\r
-information.</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee sample_seq1.fasta </span></p>\r
-\r
-</div>\r
-\r
-<p class=flagdescription><span lang=EN-US>Which is equivalent to</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee Ssample_seq1.fasta </span></p>\r
-\r
-</div>\r
-\r
-<p class=flagdescription><span lang=EN-US>When you do so, <b style='mso-bidi-font-weight:\r
-normal'>sample_seq1</b> is used as a name prefix for every file the program\r
-outputs.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958524"></a><a name="_Toc102494749"></a><a\r
-name="_Toc101065219"><span style='mso-bookmark:_Toc102494749'><span\r
-style='mso-bookmark:_Toc235958524'><span lang=AF>-parameters</span></span></span></a><span\r
-lang=AF style='background:gray;mso-highlight:gray'><o:p></o:p></span></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--parameters=parameters_file<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: no parameters file</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Indicates a file containing extra parameters.\r
-Parameters read this way behave as if they had been added on the right end of\r
-the command line that they either supersede(one value parameter) or complete\r
-(list of values). For instance, the following file (parameter.file) could be\r
-used </span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span lang=EN-US>*******sample_param_file.param********<span\r
-style='mso-tab-count:1'>   </span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US><span style='mso-tab-count:\r
-1'>      </span>-in=Ssample_seq1.fasta,Mfast_pair</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US><span style='mso-tab-count:\r
-1'>      </span>-output=msf_aln</span></p>\r
-\r
-<p class=examplefileCxSpLast><span lang=EN-US>**************************************</span></p>\r
-\r
-</div>\r
-\r
-<p class=Note><span lang=EN-US style='mso-ansi-language:EN-US'>Note: This is\r
-one of the exceptions (with \96infile) where the identifier tag (S,A,L,M\85) can be\r
-omitted. Any dataset provided this way will be assumed to be a sequence (S).\r
-These exceptions have been designed to keep the program compatible with\r
-ClustalW.<o:p></o:p></span></p>\r
-\r
-<p class=Note><span lang=EN-US style='mso-ansi-language:EN-US'>Note: This\r
-parameter file can ONLY contain valid parameters. Comments are not allowed.\r
-Parameters passed this way will be checked like normal parameters.<o:p></o:p></span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Used with:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee -parameters=sample_param_file.param</span></p>\r
-\r
-</div>\r
-\r
-<p class=flagdescription><span lang=EN-US>Will cause t_coffee to apply the\r
-fast_pair method onto to the sequences contained in sample_seq.fasta. If you\r
-wish, you can also pipe these arguments into t_coffee, by naming the parameter\r
-file &quot;stdin&quot; (as a rule, any file named stdin is expected to receive\r
-its content via the stdin)</span></p>\r
-\r
-<p class=example2><span lang=EN-US>cat sample_param_file.param<span\r
-style='mso-spacerun:yes'>  </span>| t_coffee -parameters=stdin <a\r
-name="_Toc101065220"></a></span></p>\r
-\r
-<p class=flag><span style='mso-bookmark:_Toc101065220'><a name="_Toc235958525"></a><a\r
-name="_Toc102494750"><span style='mso-bookmark:_Toc235958525'><span lang=AF>-t_coffee_defaults</span></span></a></span></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--t_coffee_defaults=&lt;file_name&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: not used.</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>This flag tells the program to use\r
-some default parameter file for t_coffee. The format of that file is the same\r
-as the one used with -parameters. The file used is either:</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'>            </span>1.\r
-&lt;file name&gt; if a name has been specified</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'>            </span>2.<span\r
-style='mso-spacerun:yes'>  </span><b>~/.t_coffee_defaults </b>if no file was\r
-specified</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'>            </span>3.\r
-The file indicated by the environment variable <b>TCOFFEE_DEFAULTS</b></span></p>\r
-\r
-<p class=flag><a name="_Toc235958526"><span lang=AF>-mode</span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage: -mode=\r
-hard coded mode<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: not used.</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>It indicates that t_coffee will use\r
-some hard coded parameters. These include:</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'>            </span><b\r
-style='mso-bidi-font-weight:normal'>quickaln</b>: very fast approximate\r
-alignment</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'>            </span><b\r
-style='mso-bidi-font-weight:normal'>dali</b>: a mode used to combine dali\r
-pairwise alignments</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'>            </span><b\r
-style='mso-bidi-font-weight:normal'>evaluate</b>: defaults for evaluating an\r
-alignment</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'>            </span><b\r
-style='mso-bidi-font-weight:normal'>3dcoffee</b>: runs t_coffee with the\r
-3dcoffee parameterization</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Other modes exist that are not yet\r
-fully supported<span style='mso-tab-count:1'> </span></span></p>\r
-\r
-<p class=flag><a name="_Toc235958527"></a><a name="_Toc102494752"></a><a\r
-name="_Toc101065222"><span style='mso-bookmark:_Toc102494752'><span\r
-style='mso-bookmark:_Toc235958527'><span lang=AF>-score</span></span></span></a><span\r
-style='mso-bookmark:_Toc102494752'><span style='mso-bookmark:_Toc235958527'><span\r
-lang=AF> [Deprecated]</span></span></span></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--score<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: not used</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Toggles on the evaluate mode and\r
-causes t_coffee to evaluates a precomputed alignment provided via <b>-infile=&lt;alignment&gt;</b>.\r
-The flag <b>-output</b> must be set to an appropriate format (i.e.\r
--output=score_ascii, score_html or score_pdf). A better default parameterization\r
-is obtained when using the flag <b>-mode=evaluate.</b></span></p>\r
-\r
-<p class=flag><a name="_Toc235958528"></a><a name="_Toc102494753"><span\r
-style='mso-bookmark:_Toc235958528'><span lang=AF>-evaluate</span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--evaluate<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: not used</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Replaces \96score. This flag toggles on\r
-the evaluate mode and causes t_coffee to evaluates a pre-computed alignment\r
-provided via <b>-infile=&lt;alignment&gt;</b>. The flag <b>-output</b> must be\r
-set to an appropriate format (i.e. -output=score_ascii, score_html or\r
-score_pdf). </span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>The main purpose of \96evaluate is to\r
-let you control every aspect of the evaluation. Yet it is advisable to use\r
-pre-defined parameterization: <b>mode=evaluate.</b></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee \96infile=sample_aln1.aln -mode=evaluate </span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee \96infile=sample_seq1.aln \96in<span style='mso-spacerun:yes'> \r
-</span>Lsample_lib1.tc_lib \96mode=evaluate </span></p>\r
-\r
-</div>\r
-\r
-<p class=flag><a name="_Toc235958529"></a><a name="_Toc102494754"></a><a\r
-name="_Toc101065223"><span style='mso-bookmark:_Toc102494754'><span\r
-style='mso-bookmark:_Toc235958529'><span lang=AF>-convert [cw]</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--convert<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: turned off</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Toggles on the conversion mode and\r
-causes T-Coffee to convert the sequences, alignments, libraries or structures\r
-provided via the <b>-infile</b> and <b>-in</b> flags. The output format must be\r
-set via the <b>-output</b> flag. This flag can also be used if you simply want\r
-to compute a library (i.e. you have an alignment and you want to turn it into a\r
-library).</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>This flag is ClustalW compliant.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958530"></a><a name="_Toc102494755"></a><a\r
-name="_Toc101065224"><span style='mso-bookmark:_Toc102494755'><span\r
-style='mso-bookmark:_Toc235958530'><span lang=AF>-do_align [cw]</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-do_align<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: turned on</span></p>\r
-\r
-<h2><a name="_Toc235958531"></a><a name="_Toc102494756"></a><a\r
-name="_Toc102494363"></a><a name="_Toc101065225"><span style='mso-bookmark:\r
-_Toc102494363'><span style='mso-bookmark:_Toc102494756'><span style='mso-bookmark:\r
-_Toc235958531'><span lang=EN-US>Special Parameters</span></span></span></span></a></h2>\r
-\r
-<p class=flag><a name="_Toc235958532"></a><a name="_Toc102494757"></a><a\r
-name="_Toc101065226"><span style='mso-bookmark:_Toc102494757'><span\r
-style='mso-bookmark:_Toc235958532'><span lang=AF>-version</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--version<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: not used</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Returns the current version number</span></p>\r
-\r
-<p class=flag><a name="_Toc102494758"></a><a name="_Toc101065227"></a><a\r
-name="_Toc235958533"><span style='mso-bookmark:_Toc101065227'><span\r
-style='mso-bookmark:_Toc102494758'><span lang=AF>-proxy</span></span></span></a><span\r
-style='mso-bookmark:_Toc101065227'><span style='mso-bookmark:_Toc102494758'></span></span></p>\r
-\r
-<p class=flagusage><span style='mso-bookmark:_Toc101065227'><span\r
-style='mso-bookmark:_Toc102494758'><span lang=EN-US style='mso-ansi-language:\r
-EN-US'>Usage: -proxy=&lt;proxy&gt;<o:p></o:p></span></span></span></p>\r
-\r
-<p class=instruction><span style='mso-bookmark:_Toc101065227'><span\r
-style='mso-bookmark:_Toc102494758'><span lang=EN-US>Default: not used</span></span></span></p>\r
-\r
-<p class=flagdescription><span style='mso-bookmark:_Toc101065227'><span\r
-style='mso-bookmark:_Toc102494758'><span lang=EN-US>Sets the proxy used by\r
-HTTP_proxy AND http_proxy. Setting with the propmpt supersedes ANY other\r
-setting.</span></span></span></p>\r
-\r
-<p class=flagdescription><span style='mso-bookmark:_Toc101065227'><span\r
-style='mso-bookmark:_Toc102494758'><span lang=EN-US>Note that if you use no\r
-proxy, you should set</span></span></span></p>\r
-\r
-<p class=flagdescription><span style='mso-bookmark:_Toc101065227'><span\r
-style='mso-bookmark:_Toc102494758'><span lang=EN-US><span style='mso-tab-count:\r
-1'>            </span>-proxy</span></span></span></p>\r
-\r
-<p class=flag><span style='mso-bookmark:_Toc101065227'><span style='mso-bookmark:\r
-_Toc102494758'><a name="_Toc235958534"><span lang=AF>-email</span></a></span></span></p>\r
-\r
-<p class=flagusage><span style='mso-bookmark:_Toc101065227'><span\r
-style='mso-bookmark:_Toc102494758'><span lang=EN-US style='mso-ansi-language:\r
-EN-US'>Usage: -email=&lt;email&gt;<o:p></o:p></span></span></span></p>\r
-\r
-<p class=instruction><span style='mso-bookmark:_Toc101065227'><span\r
-style='mso-bookmark:_Toc102494758'><span lang=EN-US>Default: not used</span></span></span></p>\r
-\r
-<p class=flagdescription><span style='mso-bookmark:_Toc101065227'><span\r
-style='mso-bookmark:_Toc102494758'><span lang=EN-US>Sets your email value as\r
-provided to web services</span></span></span></p>\r
-\r
-<p class=flag><span style='mso-bookmark:_Toc101065227'><span style='mso-bookmark:\r
-_Toc102494758'><a name="_Toc235958535"><span lang=AF>-check_configuration</span></a></span></span></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--check_configuration<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: not used</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Checks your system to determine\r
-whether all the programs T-Coffee can interact with are installed.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958536"></a><a name="_Toc102494759"></a><a\r
-name="_Toc101065228"><span style='mso-bookmark:_Toc102494759'><span\r
-style='mso-bookmark:_Toc235958536'><span lang=AF>-cache</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--cache=&lt;use, update, ignore, &lt;filename&gt;&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -cache=use</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>By default, t_coffee stores in a\r
-cache directory, the results of computationally expensive (structural\r
-alignment) or network intensive (BLAST search) operations.<a\r
-name="_Toc101065229"></a></span></p>\r
-\r
-<p class=flag><span style='mso-bookmark:_Toc101065229'><a name="_Toc235958537"></a><a\r
-name="_Toc102494760"><span style='mso-bookmark:_Toc235958537'><span lang=AF>-update</span></span></a></span></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--update<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: turned off</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Causes a <span\r
-class=StyleflagdescriptionBoldItalicChar>wget</span> access that checks whether\r
-the t_coffee version you are using needs updating.<a name="_Toc101065230"></a></span></p>\r
-\r
-<p class=flag><span style='mso-bookmark:_Toc101065230'><a name="_Toc235958538"></a><a\r
-name="_Toc102494761"><span style='mso-bookmark:_Toc235958538'><span lang=AF>-full_log</span></span></a></span></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--full_log=&lt;filename&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: turned off</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Causes t_coffee to output a full log\r
-file that contains all the input/output files.<a name="_Toc101065231"></a></span></p>\r
-\r
-<p class=flag><span style='mso-bookmark:_Toc101065231'><a name="_Toc235958539"></a><a\r
-name="_Toc102494762"><span style='mso-bookmark:_Toc235958539'><span lang=AF>-plugins</span></span></a></span></p>\r
-\r
-<p class=flagusage><span style='mso-bookmark:_Toc101065231'><span\r
-style='mso-bookmark:_Toc102494762'><span style='mso-bookmark:_Toc235958539'><span\r
-lang=EN-US style='mso-ansi-language:EN-US'>Usage: -plugins=&lt;dir&gt;<o:p></o:p></span></span></span></span></p>\r
-\r
-<p class=instruction><span style='mso-bookmark:_Toc101065231'><span\r
-style='mso-bookmark:_Toc102494762'><span style='mso-bookmark:_Toc235958539'><span\r
-lang=EN-US>Default: default</span></span></span></span></p>\r
-\r
-<p class=flagdescription><span style='mso-bookmark:_Toc101065231'><span\r
-style='mso-bookmark:_Toc102494762'><span style='mso-bookmark:_Toc235958539'><span\r
-lang=EN-US>Specifies the directory in which the companion packages (other\r
-multiple aligners used by M-Coffee, structural aligners, etc\85) are kept as an\r
-alternative, you can also set the environment variable PLUGINS_4_TCOFFEE</span></span></span></span></p>\r
-\r
-<p class=flagdescription><span style='mso-bookmark:_Toc101065231'><span\r
-style='mso-bookmark:_Toc102494762'><span style='mso-bookmark:_Toc235958539'><span\r
-lang=EN-US>The default is ~/.t_coffee/plugins/</span></span></span></span></p>\r
-\r
-<p class=flag><span style='mso-bookmark:_Toc101065231'><span style='mso-bookmark:\r
-_Toc102494762'><span style='mso-bookmark:_Toc235958539'><span lang=AF>-other_pg</span></span></span></span></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--other_pg=&lt;filename&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: turned off</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Some rumours claim that Tetris is\r
-embedded within T-Coffee and could be ran using some special set of commands.\r
-We wish to deny these rumours, although we may admit that several interesting\r
-reformatting programs are now embedded in t_coffee and can be ran through the\r
-\96other_pg flag.</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee \96other_pg=seq_reformat </span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee \96other_pg=unpack_all </span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee \96other_pg=unpack_extract_from_pdb </span></p>\r
-\r
-</div>\r
-\r
-<h2><a name="_Toc235958540"></a><a name="_Toc102494763"></a><a\r
-name="_Toc102494364"></a><a name="_Toc101065232"><span style='mso-bookmark:\r
-_Toc102494364'><span style='mso-bookmark:_Toc102494763'><span style='mso-bookmark:\r
-_Toc235958540'><span lang=EN-US>Input</span></span></span></span></a><span\r
-lang=EN-US> </span></h2>\r
-\r
-<h3><a name="_Toc235958541"></a><a name="_Toc102494764"></a><a\r
-name="_Toc102494365"></a><a name="_Toc101065233"><span style='mso-bookmark:\r
-_Toc102494365'><span style='mso-bookmark:_Toc102494764'><span style='mso-bookmark:\r
-_Toc235958541'><span lang=EN-US>Sequence Input</span></span></span></span></a></h3>\r
-\r
-<p class=flag><a name="_Toc235958542"></a><a name="_Toc102494765"></a><a\r
-name="_Toc101065234"><span style='mso-bookmark:_Toc102494765'><span\r
-style='mso-bookmark:_Toc235958542'><span lang=AF>-infile [cw]</span></span></span></a></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>To remain compatible with ClustalW,\r
-it is possible to indicate the sequences with this flag</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee -infile=sample_seq1.fasta </span></p>\r
-\r
-</div>\r
-\r
-<p class=Note><span lang=EN-US style='mso-ansi-language:EN-US'>Note: Common\r
-multiple sequence alignments format constitute a valid input format.<o:p></o:p></span></p>\r
-\r
-<p class=Note><span lang=EN-US style='mso-ansi-language:EN-US'>Note: T-Coffee\r
-automatically removes the gaps </span><i><span lang=EN-US style='mso-ansi-language:\r
-EN-US;mso-bidi-font-weight:bold'>before</span></i><span lang=EN-US\r
-style='mso-ansi-language:EN-US'> doing the alignment. This behaviour is different\r
-from that of ClustalW where the gaps are kept.<o:p></o:p></span></p>\r
-\r
-<p class=flag><a name="_Toc235958543"></a><a name="_Toc102494766"></a><a\r
-name="_Toc101065235"><span style='mso-bookmark:_Toc102494766'><span\r
-style='mso-bookmark:_Toc235958543'><span lang=AF>-in</span></span></span></a><span\r
-style='mso-bookmark:_Toc102494766'><span style='mso-bookmark:_Toc235958543'><span\r
-lang=AF> (Cf \96in from the Method and Library Input section)</span></span></span></p>\r
-\r
-<p class=flag><a name="_Toc235958544"></a><a name="_Toc102494767"></a><a\r
-name="_Toc101065236"><span style='mso-bookmark:_Toc102494767'><span\r
-style='mso-bookmark:_Toc235958544'><span lang=AF>-get_type</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--get_type<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: turned off</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Forces t_coffee to identify the\r
-sequences type (PROTEIN, DNA).</span></p>\r
-\r
-<p class=flag><a name="_Toc235958545"></a><a name="_Toc102494768"></a><a\r
-name="_Toc101065237"><span style='mso-bookmark:_Toc102494768'><span\r
-style='mso-bookmark:_Toc235958545'><span lang=AF>-type [cw]</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--type=DNA ¦ PROTEIN¦ DNA_PROTEIN<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -type=&lt;automatically set&gt;</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>This flag sets the type of the\r
-sequences. If omitted, the type is guessed automatically. This flag is\r
-compatible with ClustalW.</span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.5pt;\r
-padding:0mm 0mm 0mm 0mm;background:#F7CBB7'>\r
-\r
-<p class=Warning><span lang=EN-US>Warning:<span style='mso-spacerun:yes'> \r
-</span>In case of low complexity or short sequences, it is recommended to set\r
-the type manually.<a name="_Toc101065238"></a></span></p>\r
-\r
-</div>\r
-\r
-<p class=flag><span style='mso-bookmark:_Toc101065238'><a name="_Toc235958546"></a><a\r
-name="_Toc102494769"><span style='mso-bookmark:_Toc235958546'><span lang=AF>-seq</span></span></a></span></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--seq=[&lt;P,S&gt;&lt;name&gt;,]<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: none</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>-seq is now the recommended flag to provide\r
-your sequences. It behaves mostly like the -in flag.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958547"></a><a name="_Toc102494770"></a><a\r
-name="_Toc101065239"><span style='mso-bookmark:_Toc102494770'><span\r
-style='mso-bookmark:_Toc235958547'><span lang=AF>-seq_source</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--seq_source=&lt;ANY or<span style='mso-spacerun:yes'>  </span>_LS or LS &gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: ANY.</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>You may not want to combine all the\r
-provided sequences into a single sequence list. You can do by specifying that\r
-you do not want to treat all the \96in files as potential sequence sources.</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>-seq_source=_LA indicates that\r
-neither sequences provided via the A (Alignment) flag or via the L (Library\r
-flag) should be added to the sequence list.</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>-seq_source=S means that only\r
-sequences provided via the S tag will be considered. All the other sequences\r
-will be ignored.</span></p>\r
-\r
-<p class=Note><span lang=EN-US style='mso-ansi-language:EN-US'>Note:<span\r
-style='mso-spacerun:yes'>  </span>This flag is mostly designed for interactions\r
-between T-Coffee and T-CoffeeDPA (the large scale version of T-Coffee).</span><span\r
-lang=EN-US style='mso-ansi-language:EN-US;mso-bidi-font-weight:bold'><o:p></o:p></span></p>\r
-\r
-<h3><a name="_Toc235958548"></a><a name="_Toc102494771"></a><a\r
-name="_Toc102494366"></a><a name="_Toc101065241"><span style='mso-bookmark:\r
-_Toc102494366'><span style='mso-bookmark:_Toc102494771'><span style='mso-bookmark:\r
-_Toc235958548'><span lang=EN-US>Structure Input</span></span></span></span></a></h3>\r
-\r
-<p class=flag><a name="_Toc235958549"></a><a name="_Toc102494772"></a><a\r
-name="_Toc101065242"><span style='mso-bookmark:_Toc102494772'><span\r
-style='mso-bookmark:_Toc235958549'><span lang=AF>-pdb</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-pdb=&lt;pdbid1&gt;,&lt;pdbid2&gt;\85[Max 200]<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: None</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Reads or fetch a pdb file. It is\r
-possible to specify a chain or even a sub-chain:</span></p>\r
-\r
-<p class=example2><span lang=EN-US>PDBID(PDB_CHAIN)[opt] (FIRST,LAST)[opt]<a\r
-name="_Toc101065243"></a></span></p>\r
-\r
-<p class=flagdescription><span style='mso-bookmark:_Toc101065243'><span\r
-lang=EN-US>It is also possible to input structures via the \96in flag. In that\r
-case, you will need to use the TAG identifier:</span></span></p>\r
-\r
-<p class=example2><span style='mso-bookmark:_Toc101065243'><span lang=EN-US>-in\r
-Ppdb1 Ppdb2\85 </span></span></p>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065243'><a name="_Toc235958550"></a><a\r
-name="_Toc102494773"></a><a name="_Toc102494367"><span style='mso-bookmark:\r
-_Toc102494773'><span style='mso-bookmark:_Toc235958550'><span lang=EN-US>Tree\r
-Input</span></span></span></a></span></h3>\r
-\r
-<p class=flag><a name="_Toc235958551"></a><a name="_Toc102494774"></a><a\r
-name="_Toc101065244"><span style='mso-bookmark:_Toc102494774'><span\r
-style='mso-bookmark:_Toc235958551'><span lang=AF>-usetree</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--usetree=&lt;tree file&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: No file specified</span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Format: newick tree format (ClustalW\r
-Style)</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>This flag indicates that rather than\r
-computing a new dendrogram, t_coffee must use a pre-computed one. The tree\r
-files are in phylips format and compatible with ClustalW. In most cases, using\r
-a pre-computed tree will halve the computation time required by t_coffee. It is\r
-also possible to use trees output by ClustalW, Phylips and any other program.</span></p>\r
-\r
-<h3><a name="_Toc235958552"></a><a name="_Toc102494775"></a><a\r
-name="_Toc102494368"></a><a name="_Toc101065245"><span style='mso-bookmark:\r
-_Toc102494368'><span style='mso-bookmark:_Toc102494775'><span style='mso-bookmark:\r
-_Toc235958552'><span lang=EN-US>Structures, Sequences Methods and Library Input</span></span></span></span></a><span\r
-style='mso-bookmark:_Toc235958552'><span lang=EN-US> via the </span></span><span\r
-style='mso-bookmark:_Toc235958552'><span lang=EN-US style='font-family:Symbol;\r
-mso-ascii-font-family:"Arial Black"'>&#150;</span><span lang=EN-US>in Flag</span></span></h3>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.5pt;\r
-padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#FFFF89'>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut align=center\r
-style='text-align:center;background:#FFFF89'><a name="_Toc101065246"><span\r
-lang=EN-US style='font-size:20.0pt;mso-bidi-font-size:10.0pt'>The -in Flag and\r
-its Identifier TAGS<o:p></o:p></span></a></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span\r
-style='mso-bookmark:_Toc101065246'><span lang=EN-US><o:p>&nbsp;</o:p></span></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span\r
-style='mso-bookmark:_Toc101065246'><span lang=EN-US>&lt;-in&gt; is the real\r
-grinder of T-Coffee. Sequences, methods and alignments all pass through so that\r
-T-Coffee can turn it all into a single list of constraints (the library).\r
-Everything is done automatically with T-Coffee going through each file to\r
-extract the sequences it contains. The methods are then applied to the\r
-sequences. Pre-compiled constraint list can also be provided. Each file\r
-provided via this flag must be preceded with a symbol (Identifier TAG) that\r
-indicates its nature to T-Coffee. The TAGs currently supported are the\r
-following:</span></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span\r
-style='mso-bookmark:_Toc101065246'><span lang=EN-US><o:p>&nbsp;</o:p></span></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span\r
-style='mso-bookmark:_Toc101065246'><span lang=EN-US>P<span style='mso-tab-count:\r
-1'>         </span>PDB structure</span></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span\r
-style='mso-bookmark:_Toc101065246'><span lang=EN-US>S <span style='mso-tab-count:\r
-1'>         </span>for sequences (use it as well to treat an MSA as unaligned\r
-sequences)</span></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span\r
-style='mso-bookmark:_Toc101065246'><span lang=EN-US><o:p>&nbsp;</o:p></span></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span\r
-style='mso-bookmark:_Toc101065246'><span lang=EN-US>M <span style='mso-tab-count:\r
-1'>       </span>Methods used to build the library</span></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span\r
-style='mso-bookmark:_Toc101065246'><span lang=EN-US>L <span style='mso-tab-count:\r
-1'>        </span>Pre-computed T-Coffee library</span></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span\r
-style='mso-bookmark:_Toc101065246'><span lang=EN-US>A <span style='mso-tab-count:\r
-1'>        </span>Multiple Alignments that must be turned into a Library</span></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span\r
-style='mso-bookmark:_Toc101065246'><span lang=EN-US><o:p>&nbsp;</o:p></span></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span\r
-style='mso-bookmark:_Toc101065246'><span lang=EN-US>X <span style='mso-tab-count:\r
-1'>        </span>Substitution matrices.</span></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:\r
-35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:\r
-_Toc101065246'><span lang=EN-US>R <span style='mso-tab-count:1'>        </span><span\r
-style='mso-tab-count:1'>            </span>Profiles. This is a legal multiple\r
-alignments that will be treated as single sequences (the sequences it contains\r
-will not be realigned). </span></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:\r
-35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:\r
-_Toc101065246'><span lang=EN-US><o:p>&nbsp;</o:p></span></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:\r
-35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:\r
-_Toc101065246'><span lang=EN-US>If you do not want to use the TAGS, you will\r
-need to use the following flags in replacement of -in. Do not use the TAGS when\r
-using these flags:</span></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:\r
-35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:\r
-_Toc101065246'><span lang=EN-US><o:p>&nbsp;</o:p></span></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:\r
-35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:\r
-_Toc101065246'><span lang=EN-US>-aln <span style='mso-tab-count:3'>                            </span>Alignments\r
-<span style='mso-tab-count:1'>   </span>(A)</span></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:\r
-35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:\r
-_Toc101065246'><span lang=EN-US>-profile<span style='mso-tab-count:1'>           </span>Profiles\r
-<span style='mso-tab-count:1'>          </span>(R)</span></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:\r
-35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:\r
-_Toc101065246'><span lang=EN-US>-method<span style='mso-tab-count:1'>          </span>Method\r
-<span style='mso-tab-count:1'>         </span>(M)</span></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:\r
-35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:\r
-_Toc101065246'><span lang=EN-US>-seq<span style='mso-tab-count:3'>                             </span>Sequences\r
-<span style='mso-tab-count:1'>     </span>(S)</span></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:\r
-35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:\r
-_Toc101065246'><span lang=EN-US>-lib<span style='mso-tab-count:3'>                              </span>Libraries<span\r
-style='mso-tab-count:1'>        </span>(L)<a name="_Toc102494776"></a></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=flag><span style='mso-bookmark:_Toc101065246'><span style='mso-bookmark:\r
-_Toc102494776'><a name="_Toc235958553"><span lang=AF>-in</span></a></span></span></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--in=[&lt;P,S,A,L,M,X&gt;&lt;name&gt;,]<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default:\r
--in=Mlalign_id_pair,Mclustalw_pair</span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.5pt;\r
-padding:0mm 0mm 0mm 0mm;background:#F7CBB7'>\r
-\r
-<p class=Warning><span lang=EN-US>Note: -in can be replaced with the combined\r
-usage of -aln, iprofile, .pdb, .lib, -method.</span></p>\r
-\r
-</div>\r
-\r
-<p class=flagdescription><span lang=EN-US>See the box for an explanation of the\r
--in flag. The following argument passed via -in</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee\r
--in=Ssample_seq1.fasta,Asample_aln1.aln,Asample_aln2.msf,Mlalign_id_pair,Lsample_lib1.tc_lib\r
-\96outfile=outaln</span></p>\r
-\r
-</div>\r
-\r
-<p class=flagdescription><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>This command will trigger the following\r
-chain of events:</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>1-Gather all the sequences</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Sequences within all the provided\r
-files are pooled together. Format recognition is automatic. Duplicates are\r
-removed (if they have the same name). Duplicates in a single file are only\r
-tolerated in FASTA format file, although they will cause sequences to be\r
-renamed.</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>In the above case, the total set of\r
-sequences will be made of sequences contained in sequences1.seq,\r
-alignment1.aln, alignment2.msf and library.lib, plus the sequences initially\r
-gathered<span style='mso-spacerun:yes'>  </span>by -infile.</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>2-Turn alignments into libraries</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>alignment1.aln and alignment2.msf\r
-will be read and turned into libraries. Another library will be produced by\r
-applying the method lalign_id_pair to the set of sequences previously obtained\r
-(1). The final library used for the alignment will be the combination of all\r
-this information. </span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Note as well the following rules: </span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=flagdescription><b style='mso-bidi-font-weight:normal'><span\r
-lang=EN-US>1-Order</span></b><span lang=EN-US style='mso-bidi-font-weight:bold'>:</span><span\r
-lang=EN-US> The order in which sequences, methods, alignments and libraries are\r
-fed in is irrelevant.</span></p>\r
-\r
-<p class=flagdescription><b style='mso-bidi-font-weight:normal'><span\r
-lang=EN-US>2-Heterogeneity</span></b><span lang=EN-US style='mso-bidi-font-weight:\r
-bold'>:</span><span lang=EN-US> There is no need for each element (A, S, L) to\r
-contain the same sequences.</span></p>\r
-\r
-<p class=flagdescription><b style='mso-bidi-font-weight:normal'><span\r
-lang=EN-US>3-No Duplicate</span></b><span lang=EN-US style='mso-bidi-font-weight:\r
-bold'>:</span><span lang=EN-US> Each file should contain only one copy of each\r
-sequence. Duplicates are only allowed in FASTA files but will cause the\r
-sequences to be renamed.</span></p>\r
-\r
-<p class=flagdescription><b style='mso-bidi-font-weight:normal'><span\r
-lang=EN-US>4-Reconciliation</span></b><span lang=EN-US style='mso-bidi-font-weight:\r
-bold'>:</span><span lang=EN-US> If two files (for instance two alignments)\r
-contain different versions of the same sequence due to an indel, a new sequence\r
-will be reconstructed and used instead:</span></p>\r
-\r
-<p class=example2CxSpFirst><span lang=EN-US>aln 1:hgab1 <span style='mso-tab-count:\r
-1'>  </span>AAAAABAAAAA</span></p>\r
-\r
-<p class=example2CxSpLast><span lang=EN-US>aln 2:hgab1<span style='mso-tab-count:\r
-1'>   </span>AAAAAAAAAACCC</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>will cause the program to reconstruct\r
-and use the following sequence </span></p>\r
-\r
-<p class=example2><span lang=EN-US>hgab1<span style='mso-tab-count:1'>   </span>AAAAABAAAAACCC\r
-</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>This can be useful if you are trying\r
-to combine several runs of blast, or structural information where residues may\r
-have been deleted. However substitutions are forbidden. If two sequences with\r
-the same name cannot be merged, they will cause the program to exit with an\r
-information message.</span></p>\r
-\r
-<p class=flagdescription><b style='mso-bidi-font-weight:normal'><span\r
-lang=EN-US>5-Methods</span></b><span lang=EN-US style='mso-bidi-font-weight:\r
-bold'>:</span><span lang=EN-US> The method describer can either be built in\r
-(See ### for a list of all the available methods) or be a file describing the\r
-method to be used. The exact syntax is provided in part 4 of this manual.</span></p>\r
-\r
-<p class=flagdescription><b style='mso-bidi-font-weight:normal'><span\r
-lang=EN-US>6-Substitution Matrices</span></b><span lang=EN-US style='mso-bidi-font-weight:\r
-bold'>: </span><span lang=EN-US>If the method is a substitution matrix (X) then\r
-no other type of information should be provided. For instance:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee sample_seq1.fasta -in=Xpam250mt<span style='mso-spacerun:yes'> \r
-</span>-gapopen=-10<span style='mso-spacerun:yes'>  </span>-gapext=-1 </span></p>\r
-\r
-</div>\r
-\r
-<p class=flagdescription><span lang=EN-US>This command results in a progressive\r
-alignment carried out on the sequences in seqfile. The procedure does not use\r
-any more the T-Coffee concistency based algorithm, but switches to a standard\r
-progressive alignment algorithm (like ClustalW or Pileup) much less accurate.\r
-In this context, appropriate gap penalties should be provided. The matrices are\r
-in the file source/matrices.h. Add-Hoc matrices can also be provided by the\r
-user (see the matrices format section at the end of this manual).</span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.5pt;\r
-padding:0mm 0mm 0mm 0mm;background:#F7CBB7'>\r
-\r
-<p class=Warning><span lang=EN-US>Warning: Xmatrix does not have the same\r
-effect as using the -matrix flag.<span style='mso-spacerun:yes'>  </span>The\r
--matrix defines the matrix that will be used while compiling the library while\r
-the Xmatrix defines the matrix used when assembling the final alignment.</span></p>\r
-\r
-</div>\r
-\r
-<h3><a name="_Toc235958554"></a><a name="_Toc102494777"></a><a\r
-name="_Toc102494369"></a><a name="_Toc101065247"><span style='mso-bookmark:\r
-_Toc102494369'><span style='mso-bookmark:_Toc102494777'><span style='mso-bookmark:\r
-_Toc235958554'><span lang=EN-US>Profile Input</span></span></span></span></a></h3>\r
-\r
-<p class=flag><a name="_Toc235958555"></a><a name="_Toc102494778"></a><a\r
-name="_Toc101065248"><span style='mso-bookmark:_Toc102494778'><span\r
-style='mso-bookmark:_Toc235958555'><span lang=AF>-profile</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--profile=[&lt;name&gt;,] maximum of 200 profiles.<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: no default</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>This flag causes T-Coffee to treat\r
-multiple alignments as a single sequences, thus making it possible to make\r
-multiple profile alignments. The profile-profile alignment is controlled by <span\r
-style='mso-bidi-font-weight:bold'>-profile_mode</span> and <span\r
-style='mso-bidi-font-weight:bold'>-profile_comparison</span>. When provided\r
-with the <b style='mso-bidi-font-weight:normal'>-in</b> flag, profiles must be\r
-preceded with the letter R.</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee \96profile sample_aln1.aln,sample_aln2.aln \96outfile=profile_aln</span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee \96in Rsample_aln1.aln,Rsample_aln2.aln,Mslow_pair,Mlalign_id_pair\r
-\96outfile=profile_aln</span></p>\r
-\r
-</div>\r
-\r
-<p class=flagdescription><span lang=EN-US>Note that when using \96template_file,\r
-the program will also look for the templates associated with the profiles, even\r
-if the profiles have been provided as templates themselves (however it will not\r
-look for the template of the profile templates of the profile templates\85)</span></p>\r
-\r
-<p class=flag><a name="_Toc235958556"></a><a name="_Toc102494779"></a><a\r
-name="_Toc101065249"><span style='mso-bookmark:_Toc102494779'><span\r
-style='mso-bookmark:_Toc235958556'><span lang=AF>-profile1 [cw]</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--profile1=[&lt;name&gt;], one name only<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: no default</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Similar to the previous one and was\r
-provided for compatibility with ClustalW.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958557"></a><a name="_Toc102494780"></a><a\r
-name="_Toc101065250"><span style='mso-bookmark:_Toc102494780'><span\r
-style='mso-bookmark:_Toc235958557'><span lang=AF>-profile2 [cw]</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--profile1=[&lt;name&gt;], one name only<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: no default</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Similar to the previous one and was\r
-provided for compatibility with ClustalW.</span></p>\r
-\r
-<h2><a name="_Toc235958558"></a><a name="_Toc102494781"></a><a\r
-name="_Toc102494370"></a><a name="_Toc101065251"><span style='mso-bookmark:\r
-_Toc102494370'><span style='mso-bookmark:_Toc102494781'><span style='mso-bookmark:\r
-_Toc235958558'><span lang=EN-US>Alignment Computation</span></span></span></span></a></h2>\r
-\r
-<h3><a name="_Toc235958559"></a><a name="_Toc102494782"></a><a\r
-name="_Toc102494371"></a><a name="_Toc101065252"><span style='mso-bookmark:\r
-_Toc102494371'><span style='mso-bookmark:_Toc102494782'><span style='mso-bookmark:\r
-_Toc235958559'><span lang=EN-US>Library Computation: Methods</span></span></span></span></a></h3>\r
-\r
-<p class=flag><a name="_Toc235958560"></a><a name="_Toc102494783"><span\r
-style='mso-bookmark:_Toc235958560'><span lang=AF>-lalign_n_top</span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--lalign_n_top=&lt;Integer&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -lalign_n_top=10</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Number of alignment reported by the\r
-local method (lalign).</span></p>\r
-\r
-<p class=flag><a name="_Toc235958561"></a><a name="_Toc102494784"><span\r
-style='mso-bookmark:_Toc235958561'><span lang=AF>-align_pdb_param_file</span></span></a></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Unsuported</span></p>\r
-\r
-<p class=flag><a name="_Toc235958562"></a><a name="_Toc102494785"><span\r
-style='mso-bookmark:_Toc235958562'><span lang=AF>-align_pdb_hasch_mode</span></span></a></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Unsuported<a name="_Toc101065253"></a></span></p>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065253'><a name="_Toc235958563"></a><a\r
-name="_Toc102494786"></a><a name="_Toc102494372"><span style='mso-bookmark:\r
-_Toc102494786'><span style='mso-bookmark:_Toc235958563'><span lang=EN-US>Library\r
-Computation: Extension</span></span></span></a></span></h3>\r
-\r
-<p class=flag><a name="_Toc101065255"></a><a name="_Toc235958564"></a><a\r
-name="_Toc102494787"></a><a name="_Toc101065254"><span style='mso-bookmark:\r
-_Toc102494787'><span style='mso-bookmark:_Toc235958564'><span style='mso-bookmark:\r
-_Toc101065255'><span lang=AF>-</span></span></span></span></a><span\r
-style='mso-bookmark:_Toc102494787'><span style='mso-bookmark:_Toc235958564'><span\r
-style='mso-bookmark:_Toc101065255'><span lang=AF>lib_list [Unsupported]</span></span></span></span><span\r
-style='mso-bookmark:_Toc101065255'></span></p>\r
-\r
-<p class=flagusage><span style='mso-bookmark:_Toc101065255'><span lang=EN-US\r
-style='mso-ansi-language:EN-US'>Usage:<span style='mso-spacerun:yes'> \r
-</span>-lib_list=&lt;filename&gt; <o:p></o:p></span></span></p>\r
-\r
-<p class=instruction><span style='mso-bookmark:_Toc101065255'><span lang=EN-US>Default:unset</span></span></p>\r
-\r
-<p class=flagdescription><span style='mso-bookmark:_Toc101065255'><span\r
-lang=EN-US>Use this flag if you do not want the library computation to take\r
-into account all the possible pairs in your dataset. For instance</span></span></p>\r
-\r
-<p class=flagdescription><span style='mso-bookmark:_Toc101065255'><span\r
-lang=EN-US>Format:</span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc101065255'><span\r
-lang=EN-US><span style='mso-tab-count:1'>      </span>2 Name1 name2 </span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065255'><span\r
-lang=EN-US><span style='mso-tab-count:1'>      </span>2 Name1 name4</span></span></p>\r
-\r
-<p class=examplefileCxSpLast><span style='mso-bookmark:_Toc101065255'><span\r
-lang=EN-US><span style='mso-tab-count:1'>      </span>3 Name1 Name2 Name3\85</span></span></p>\r
-\r
-</div>\r
-\r
-<p class=flagdescription><span style='mso-bookmark:_Toc101065255'><span\r
-lang=EN-US><span style='mso-tab-count:1'>            </span>(the line 3 would\r
-be used by a multiple alignment method).</span></span></p>\r
-\r
-<p class=flag><span style='mso-bookmark:_Toc101065255'><a name="_Toc235958565"></a><a\r
-name="_Toc102494788"><span style='mso-bookmark:_Toc235958565'><span lang=AF>-do_normalise</span></span></a></span></p>\r
-\r
-<p class=flagusage><span style='mso-bookmark:_Toc101065255'><span lang=EN-US\r
-style='mso-ansi-language:EN-US'>Usage:<span style='mso-spacerun:yes'> \r
-</span>-do_normalise=&lt;0 or a positive value&gt; <o:p></o:p></span></span></p>\r
-\r
-<p class=instruction><span style='mso-bookmark:_Toc101065255'><span lang=EN-US>Default:-do_normalise=1000</span></span></p>\r
-\r
-<p class=instruction><span style='mso-bookmark:_Toc101065255'><span lang=EN-US>Development\r
-Only</span></span></p>\r
-\r
-<p class=flagdescription><span style='mso-bookmark:_Toc101065255'><span\r
-lang=EN-US>When using a value different from 0, this flag sets the score of the\r
-highest scoring pair to 1000. </span></span></p>\r
-\r
-<p class=flag><span style='mso-bookmark:_Toc101065255'><a name="_Toc235958566"></a><a\r
-name="_Toc102494789"><span style='mso-bookmark:_Toc235958566'><span lang=AF>-extend</span></span></a></span></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-extend=&lt;0,1 or a positive value&gt; <o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default:-extend=1</span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Development Only</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>When turned on, this flag indicates\r
-that the library extension should be carried out when performing the multiple\r
-alignment. If <b>-extend =0</b>, the extension is not made, if it is set to 1,\r
-the extension is made on all the pairs in the library. If the extension is set\r
-to another positive value, the extension is only carried out on pairs having a weight\r
-value superior to the specified limit.<a name="_Toc101065256"></a></span></p>\r
-\r
-<p class=flag><span style='mso-bookmark:_Toc101065256'><a name="_Toc235958567"></a><a\r
-name="_Toc102494790"><span style='mso-bookmark:_Toc235958567'><span lang=AF>-extend_mode</span></span></a></span></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-extend=&lt;string&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default:-extend=very_fast_triplet</span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Warning: Development Only</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Controls the algorithm for matrix\r
-extension. Available modes include:</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>relative_triplet<span\r
-style='mso-tab-count:2'>                  </span>Unsupported</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>g_coffee<span style='mso-tab-count:\r
-3'>                                           </span>Unsupported</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>g_coffee_quadruplets<span\r
-style='mso-tab-count:1'>    </span>Unsupported</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>fast_triplet<span style='mso-tab-count:\r
-2'>                        </span>Fast triplet extension</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>very_fast_triplet<span\r
-style='mso-tab-count:2'>                             </span>slow triplet\r
-extension, limited to the <b>-max_n_pair</b> best sequence pairs when aligning\r
-two profiles</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>slow_triplet<span style='mso-tab-count:\r
-2'>                       </span>Exhaustive use of all the triplets</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>mixt<span style='mso-tab-count:3'>                                   </span>Unsupported</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>quadruplet<span style='mso-tab-count:\r
-2'>                        </span>Unsupported</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>test<span style='mso-tab-count:3'>                                     </span>Unsupported</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>matrix<span style='mso-tab-count:\r
-3'>                                               </span>Use of the matrix <b>-matrix<o:p></o:p></b></span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>fast_matrix<span style='mso-tab-count:\r
-2'>                      </span>Use of the matrix <b>-matrix</b>. Profiles are\r
-turned into consensus</span></p>\r
-\r
-<p class=flag><a name="_Toc235958568"></a><a name="_Toc102494791"></a><a\r
-name="_Toc101065257"><span style='mso-bookmark:_Toc102494791'><span\r
-style='mso-bookmark:_Toc235958568'><span lang=AF>-max_n_pair</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-max_n_pair=&lt;integer&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default:-extend=10</span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Development Only</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Controls the number of pairs\r
-considered by the <b>-extend_mode</b>=very_fast_triplet. Setting it to 0 forces\r
-all the pairs to be considered (equivalent to <b>-extend_mode</b>=slow_triplet).</span></p>\r
-\r
-<p class=flag><a name="_Toc235958569"></a><a name="_Toc102494792"></a><a\r
-name="_Toc101065258"><span style='mso-bookmark:_Toc102494792'><span\r
-style='mso-bookmark:_Toc235958569'><span lang=AF>-seq_name_for_quadruplet</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>Unsupported<o:p></o:p></span></p>\r
-\r
-<p class=flag><a name="_Toc235958570"></a><a name="_Toc102494793"></a><a\r
-name="_Toc101065259"><span style='mso-bookmark:_Toc102494793'><span\r
-style='mso-bookmark:_Toc235958570'><span lang=AF>-compact</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>Unsupported<o:p></o:p></span></p>\r
-\r
-<p class=flag><a name="_Toc235958571"></a><a name="_Toc102494794"></a><a\r
-name="_Toc101065260"><span style='mso-bookmark:_Toc102494794'><span\r
-style='mso-bookmark:_Toc235958571'><span lang=AF>-clean</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>Unsupported<o:p></o:p></span></p>\r
-\r
-<p class=flag><a name="_Toc235958572"></a><a name="_Toc102494795"></a><a\r
-name="_Toc101065261"><span style='mso-bookmark:_Toc102494795'><span\r
-style='mso-bookmark:_Toc235958572'><span lang=AF>-maximise</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>Unsupported<o:p></o:p></span></p>\r
-\r
-<p class=flag><a name="_Toc235958573"></a><a name="_Toc102494796"></a><a\r
-name="_Toc101065262"><span style='mso-bookmark:_Toc102494796'><span\r
-style='mso-bookmark:_Toc235958573'><span lang=AF>-do_self</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>Flag -do_self<o:p></o:p></span></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Default: No<o:p></o:p></span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>This flag causes the extension to\r
-carried out within the sequences (as opposed to between sequences). This is\r
-necessary when looking for internal repeats with Mocca.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958574"></a><a name="_Toc102494797"></a><a\r
-name="_Toc101065263"><span style='mso-bookmark:_Toc102494797'><span\r
-style='mso-bookmark:_Toc235958574'><span lang=AF>-seq_name_for_quadruplet</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>Unsupported<o:p></o:p></span></p>\r
-\r
-<p class=flag><a name="_Toc235958575"></a><a name="_Toc102494798"></a><a\r
-name="_Toc101065264"><span style='mso-bookmark:_Toc102494798'><span\r
-style='mso-bookmark:_Toc235958575'><span lang=AF>-weight</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-weight=&lt;winsimN, sim or\r
-sim_&lt;matrix_name or matrix_file&gt; or &lt;integer value&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -weight=sim</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Weight defines the way alignments are\r
-weighted when turned into a library. <span\r
-style='mso-spacerun:yes'> </span>Overweighting can be obtained with the\r
-OW&lt;X&gt; weight mode.</span></p>\r
-\r
-<p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar><span\r
-lang=EN-US><o:p>&nbsp;</o:p></span></span></p>\r
-\r
-<p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar><span\r
-lang=EN-US>winsimN </span></span><span lang=EN-US>indicates that the weight\r
-assigned to a given pair will be equal to the percent identity within a window\r
-of 2N+1 length centered on that pair. For instance winsim10 defines a window of\r
-10 residues around the pair being considered. This gives its own weight to each\r
-residue in the output library. In our hands, this type of weighting scheme has\r
-not provided any significant improvement over the standard sim value.</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee sample_seq1.fasta -weight=winsim10 \96out_lib=test.tc_lib </span></p>\r
-\r
-</div>\r
-\r
-<p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar><span\r
-lang=EN-US>sim</span></span><span lang=EN-US> indicates that the weight equals\r
-the average identity within the sequences containing the matched residues.</span></p>\r
-\r
-<p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar><span\r
-lang=EN-US>OW&lt;X&gt;</span></span><span\r
-class=StyleflagdescriptionBoldItalicChar><span lang=EN-US style='font-style:\r
-normal;mso-bidi-font-style:italic'> </span></span><span\r
-class=StyleflagdescriptionBoldItalicChar><span lang=EN-US style='font-weight:\r
-normal;mso-bidi-font-weight:bold;font-style:normal;mso-bidi-font-style:italic'>Will\r
-cause the sim weight to be multiplied by X<o:p></o:p></span></span></p>\r
-\r
-<p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar><span\r
-lang=EN-US>sim_matrix_name</span></span><span lang=EN-US> indicates the average\r
-identity with two residues regarded as identical when their substitution value\r
-is positive. The valid matrices names are in <i style='mso-bidi-font-style:\r
-normal'>matrices.h (pam250mt) .</i>Matrices not found in this header are\r
-considered to be filenames. See the format section for matrices. For instance, <i\r
-style='mso-bidi-font-style:normal'>-weight=sim_pam250mt</i> indicates that the\r
-grouping used for similarity will be the set of classes with positive\r
-substitutions. </span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee sample_seq1.fasta -weight=winsim10 \96out_lib=test.tc_lib </span></p>\r
-\r
-</div>\r
-\r
-<p class=flagdescription><span lang=EN-US>Other groups include </span></p>\r
-\r
-<p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar><span\r
-lang=EN-US>sim_clustalw_col</span></span><i style='mso-bidi-font-style:normal'><span\r
-lang=EN-US> </span></i><span lang=EN-US>( categories of clustalw marked with :)</span></p>\r
-\r
-<p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar><span\r
-lang=EN-US>sim_clustalw_dot</span></span><span lang=EN-US> ( categories of\r
-clustalw marked with .)</span></p>\r
-\r
-<p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar><span\r
-lang=EN-US>Value</span></span><i style='mso-bidi-font-style:normal'><span\r
-lang=EN-US> </span></i><span lang=EN-US>indicates that all the pairs found in\r
-the alignments must be given the same weight equal to value. This is useful\r
-when the alignment one wishes to turn into a library must be given a\r
-pre-specified score (for instance if they come from a structure\r
-super-imposition program). Value is an integer:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee sample_seq1.fasta -weight=1000 \96out_lib=test.tc_lib </span></p>\r
-\r
-</div>\r
-\r
-<h3><a name="_Toc235958576"></a><a name="_Toc102494799"></a><a\r
-name="_Toc102494373"></a><a name="_Toc101065265"><span style='mso-bookmark:\r
-_Toc102494373'><span style='mso-bookmark:_Toc102494799'><span style='mso-bookmark:\r
-_Toc235958576'><span lang=EN-US>Tree Computation</span></span></span></span></a></h3>\r
-\r
-<p class=flag><a name="_Toc235958577"></a><a name="_Toc102494800"></a><a\r
-name="_Toc101065266"><span style='mso-bookmark:_Toc102494800'><span\r
-style='mso-bookmark:_Toc235958577'><span lang=AF>-</span></span></span></a><span\r
-style='mso-bookmark:_Toc235958577'><span lang=AF>distance_matrix_mode</span></span></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--distance_matrix_mode=&lt;slow, fast, very_fast&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: very_fast</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>This flag indicates the method used\r
-for computing the distance matrix (distance between every pair of sequences)\r
-required for the computation of the dendrogram. </span></p>\r
-\r
-<p class=flagdescription><b style='mso-bidi-font-weight:normal'><span\r
-lang=EN-US>Slow</span></b><span lang=EN-US> <span style='mso-tab-count:1'>  </span>The\r
-chosen dp_mode using the extended library, </span></p>\r
-\r
-<p class=flagdescription><b style='mso-bidi-font-weight:normal'><span\r
-lang=EN-US>fast</span></b><span lang=EN-US>:<span style='mso-spacerun:yes'>  \r
-</span><span style='mso-tab-count:1'> </span>The fasta dp_mode using the\r
-extended library.</span></p>\r
-\r
-<p class=flagdescription><b style='mso-bidi-font-weight:normal'><span\r
-lang=EN-US>very_fast</span></b><span lang=EN-US><span style='mso-tab-count:\r
-1'>          </span>The fasta dp_mode using blosum62mt.</span></p>\r
-\r
-<p class=flagdescription><b style='mso-bidi-font-weight:normal'><span\r
-lang=EN-US>ktup<span style='mso-tab-count:1'>    </span></span></b><span\r
-lang=EN-US>Ktup matching (Muscle kind) </span></p>\r
-\r
-<p class=flagdescription><b style='mso-bidi-font-weight:normal'><span\r
-lang=EN-US>aln<span style='mso-tab-count:2'>                      </span></span></b><span\r
-lang=EN-US>Read the distances on a precomputed MSA</span></p>\r
-\r
-<p class=flag><a name="_Toc235958578"></a><a name="_Toc102494801"></a><a\r
-name="_Toc101065267"><span style='mso-bookmark:_Toc102494801'><span\r
-style='mso-bookmark:_Toc235958578'><span lang=AF>-quicktree [CW]</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--quicktree<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Description: Causes T-Coffee to compute a\r
-fast approximate guide tree</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>This flag is kept for compatibility with\r
-ClustalW. It indicates that:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee sample_seq1.fasta \96distance_matrix_mode=very_fast </span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee sample_seq1.fasta \96quicktree </span></p>\r
-\r
-</div>\r
-\r
-<h3><a name="_Toc235958579"></a><a name="_Toc102494802"></a><a\r
-name="_Toc102494374"></a><a name="_Toc101065268"><span style='mso-bookmark:\r
-_Toc102494374'><span style='mso-bookmark:_Toc102494802'><span style='mso-bookmark:\r
-_Toc235958579'><span lang=EN-US>Pair-wise Alignment Computation</span></span></span></span></a></h3>\r
-\r
-<p class=Noteboxtitle><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.5pt;\r
-padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#FFFF89'>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut align=center\r
-style='text-align:center;background:#FFFF89'><span lang=EN-US style='font-size:\r
-20.0pt'>Controlling Alignment Computation<o:p></o:p></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US>Most\r
-parameters in this section refer to the alignment mode fasta_pair_wise and\r
-cfatsa_pair_wise. When using these alignment modes, things proceed as follow:</span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US>1-Sequences\r
-are recoded using a degenerated alphabet provided with &lt;-sim_matrix&gt; </span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US>2-Recoded\r
-sequences are then hashed into ktuples of size <u>&lt;-ktup&gt;</u></span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US>3-Dynamic\r
-programming runs on the <u>&lt;-ndiag&gt;</u> best diagonals whose score is\r
-higher than <u>&lt;-diag_threshold&gt;</u>, the way diagonals are scored is\r
-controlled via <u>&lt;-diag_mode&gt;</u> .</span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US>4-The\r
-Dynamic computation is made to optimize either the library scoring scheme (as\r
-defined by the <u>-in</u> flag) or a substitution matrix as provided via the <u>-matrix</u>\r
-flag. The penalty scheme is defined by <u>-gapopen</u> and <u>-gapext</u>. If <u>-gapopen</u>\r
-is undefined, the value defined in <u>-cosmetic_penalty</u> is used instead.</span></p>\r
-\r
-<p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US>5-Terminal\r
-gaps are scored according to <u>-tg_mode</u></span></p>\r
-\r
-</div>\r
-\r
-<p class=noteboxbody><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=flag><a name="_Toc235958580"></a><a name="_Toc102494803"></a><a\r
-name="_Toc101065269"><span style='mso-bookmark:_Toc102494803'><span\r
-style='mso-bookmark:_Toc235958580'><span lang=AF>-dp_mode</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-dp_mode=&lt;string&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -dp_mode=cfasta_fair_wise</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>This flag indicates the type of\r
-dynamic programming used by the program:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee sample_seq1.fasta \96dp_mode myers_miller_pair_wise </span></p>\r
-\r
-</div>\r
-\r
-<p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar><span\r
-lang=EN-US>gotoh_pair_wise</span></span><span lang=EN-US>: implementation of\r
-the gotoh algorithm (quadratic in memory and time)</span></p>\r
-\r
-<p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar><span\r
-lang=EN-US>myers_miller_pair_wise</span></span><span lang=EN-US>:\r
-implementation of the Myers and Miller dynamic programming algorithm (\r
-quadratic in time and linear in space). This algorithm is recommended for very\r
-long sequences. It is about 2 times slower than gotoh and only accepts <i\r
-style='mso-bidi-font-style:normal'>tg_mode=1or 2 (i.e. gaps penalized for\r
-opening).<o:p></o:p></i></span></p>\r
-\r
-<p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar><span\r
-lang=EN-US>fasta_pair_wise</span></span><i style='mso-bidi-font-style:normal'><span\r
-lang=EN-US>: </span></i><span lang=EN-US>implementation of the fasta algorithm.\r
-The sequence is hashed, looking for <i style='mso-bidi-font-style:normal'>ktuples</i>\r
-words. Dynamic programming is only carried out on the <i style='mso-bidi-font-style:\r
-normal'>ndiag</i> best scoring diagonals. This is much faster but less accurate\r
-than the two previous. This mode is controlled by the parameters <b>-ktuple,\r
--diag_mode and -ndiag<o:p></o:p></b></span></p>\r
-\r
-<p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar><span\r
-lang=EN-US>cfasta_pair_wise</span></span><span lang=EN-US>: c stands for\r
-checked. It is the same algorithm. The dynamic programming is made on the <i\r
-style='mso-bidi-font-style:normal'>ndiag</i> best diagonals, and then on the\r
-2*ndiags, and so on until the scores converge. Complexity will depend on the\r
-level of divergence of the sequences, but will usually be L*log(L), with an\r
-accuracy comparable to the two first mode ( this was checked on BaliBase). This\r
-mode is controlled by the parameters <b>-ktuple, -diag_mode and \96ndiag<o:p></o:p></b></span></p>\r
-\r
-<p class=Note><span lang=EN-US style='mso-ansi-language:EN-US'>Note: Users may\r
-find by looking into the code that other modes with fancy names exists\r
-(viterby_pair_wise\85) Unless mentioned in this documentation, these modes are\r
-not supported.<o:p></o:p></span></p>\r
-\r
-<p class=flag><a name="_Toc235958581"></a><a name="_Toc102494804"></a><a\r
-name="_Toc101065270"><span style='mso-bookmark:_Toc102494804'><span\r
-style='mso-bookmark:_Toc235958581'><span lang=AF>-ktuple</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-ktuple=&lt;value&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -ktuple=1 or 2</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Indicates the ktuple size for\r
-cfasta_pair_wise dp_mode and fasta_pair_wise. It is set to 1 for proteins, and\r
-2 for DNA. The alphabet used for protein can be a degenerated version, set with\r
-<b><u>-sim_matrix.</u></b>. </span></p>\r
-\r
-<p class=flag><a name="_Toc235958582"></a><a name="_Toc102494805"></a><a\r
-name="_Toc101065271"><span style='mso-bookmark:_Toc102494805'><span\r
-style='mso-bookmark:_Toc235958582'><span lang=AF>-ndiag</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-ndiag=&lt;value&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -ndiag=0</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Indicates the number of diagonals\r
-used by the <i>fasta_pair_wise</i> algorithm (cf <b>-dp_mode</b>). When<span\r
-style='mso-spacerun:yes'>  </span><b>-ndiag=0</b>, n_diag=Log (length of the\r
-smallest sequence)+1. </span></p>\r
-\r
-<p class=Note><span lang=EN-US style='mso-ansi-language:EN-US'>When \96ndiag and\r
-\96diag_threshold are set, diagonals are selected if and only if they fulfill\r
-both conditions.<o:p></o:p></span></p>\r
-\r
-<p class=flag><a name="_Toc235958583"></a><a name="_Toc102494806"></a><a\r
-name="_Toc101065272"><span style='mso-bookmark:_Toc102494806'><span\r
-style='mso-bookmark:_Toc235958583'><span lang=AF>-diag_mode</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-diag_mode=&lt;value&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -diag_mode=0</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Indicates the manner in which\r
-diagonals are scored during the fasta hashing. </span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>0: indicates that the score of a\r
-diagonal is equal to the sum of the scores of the exact matches it contains. </span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>1 indicates that this score is set\r
-equal to the score of the best uninterrupted segment (useful when dealing with\r
-fragments of sequences).</span></p>\r
-\r
-<p class=flag><a name="_Toc235958584"></a><a name="_Toc102494807"></a><a\r
-name="_Toc101065273"><span style='mso-bookmark:_Toc102494807'><span\r
-style='mso-bookmark:_Toc235958584'><span lang=AF>-diag_threshold</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-diag_threshold=&lt;value&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -diag_threshold=0</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Sets the value of the threshold when\r
-selecting diagonals. </span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>0: indicates that \96ndiag should be\r
-used to select the diagonals (cf \96ndiag section).</span></p>\r
-\r
-<p class=flag><a name="_Toc235958585"></a><a name="_Toc102494808"></a><a\r
-name="_Toc101065274"><span style='mso-bookmark:_Toc102494808'><span\r
-style='mso-bookmark:_Toc235958585'><span lang=AF>-sim_matrix</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-sim_matrix=&lt;string&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -sim_matrix=vasiliky</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Indicates the manner in which the\r
-amino acid alphabet is degenerated when hashing in the fasta_pairwise dynamic\r
-programming. Standard ClustalW matrices are all valid. They are used to define\r
-groups of amino acids having positive substitution values. In T-Coffee, the\r
-default is a 13 letter grouping named Vasiliky, with residues grouped as\r
-follows:</span></p>\r
-\r
-<p class=example2><span lang=EN-US>rk, de, qh, vilm, fy (other residues kept\r
-alone).</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>This alphabet is set with the flag <b>-sim_matrix=vasiliky</b>.\r
-In order to keep the alphabet non degenerated, <b>-sim_matrix=idmat </b>can be\r
-used to retain the standard alphabet.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958586"></a><a name="_Toc102494809"></a><a\r
-name="_Toc101065275"><span style='mso-bookmark:_Toc102494809'><span\r
-style='mso-bookmark:_Toc235958586'><span lang=AF>-matrix [CW]</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-matrix=&lt;blosum62mt&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -matrix=blosum62mt</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>The usage of this flag has been\r
-modified from previous versions, due to frequent mistakes in its usage. This\r
-flag sets the matrix that will be used by alignment methods within t_coffee\r
-(slow_pair, lalign_id_pair). It does not affect external methods (like\r
-clustal_pair, clustal_aln\85). </span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Users can also provide their own\r
-matrices, using the matrix format described in the appendix.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958587"></a><a name="_Toc102494810"></a><a\r
-name="_Toc101065276"><span style='mso-bookmark:_Toc102494810'><span\r
-style='mso-bookmark:_Toc235958587'><span lang=AF>-nomatch</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-nomatch=&lt;positive value&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -nomatch=0</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Indicates the penalty to associate\r
-with a match. When using a library, all matches are positive or equal to 0.\r
-Matches equal to 0 are unsupported by the library but non-penalized. Setting\r
-nomatch to a non-negative value makes it possible to penalize these null\r
-matches and prevent unrelated sequences from being aligned (this can be useful\r
-when the alignments are meant to be used for structural modeling).</span></p>\r
-\r
-<p class=flag><a name="_Toc235958588"></a><a name="_Toc102494811"></a><a\r
-name="_Toc101065277"><span style='mso-bookmark:_Toc102494811'><span\r
-style='mso-bookmark:_Toc235958588'><span lang=AF>-gapopen</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-gapopen=&lt;negative value&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -gapopen=0</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Indicates the penalty applied for\r
-opening a gap. The penalty must be negative. If no value is provided when using\r
-a substitution matrix, a value will be automatically computed.</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Here are some guidelines regarding\r
-the tuning of gapopen and gapext. In T-Coffee matches get a score between 0\r
-(match) and 1000 (match perfectly consistent with the library). The default\r
-cosmetic penalty is set to -50 (5% of a perfect match). If you want to tune\r
--gapoen and see a strong effect, you should therefore consider values between 0\r
-and -1000. </span></p>\r
-\r
-<p class=flag><a name="_Toc235958589"></a><a name="_Toc102494812"></a><a\r
-name="_Toc101065278"><span style='mso-bookmark:_Toc102494812'><span\r
-style='mso-bookmark:_Toc235958589'><span lang=AF>-gapext</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-gapext=&lt;negative value&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -gapext=0</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Indicates the penalty applied for\r
-extending a gap (cf <b><u>-gapopen</u></b>)</span></p>\r
-\r
-<p class=flag><a name="_Toc235958590"></a><a name="_Toc102494813"></a><a\r
-name="_Toc101065279"><span style='mso-bookmark:_Toc102494813'><span\r
-style='mso-bookmark:_Toc235958590'><span lang=AF>-fgapopen</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Unsupported<o:p></o:p></span></p>\r
-\r
-<p class=flag><a name="_Toc235958591"></a><a name="_Toc102494814"></a><a\r
-name="_Toc101065280"><span style='mso-bookmark:_Toc102494814'><span\r
-style='mso-bookmark:_Toc235958591'><span lang=AF>-fgapext</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Unsupported<o:p></o:p></span></p>\r
-\r
-<p class=flag><a name="_Toc235958592"></a><a name="_Toc102494815"></a><a\r
-name="_Toc101065281"><span style='mso-bookmark:_Toc102494815'><span\r
-style='mso-bookmark:_Toc235958592'><span lang=AF>-cosmetic_penalty</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-cosmetic_penalty=&lt;negative value&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -cosmetic_penalty=-50</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Indicates the penalty applied for\r
-opening a gap. This penalty is set to a very low value. It will only have an\r
-influence on the portions of the alignment that are unalignable. It will not\r
-make them more correct, but only more pleasing to the eye ( i.e. Avoid\r
-stretches of lonely residues).</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>The cosmetic penalty is automatically\r
-turned off if a substitution matrix is used rather than a library.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958593"></a><a name="_Toc102494816"></a><a\r
-name="_Toc101065282"><span style='mso-bookmark:_Toc102494816'><span\r
-style='mso-bookmark:_Toc235958593'><span lang=AF>-tg_mode</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-tg_mode=&lt;0, 1, or 2&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -tg_mode=1</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>0: terminal gaps penalized with <span\r
-class=StyleflagdescriptionBoldItalicChar>-gapopen + -gapext*len<o:p></o:p></span></span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>1: terminal gaps penalized with a <span\r
-class=StyleflagdescriptionBoldItalicChar>-gapext*len<o:p></o:p></span></span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>2: terminal gaps unpenalized.</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<h3><a name="_Toc235958594"></a><a name="_Toc102494817"></a><a\r
-name="_Toc102494375"></a><a name="_Toc101065283"><span style='mso-bookmark:\r
-_Toc102494375'><span style='mso-bookmark:_Toc102494817'><span style='mso-bookmark:\r
-_Toc235958594'><span lang=EN-US>Weighting Schemes</span></span></span></span></a></h3>\r
-\r
-<p class=flag><a name="_Toc235958595"></a><a name="_Toc102494818"></a><a\r
-name="_Toc101065284"><span style='mso-bookmark:_Toc102494818'><span\r
-style='mso-bookmark:_Toc235958595'><span lang=AF>-seq_weight</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--seq_weight=&lt;t_coffee or &lt;file_name&gt;&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -seq_weight=t_coffee</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>These are the individual weights\r
-assigned to each sequence. The t_coffee weights try to compensate the bias in\r
-consistency caused by redundancy in the sequences.</span></p>\r
-\r
-<p class=Formula><span lang=EN-US><span style='mso-tab-count:1'>            </span>sim(A,B)=%similarity\r
-between A and B, between 0 and 1. </span></p>\r
-\r
-<p class=Formula><span lang=EN-US><span style='mso-tab-count:1'>            </span>weight(A)=1/sum(sim(A,X)^3)</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Weights are normalized so that their\r
-sum equals the number of sequences. They are applied onto the primary library\r
-in the following manner:</span></p>\r
-\r
-<p class=Formula><span lang=EN-US><span style='mso-tab-count:1'>            </span>res_score(Ax,By)=Min(weight(A),\r
-weight(B))*res_score(Ax, By)</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>These are very simple weights. Their\r
-main goal is to prevent a single sequence present in many copies to dominate\r
-the alignment.</span></p>\r
-\r
-<p class=Note><span lang=EN-US style='mso-ansi-language:EN-US'>Note: The\r
-library output by -out_lib is the un-weighted<span style='mso-spacerun:yes'> \r
-</span>library. <o:p></o:p></span></p>\r
-\r
-<p class=Note><span lang=EN-US style='mso-ansi-language:EN-US'>Note: Weights\r
-can be output using the -outseqweight flag.<o:p></o:p></span></p>\r
-\r
-<p class=Note><span lang=EN-US style='mso-ansi-language:EN-US'>Note: You can\r
-use your own weights (see the format section). <o:p></o:p></span></p>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<h3><a name="_Toc235958596"></a><a name="_Toc102494819"></a><a\r
-name="_Toc102494376"></a><a name="_Toc101065285"><span style='mso-bookmark:\r
-_Toc102494376'><span style='mso-bookmark:_Toc102494819'><span style='mso-bookmark:\r
-_Toc235958596'><span lang=EN-US>Multiple Alignment Computation</span></span></span></span></a></h3>\r
-\r
-<p class=flag><a name="_Toc235958597"></a><a name="_Toc102494820"></a><a\r
-name="_Toc101065286"><span style='mso-bookmark:_Toc102494820'><span\r
-style='mso-bookmark:_Toc235958597'><span lang=AF>-msa_mode</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--msa_mode=&lt;tree,graph,precomputed&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -evaluate_mode=tree</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Unsupported</span></p>\r
-\r
-<p class=flag><a name="_Toc102494821"></a><a name="_Toc101065287"></a><a\r
-name="_Toc235958598"><span style='mso-bookmark:_Toc101065287'><span\r
-style='mso-bookmark:_Toc102494821'><span lang=AF>-one2all</span></span></span></a><span\r
-style='mso-bookmark:_Toc101065287'><span style='mso-bookmark:_Toc102494821'></span></span></p>\r
-\r
-<p class=flagusage><span style='mso-bookmark:_Toc101065287'><span\r
-style='mso-bookmark:_Toc102494821'><span lang=EN-US style='mso-ansi-language:\r
-EN-US'>Usage: -one2all=&lt;name&gt;<o:p></o:p></span></span></span></p>\r
-\r
-<p class=instruction><span style='mso-bookmark:_Toc101065287'><span\r
-style='mso-bookmark:_Toc102494821'><span lang=EN-US>Default: not used</span></span></span></p>\r
-\r
-<p class=flagdescription><span style='mso-bookmark:_Toc101065287'><span\r
-style='mso-bookmark:_Toc102494821'><span lang=EN-US>Will generate a one to all\r
-library with respect to the specified sequence and will then align all the\r
-sequences in turn to that sequence, in a sequence determined by the order in\r
-which the sequences were provided.<span style='mso-spacerun:yes'>  </span></span></span></span></p>\r
-\r
-<p class=flagdescription><span style='mso-bookmark:_Toc101065287'><span\r
-style='mso-bookmark:_Toc102494821'><b style='mso-bidi-font-weight:normal'><span\r
-lang=EN-US>\96profile_comparison =profile</span></b><span lang=EN-US>, the MSAs\r
-provided via \96profile are vectorized and the function specified by\r
-\96profile_comparison is used to make profile profile alignments. In that case,\r
-the complexity is NL^2</span></span></span></p>\r
-\r
-<p class=flag><span style='mso-bookmark:_Toc101065287'><span style='mso-bookmark:\r
-_Toc102494821'><a name="_Toc235958599"><span lang=AF>-profile</span></a></span></span><span\r
-style='mso-bookmark:_Toc235958599'><span lang=AF>_comparison</span></span></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--profile_mode=&lt;fullN,profile&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -profile_mode=full50</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>The profile mode flag controls the\r
-multiple profile alignments in T-Coffee. There are two instances where t_coffee\r
-can make multiple profile alignments:</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>1-When N, the number of sequences is\r
-higher than <b style='mso-bidi-font-weight:normal'>\96maxnseq, </b>the program\r
-switches to its multiple profile alignment mode (t_coffee_dpa).</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>2-When MSAs are provided via the <b\r
-style='mso-bidi-font-weight:normal'>\96profile</b> flag or via <b\r
-style='mso-bidi-font-weight:normal'>\96profile1</b> and <b style='mso-bidi-font-weight:\r
-normal'>\96profile2</b>. </span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>In these situations, the\r
-\96profile_mode value influences the alignment computation, these values are:</span></p>\r
-\r
-<p class=flagdescription><b style='mso-bidi-font-weight:normal'><span\r
-lang=EN-US>\96profile_comparison =profile</span></b><span lang=EN-US>, the MSAs\r
-provided via \96profile are vectorized and the function specified by\r
-\96profile_comparison is used to make profile profile alignments. In that case,\r
-the complexity is NL^2</span></p>\r
-\r
-<p class=flagdescription><span class=ListChar><b style='mso-bidi-font-weight:\r
-normal'><span lang=EN-US style='font-size:12.0pt;mso-bidi-font-size:10.0pt'>-profile_comparison=fullN</span></b></span><span\r
-lang=EN-US>, N is an integer value that can omitted. <i style='mso-bidi-font-style:\r
-normal'>Full</i> indicates that given two profiles, the alignment will be based\r
-on a library that includes every possible pair of sequences between the two\r
-profiles. If N is set, then the library will be restricted to the N most\r
-similar pairs of sequences between the two profiles, as judged from a measure\r
-made on a pairwise alignment of these two profiles.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958600"></a><a name="_Toc102494822"></a><a\r
-name="_Toc101065288"><span style='mso-bookmark:_Toc102494822'><span\r
-style='mso-bookmark:_Toc235958600'><span lang=AF>-profile_</span></span></span></a><span\r
-style='mso-bookmark:_Toc235958600'><span lang=AF>mode</span></span></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--profile_mode=&lt;cw_profile_profile, muscle_profile_profile, multi_channel&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -profile_mode=cw_profile_profile</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>When <b style='mso-bidi-font-weight:\r
-normal'>\96profile_comparison=profile</b>, this flag selects a profile scoring\r
-function.</span></p>\r
-\r
-<h3><a name="_Toc235958601"></a><a name="_Toc102494823"></a><a\r
-name="_Toc102494377"></a><a name="_Toc101065289"><span style='mso-bookmark:\r
-_Toc102494377'><span style='mso-bookmark:_Toc102494823'><span style='mso-bookmark:\r
-_Toc235958601'><span lang=EN-US>Alignment Post-Processing</span></span></span></span></a></h3>\r
-\r
-<p class=flag><a name="_Toc235958602"></a><a name="_Toc102494824"></a><a\r
-name="_Toc101065290"><span style='mso-bookmark:_Toc102494824'><span\r
-style='mso-bookmark:_Toc235958602'><span lang=AF>-clean_aln</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-clean_aln<span style='mso-spacerun:yes'> \r
-</span><o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default:-clean_aln</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>This flag causes T-Coffee to\r
-post-process the multiple alignment. Residues that have a reliability score\r
-smaller or equal to -clean_threshold (as given by an evaluation that uses\r
--clean_evaluate_mode)<span style='mso-spacerun:yes'>  </span>are realigned to\r
-the rest of the alignment. Residues with a score higher than the threshold\r
-constitute a rigid framework that cannot be altered.</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>The cleaning algorithm is greedy. It\r
-starts from the top left segment of low constituency residues and works its way\r
-left to right, top to bottom along the alignment. You can require this\r
-operation to be carried out for several cycles using the -clean_iterations\r
-flag.</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>The rationale behind this operation\r
-is mostly cosmetic. In order to ensure a decent looking alignment, the gop is\r
-set to -20 and the gep to -1. There is no penalty for terminal gaps, and the\r
-matrix is blosum62mt.</span></p>\r
-\r
-<p class=Note><span lang=EN-US style='mso-ansi-language:EN-US'>Note: Gaps are\r
-always considered to have a reliability score of 0.<o:p></o:p></span></p>\r
-\r
-<p class=Note><span class=WarningChar><span lang=EN-US>Note: The use of the\r
-cleaning option can result in memory overflow when aligning large</span></span><span\r
-lang=EN-US style='mso-ansi-language:EN-US'> </span><span class=WarningChar><span\r
-lang=EN-US>sequences,<o:p></o:p></span></span></p>\r
-\r
-<p class=flag><a name="_Toc235958603"></a><a name="_Toc102494825"></a><a\r
-name="_Toc101065291"><span style='mso-bookmark:_Toc102494825'><span\r
-style='mso-bookmark:_Toc235958603'><span lang=AF>-clean_threshold</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-clean_threshold=&lt;0-9&gt;<span\r
-style='mso-spacerun:yes'>  </span><o:p></o:p></span></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Default:-clean_aln=1<o:p></o:p></span></p>\r
-\r
-<p class=MyNormal><span lang=AF>See -clean_aln for details.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958604"></a><a name="_Toc102494826"></a><a\r
-name="_Toc101065292"><span style='mso-bookmark:_Toc102494826'><span\r
-style='mso-bookmark:_Toc235958604'><span lang=AF>-clean_iteration</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-clean_iteration=&lt;value between 1 and\r
-&gt;<span style='mso-spacerun:yes'>  </span><o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default:-clean_iteration=1</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>See -clean_aln for details.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958605"></a><a name="_Toc102494827"></a><a\r
-name="_Toc101065293"><span style='mso-bookmark:_Toc102494827'><span\r
-style='mso-bookmark:_Toc235958605'><span lang=AF>-clean_evaluation_mode</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-clean_iteration=&lt;evaluation_mode\r
-&gt;<span style='mso-spacerun:yes'>  </span><o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default:-clean_iteration=t_coffee_non_extended</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Indicates the mode used for the\r
-evaluation that will indicate the segments that should be realigned. See\r
--evaluation_mode for the list of accepted modes.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958606"></a><a name="_Toc102494828"></a><a\r
-name="_Toc101065294"><span style='mso-bookmark:_Toc102494828'><span\r
-style='mso-bookmark:_Toc235958606'><span lang=AF>-iterate</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--iterate=&lt;integer&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -iterate=0</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Sequences are extracted in turn and\r
-realigned to the MSA. If iterate is set to -1, each sequence is realigned,\r
-otherwise the number of iterations is set by \96iterate.</span></p>\r
-\r
-<h2><a name="_Toc235958607"></a><a name="_Toc102494829"></a><a\r
-name="_Toc102494378"></a><a name="_Toc101065295"><span style='mso-bookmark:\r
-_Toc102494378'><span style='mso-bookmark:_Toc102494829'><span style='mso-bookmark:\r
-_Toc235958607'><span lang=EN-US>CPU Control</span></span></span></span></a></h2>\r
-\r
-<h3><a name="_Toc235958608"></a><a name="_Toc102494830"></a><a\r
-name="_Toc102494379"></a><a name="_Toc101065296"><span style='mso-bookmark:\r
-_Toc102494379'><span style='mso-bookmark:_Toc102494830'><span style='mso-bookmark:\r
-_Toc235958608'><span lang=EN-US>Multithreading</span></span></span></span></a></h3>\r
-\r
-<p class=flag><a name="_Toc235958609"></a><a name="_Toc102494831"></a><a\r
-name="_Toc101065297"><span style='mso-bookmark:_Toc102494831'><span\r
-style='mso-bookmark:_Toc235958609'><span lang=AF>-multi_core </span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-multi_core=</span> templates_jobs_relax_msa<span\r
-lang=EN-US style='mso-ansi-language:EN-US'><o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: 0</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Specifies that the steps of T-Coffee\r
-that should be multi threaded. by default all relevant steps are.</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee sample_seq2.fasta -multi_core jobs</span></p>\r
-\r
-</div>\r
-\r
-<p class=flag><a name="_Toc235958610"></a><a name="_Toc102494832"></a><a\r
-name="_Toc102494380"></a><a name="_Toc101065298"><span style='mso-bookmark:\r
-_Toc102494380'><span style='mso-bookmark:_Toc102494832'><span style='mso-bookmark:\r
-_Toc235958610'><span lang=AF>-n_core </span></span></span></span></a></p>\r
-\r
-<p class=flagusage><span style='mso-bookmark:_Toc101065298'><span\r
-style='mso-bookmark:_Toc102494380'><span style='mso-bookmark:_Toc102494832'><span\r
-style='mso-bookmark:_Toc235958610'><span lang=EN-US style='mso-ansi-language:\r
-EN-US'>Usage:<span style='mso-spacerun:yes'>  </span>-n_core=</span><span\r
-lang=EN-US> </span>&lt;number of cores&gt;</span></span></span></span><span\r
-style='mso-bookmark:_Toc101065298'><span style='mso-bookmark:_Toc102494380'><span\r
-style='mso-bookmark:_Toc102494832'><span style='mso-bookmark:_Toc235958610'><span\r
-lang=EN-US style='mso-ansi-language:EN-US'><o:p></o:p></span></span></span></span></span></p>\r
-\r
-<p class=instruction><span style='mso-bookmark:_Toc101065298'><span\r
-style='mso-bookmark:_Toc102494380'><span style='mso-bookmark:_Toc102494832'><span\r
-style='mso-bookmark:_Toc235958610'><span lang=EN-US>Default: 0</span></span></span></span></span></p>\r
-\r
-<p class=flagdescription><span style='mso-bookmark:_Toc101065298'><span\r
-style='mso-bookmark:_Toc102494380'><span style='mso-bookmark:_Toc102494832'><span\r
-style='mso-bookmark:_Toc235958610'><span lang=EN-US>Default indicates that all\r
-cores will be used, as indicated by the environment via:</span></span></span></span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span\r
-style='mso-bookmark:_Toc101065298'><span style='mso-bookmark:_Toc102494380'><span\r
-style='mso-bookmark:_Toc102494832'><span style='mso-bookmark:_Toc235958610'><span\r
-lang=EN-US>PROMPT: t_coffee sample_seq2.fasta -multi_core jobs</span></span></span></span></span></p>\r
-\r
-</div>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065298'><span style='mso-bookmark:_Toc102494380'><span\r
-style='mso-bookmark:_Toc102494832'><span style='mso-bookmark:_Toc235958610'><span\r
-lang=EN-US><o:p>&nbsp;</o:p></span></span></span></span></span></h3>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065298'><span style='mso-bookmark:_Toc102494380'><span\r
-style='mso-bookmark:_Toc102494832'><span style='mso-bookmark:_Toc235958610'><span\r
-lang=EN-US>Limits</span></span></span></span></span></h3>\r
-\r
-<p class=flag><a name="_Toc235958611"></a><a name="_Toc102494833"></a><a\r
-name="_Toc101065299"><span style='mso-bookmark:_Toc102494833'><span\r
-style='mso-bookmark:_Toc235958611'><span lang=AF>-mem_mode</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>deprecated</span><span lang=EN-US\r
-style='mso-ansi-language:EN-US;mso-bidi-font-weight:bold'><o:p></o:p></span></p>\r
-\r
-<p class=flag><a name="_Toc235958612"></a><a name="_Toc102494834"></a><a\r
-name="_Toc101065300"><span style='mso-bookmark:_Toc102494834'><span\r
-style='mso-bookmark:_Toc235958612'><span lang=AF>-ulimit</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-ulimit=&lt;value&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -ulimit=0</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Specifies the upper limit of memory\r
-usage (in Megabytes). Processes exceeding this limit will automatically exit. A\r
-value 0 indicates that no limit applies.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958613"></a><a name="_Toc102494835"></a><a\r
-name="_Toc101065301"><span style='mso-bookmark:_Toc102494835'><span\r
-style='mso-bookmark:_Toc235958613'><span lang=AF>-maxlen</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-maxlen=&lt;value, 0=nolimit&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -maxlen=1000</span><span\r
-lang=EN-US style='mso-bidi-font-weight:bold'><o:p></o:p></span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Indicates the maximum length of the\r
-sequences. <a name="_Toc101065302"></a></span></p>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065302'><a name="_Toc235958614"></a><a\r
-name="_Toc102494836"></a><a name="_Toc102494381"><span style='mso-bookmark:\r
-_Toc102494836'><span style='mso-bookmark:_Toc235958614'><span lang=EN-US>Aligning\r
-more than 100 sequences with DPA</span></span></span></a></span></h3>\r
-\r
-<p class=flag><a name="_Toc235958615"></a><a name="_Toc102494837"></a><a\r
-name="_Toc101065303"><span style='mso-bookmark:_Toc102494837'><span\r
-style='mso-bookmark:_Toc235958615'><span lang=AF>-maxnseq</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-maxnseq=&lt;value, 0=nolimit&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -maxnseq=50</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Indicates the maximum number of\r
-sequences before triggering the use of t_coffee_dpa.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958616"></a><a name="_Toc102494838"></a><a\r
-name="_Toc101065304"><span style='mso-bookmark:_Toc102494838'><span\r
-style='mso-bookmark:_Toc235958616'><span lang=AF>-dpa_master_aln</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--dpa_master_aln=&lt;File, method&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -dpa_master_aln=NO</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>When using dpa, t_coffee needs a seed\r
-alignment that can be computed using any appropriate method. By default,\r
-t_coffee computes a fast approximate alignment.</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>A pre-alignment can be provided\r
-through this flag, as well as any program using the following syntax:</span></p>\r
-\r
-<p class=example2><span lang=EN-US>your_script \96in &lt;fasta_file&gt; -out\r
-&lt;file_name&gt;</span></p>\r
-\r
-<p class=flag><a name="_Toc235958617"></a><a name="_Toc102494839"></a><a\r
-name="_Toc101065305"><span style='mso-bookmark:_Toc102494839'><span\r
-style='mso-bookmark:_Toc235958617'><span lang=AF>-dpa_maxnseq</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--dpa_maxnseq=&lt;integer value&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -dpa_maxnseq=30</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Maximum number of sequences aligned\r
-simultaneously when DPA is ran. Given the tree computed from the master\r
-alignment, a node is sent to computation if it controls more than <b\r
-style='mso-bidi-font-weight:normal'>\96dpa_maxnseq</b> OR if it controls a pair\r
-of sequences having less than <b style='mso-bidi-font-weight:normal'>\96dpa_min_score2</b>\r
-percent ID.<a name="_Toc101065306"></a></span></p>\r
-\r
-<p class=flag><span style='mso-bookmark:_Toc101065306'><a name="_Toc235958618"></a><a\r
-name="_Toc102494840"><span style='mso-bookmark:_Toc235958618'><span lang=AF>-dpa_min_score1</span></span></a></span></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--dpa_min_score1=&lt;integer value&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -dpa_min_score1=95</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Threshold for not realigning the\r
-sequences within the master alignment. Given this alignment and the associated\r
-tree, sequences below a node are not realigned if none of them has less than<b\r
-style='mso-bidi-font-weight:normal'> \96dpa_min_score1</b> % identity.<a\r
-name="_Toc101065307"></a></span></p>\r
-\r
-<p class=flag><span style='mso-bookmark:_Toc101065307'><a name="_Toc235958619"></a><a\r
-name="_Toc102494841"><span style='mso-bookmark:_Toc235958619'><span lang=AF>-dpa_min_score2</span></span></a></span></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--dpa_min_score2<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -dpa_min_score2</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Maximum number of sequences aligned\r
-simultaneously when DPA is ran. Given the tree computed from the master\r
-alignment, a node is sent to computation if it controls more than <b\r
-style='mso-bidi-font-weight:normal'>\96dpa_maxnseq</b> OR if it controls a pair\r
-of sequences having less than <b style='mso-bidi-font-weight:normal'>\96dpa_min_score2</b>\r
-percent ID.<a name="_Toc101065308"></a></span></p>\r
-\r
-<p class=flag><span style='mso-bookmark:_Toc101065308'><a name="_Toc235958620"></a><a\r
-name="_Toc102494842"><span style='mso-bookmark:_Toc235958620'><span lang=AF>-dap_tree\r
-[NOT IMPLEMENTED]</span></span></a></span></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-dpa_tree=&lt;filename&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -unset</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Guide tree used in DPA. This is a\r
-newick tree where the distance associated with each node is set to the minimum\r
-pairwise distance among all considered sequences.</span></p>\r
-\r
-<h2><a name="_Toc235958621"></a><a name="_Toc102494843"></a><a\r
-name="_Toc102494382"></a><a name="_Toc101065309"><span style='mso-bookmark:\r
-_Toc102494382'><span style='mso-bookmark:_Toc102494843'><span style='mso-bookmark:\r
-_Toc235958621'><span lang=EN-US>Using Structures</span></span></span></span></a><a\r
-name="_Toc101065310"></a></h2>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065310'><a name="_Toc235958622"></a><a\r
-name="_Toc102494844"></a><a name="_Toc102494383"><span style='mso-bookmark:\r
-_Toc102494844'><span style='mso-bookmark:_Toc235958622'><span lang=EN-US>Generic</span></span></span></a></span></h3>\r
-\r
-<p class=flag><a name="_Toc235958623"><span lang=AF>-mode</span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage: -mode=3dcoffee<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: turned off</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Runs t_coffee with the 3dcoffee mode\r
-(cf next section).</span></p>\r
-\r
-<p class=flag><a name="_Toc235958624"></a><a name="_Toc102494846"></a><a\r
-name="_Toc101065312"><span style='mso-bookmark:_Toc102494846'><span\r
-style='mso-bookmark:_Toc235958624'><span lang=AF>-check_pdb_status</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--check_pdb_status<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: turned off</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Forces t_coffee to run\r
-extract_from_pdb to check the pdb status of each sequence. This can\r
-considerably slow down the program.</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<h3><a name="_Toc235958625"></a><a name="_Toc102494847"></a><a\r
-name="_Toc102494384"></a><a name="_Toc101065313"><span style='mso-bookmark:\r
-_Toc102494384'><span style='mso-bookmark:_Toc102494847'><span style='mso-bookmark:\r
-_Toc235958625'><span lang=EN-US>3D Coffee: Using SAP</span></span></span></span></a></h3>\r
-\r
-<p class=flagdescription><span lang=EN-US>It is possible to use t_coffee to\r
-compute multiple structural alignments. To do so, ensure that you have the sap\r
-program installed.</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee \96pdb=struc1.pdb,struc2.pdb,struc3.pdb -method sap_pair</span></p>\r
-\r
-</div>\r
-\r
-<p class=flagdescription><span lang=EN-US>Will combine the pairwise alignments\r
-produced by SAP.<span style='mso-spacerun:yes'>  </span>There are currently\r
-four methods that can be interfaced with t_coffee:</span></p>\r
-\r
-<p class=flagdescription style='text-indent:28.25pt'><span lang=EN-US>sap_pair:\r
-that uses the sap algorithm</span></p>\r
-\r
-<p class=flagdescription style='text-indent:28.25pt'><span lang=EN-US>align_pdb:\r
-uses a t_coffee implementation of sap, not as accurate.</span></p>\r
-\r
-<p class=flagdescription style='text-indent:28.25pt'><span lang=EN-US>tmaliagn_pair\r
-(http://zhang.bioinformatics.ku.edu/TM-align/)</span></p>\r
-\r
-<p class=flagdescription style='text-indent:28.25pt'><span lang=EN-US>mustang_pair\r
-(http://www.cs.mu.oz.au/~arun/mustang)</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>When providing a PDB file, the\r
-computation is only carried out on the first chain of this file. If your\r
-original file contains several chain, you should extract the chain you want to\r
-work on. You can use <b style='mso-bidi-font-weight:normal'>t_coffee \96other_pg\r
-extract_from_pdb </b>or any pdb handling program.</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>If you are working with public PDB\r
-files, you can use the PDB identifier and specify the chain by adding its index\r
-to the identifier (i.e. 1pdbC). If your structure is an NMR structure, you are\r
-advised to provide the program with one structure only.</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>If you wish to align only a portion\r
-of the structure, you should extract it yourself from the pdb file, using <b\r
-style='mso-bidi-font-weight:normal'>t_coffee \96other_pg extract_from_pdb </b>or\r
-any pdb handling program.</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>You can provide t_coffee with a\r
-mixture of sequences and structure. In this case, you should use the special\r
-mode:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee \96mode 3dcoffee \96seq 3d_sample3.fasta -template_file\r
-template_file.template</span></p>\r
-\r
-</div>\r
-\r
-<h3><a name="_Toc235958626"></a><a name="_Toc102494848"></a><a\r
-name="_Toc102494385"></a><a name="_Toc101065314"><span style='mso-bookmark:\r
-_Toc102494385'><span style='mso-bookmark:_Toc102494848'><span style='mso-bookmark:\r
-_Toc235958626'><span lang=EN-US>Using/finding PDB templates for the Sequences</span></span></span></span></a></h3>\r
-\r
-<p class=flag><a name="_Toc235958627"></a><a name="_Toc102494849"></a><a\r
-name="_Toc101065315"><span style='mso-bookmark:_Toc102494849'><span\r
-style='mso-bookmark:_Toc235958627'><span lang=AF>-template_file</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US;mso-bidi-font-weight:\r
-bold'>Usage</span><span lang=EN-US style='mso-ansi-language:EN-US'>:\r
--template_file =<o:p></o:p></span></p>\r
-\r
-<p class=flagusage style='text-indent:28.25pt'><span lang=EN-US\r
-style='mso-ansi-language:EN-US'>&lt;filename, <o:p></o:p></span></p>\r
-\r
-<p class=flagusage style='margin-left:77.95pt'><span lang=EN-US\r
-style='mso-ansi-language:EN-US'>SCRIPT_scriptame, <o:p></o:p></span></p>\r
-\r
-<p class=flagusage style='margin-left:77.95pt'><span lang=EN-US\r
-style='mso-ansi-language:EN-US'>SELF_TAG <o:p></o:p></span></p>\r
-\r
-<p class=flagusage style='margin-left:77.95pt'><span lang=EN-US\r
-style='mso-ansi-language:EN-US'>SEQFILE_TAG_filename,<o:p></o:p></span></p>\r
-\r
-<p class=flagusage style='margin-left:77.95pt'><span lang=EN-US\r
-style='mso-ansi-language:EN-US'>no&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: no</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>This flag instructs t_coffee on the\r
-templates that will be used when combining several types of information. For\r
-instance, when using structural information, this file will indicate the\r
-structural template that corresponds to your sequences. The identifier T\r
-indicates that the file should be a FASTA like file, formatted as follows.\r
-There are several ways to pass the templates:</span></p>\r
-\r
-<p class=flagheading2><span lang=EN-US>Predefined Modes</span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>EXPRESSO: will use the EBI server to find\r
-_P_ templates</span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF>PSIBLAST: will use the EBI sever to find\r
-profiles </span></p>\r
-\r
-<p class=MyNormaBoldl><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=flagheading2><span lang=EN-US>File name</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>This file contains the\r
-sequence/template association it uses a FASTA-like format, as follows:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span lang=EN-US>&gt;&lt;sequence name&gt; _P_\r
-&lt;pdb template&gt;</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>&gt;&lt;sequence name&gt; _G_\r
-&lt;gene template&gt;</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>&gt;&lt;sequence name&gt; _R_\r
-&lt;MSA template&gt;</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>&gt;&lt;sequence name&gt; _F_\r
-&lt;RNA Secondary Structure&gt;</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>&gt;&lt;sequence name&gt; _T_\r
-&lt;Transmembrane Secondary Structure&gt;</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>&gt;&lt;sequence name&gt; _E_\r
-&lt;Protein Secondary Structure&gt;</span></p>\r
-\r
-<p class=examplefileCxSpLast><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-</div>\r
-\r
-<p class=flagdescription><span lang=EN-US>Each template will be used in place\r
-of the sequence with the appropriate method. For instance, structural templates\r
-will be aligned with sap_pair and the information thus generated will be\r
-transferred onto the alignment.</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Note the following rule:</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'>            </span>-Each\r
-sequence can have one template of each type (structural, genomics\85)</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'>            </span>-Each\r
-sequence can only have one template of a given type</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'>            </span>-Several\r
-sequences can share the same template</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'>            </span>-All\r
-the sequences do not need to have a template</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>The type of template on which a\r
-method works is declared with the SEQ_TYPE parameter in the method\r
-configuration file:</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'>            </span>SEQ_TYPE<span\r
-style='mso-tab-count:1'>          </span>S: a method that uses sequences </span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'>            </span>SEQ_TYPE<span\r
-style='mso-tab-count:1'>          </span>PS: a pairwise method that aligns\r
-sequences and structures</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'>            </span>SEQ_TYPE<span\r
-style='mso-tab-count:1'>          </span>P: a method that aligns structures\r
-(sap for instance)</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>There are 4 tags identifying the\r
-template type:</span></p>\r
-\r
-<p class=flagdescription style='text-indent:28.25pt'><span lang=EN-US>_P_<span\r
-style='mso-tab-count:1'>         </span>Structural templates: a pdb identifier\r
-OR a pdb file</span></p>\r
-\r
-<p class=flagdescription style='margin-left:106.2pt;text-indent:-35.4pt'><span\r
-lang=EN-US>_G_<span style='mso-tab-count:1'>        </span>Genomic templates: a\r
-protein sequence where boundary amino-acid have been recoded with ( o:0, i:1,\r
-j:2)</span></p>\r
-\r
-<p class=flagdescription style='text-indent:28.25pt'><span lang=EN-US>_R_<span\r
-style='mso-tab-count:1'>        </span>Profile Templates: a file containing a\r
-multiple sequence alignment</span></p>\r
-\r
-<p class=flagdescription style='text-indent:28.25pt'><span lang=EN-US>_F_<span\r
-style='mso-tab-count:1'>         </span>RNA secondary Structures</span></p>\r
-\r
-<p class=flagdescription style='text-indent:28.25pt'><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>More than one template file can be\r
-provided. There is no need to have one template for every sequence in the\r
-dataset. </span></p>\r
-\r
-<p class=flagdescription style='text-indent:28.25pt'><span lang=EN-US>_P_, _G_,\r
-and _R_ are known as <b style='mso-bidi-font-weight:normal'>template TAGS<o:p></o:p></b></span></p>\r
-\r
-<p class=flagheading2><span lang=EN-US>2-SCRIPT_&lt;scriptname&gt;</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Indicates that filename is a script\r
-that will be used to generate a valid template file. The script will run on a\r
-file containing all your sequences using the following syntax:</span></p>\r
-\r
-<p class=example2><span lang=EN-US>scriptname \96infile=&lt;your sequences&gt;\r
--outfile=&lt;template_file&gt;</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>It is also possible to pass some\r
-parameters, use @ as a separator and # in place of the = sign. For instance, if\r
-you want to call the a script named blast.pl with the foloowing parameters;</span></p>\r
-\r
-<p class=example2><span lang=EN-US>blast.pl -db=pdb -dir=/local/test</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Use</span></p>\r
-\r
-<p class=example2><span lang=EN-US>SCRIPT_blast.pl@db#pdb@dir#/local/test</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Bear in mind that the input output\r
-flags will then be concatenated to this command line so that t_coffee ends up\r
-calling the program using the following system call:</span></p>\r
-\r
-<p class=example2><span lang=EN-US>blast.pl -db=pdb -dir=/local/test\r
--infile=&lt;some tmp file&gt; -outfile=&lt;another tmp file&gt;</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=flagheading2><span lang=EN-US>3-SELF_TAG</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>TAG can take the value of any of the known\r
-TAGS (_S_, _G_, _P_). SELF indicates that the original name of the sequence\r
-will be used to fetch the template: </span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee 3d_sample2.fasta \96template_file SELF_P_</span></p>\r
-\r
-</div>\r
-\r
-<p class=flagdescription><span lang=EN-US>The previous command will work\r
-because the sequences in 3d_sample3 are named </span></p>\r
-\r
-<p class=flagheading2><span lang=EN-US>4-SEQFILE_TAG_filename</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Use this flag if your templates are\r
-in filename, and are named according to the sequences. For instance, if your\r
-protein sequences have been recoded with Exon/Intron information, you should\r
-have the recoded sequences names according to the original:</span></p>\r
-\r
-<p class=example2><span lang=EN-US>SEQFILE_G_recodedprotein.fasta<span\r
-style='mso-tab-count:1'>  </span></span></p>\r
-\r
-<p class=flag><a name="_Toc235958628"></a><a name="_Toc102494850"></a><a\r
-name="_Toc101065316"><span style='mso-bookmark:_Toc102494850'><span\r
-style='mso-bookmark:_Toc235958628'><span lang=AF>-struc_to_use</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--struc_to_use=&lt;struc1, struc2\85&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -struc_to_use=NULL</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Restricts the 3Dcoffee to a set of\r
-pre-defined structures.</span></p>\r
-\r
-<h2><a name="_Toc235958629"></a><a name="_Toc102494851"></a><a\r
-name="_Toc102494386"></a><a name="_Toc101065317"><span style='mso-bookmark:\r
-_Toc102494386'><span style='mso-bookmark:_Toc102494851'><span style='mso-bookmark:\r
-_Toc235958629'><span lang=EN-US>Multiple Local Alignments</span></span></span></span></a></h2>\r
-\r
-<p class=MyNormal><span lang=AF>It is possible to compute multiple local alignments,\r
-using the moca routine. MOCA is a routine that allows extracting all the local\r
-alignments that show some similarity with another predefined fragment.</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>'mocca' is a perl script that calls t-coffee\r
-and provides it with the appropriate parameters.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958630"></a><a name="_Toc102494852"></a><a\r
-name="_Toc101065318"><span style='mso-bookmark:_Toc102494852'><span\r
-style='mso-bookmark:_Toc235958630'><span lang=AF>-domain</span></span></span></a><span\r
-style='mso-bookmark:_Toc102494852'><span style='mso-bookmark:_Toc235958630'><span\r
-lang=AF>/-mocca</span></span></span></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--domain<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: not set</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>This flag indicates that t_coffee\r
-will run using the domain mode. All the sequences will be concatenated, and the\r
-resulting sequence will be compared to itself using lalign_rs_s_pair mode\r
-(lalign of the sequence against itself using keeping the lalign raw score).\r
-This step is the most computer intensive, and it is advisable to save the\r
-resulting file.</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee -in Ssample_seq1.fasta,Mlalign_rs_s_pair\r
--out_lib=sample_lib1.mocca_lib -domain -start=100 -len=50 </span></p>\r
-\r
-</div>\r
-\r
-<p class=flagdescription><span lang=EN-US>This instruction will use the\r
-fragment 100-150 on the concatenated sequences, as a template for the extracted\r
-repeats. The extraction will only be made once. The library will be placed in\r
-the file &lt;lib name&gt;.</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>If you want, you can test other\r
-coordinates for the repeat, such as </span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee -in sample_lib1.mocca_lib -domain -start=100 -len=60 </span></p>\r
-\r
-</div>\r
-\r
-<p class=flagdescription><span lang=EN-US>This run will use the fragment\r
-100-160, and will be much faster because it does not need to re-compute the\r
-lalign library. </span></p>\r
-\r
-<p class=flag><a name="_Toc235958631"></a><a name="_Toc102494853"></a><a\r
-name="_Toc101065319"><span style='mso-bookmark:_Toc102494853'><span\r
-style='mso-bookmark:_Toc235958631'><span lang=AF>-start</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--start=&lt;int value&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: not set</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>This flag indicates the starting\r
-position of the portion of sequence that will be used as a template for the\r
-repeat extraction. The value assumes that all the sequences have been\r
-concatenated, and is given on the resulting sequence.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958632"></a><a name="_Toc102494854"></a><a\r
-name="_Toc101065320"><span style='mso-bookmark:_Toc102494854'><span\r
-style='mso-bookmark:_Toc235958632'><span lang=AF>-len</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--len=&lt;int value&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: not set</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>This flag indicates the length of the\r
-portion of sequence that will be used as a template.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958633"></a><a name="_Toc102494855"></a><a\r
-name="_Toc101065321"><span style='mso-bookmark:_Toc102494855'><span\r
-style='mso-bookmark:_Toc235958633'><span lang=AF>-scale</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--scale=&lt;int value&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -scale=-100</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>This flag indicates the value of the\r
-threshold for extracting the repeats. The actual threshold is equal to:</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'>            </span>motif_len*scale</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Increase the scale </span><span\r
-lang=EN-US style='font-family:Wingdings;mso-ascii-font-family:"Times New Roman";\r
-mso-hansi-font-family:"Times New Roman";mso-char-type:symbol;mso-symbol-font-family:\r
-Wingdings'><span style='mso-char-type:symbol;mso-symbol-font-family:Wingdings'>ó</span></span><span\r
-lang=EN-US>Increase sensitivity </span><span lang=EN-US style='font-family:\r
-Wingdings;mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman";\r
-mso-char-type:symbol;mso-symbol-font-family:Wingdings'><span style='mso-char-type:\r
-symbol;mso-symbol-font-family:Wingdings'>ó</span></span><span lang=EN-US> More\r
-alignments( i.e. -50).</span></p>\r
-\r
-<p class=flag><a name="_Toc235958634"></a><a name="_Toc102494856"></a><a\r
-name="_Toc101065322"><span style='mso-bookmark:_Toc102494856'><span\r
-style='mso-bookmark:_Toc235958634'><span lang=AF>-domain_interactive [Examples]</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--domain_interactive<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: unset</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Launches an interactive mocca\r
-session.</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee -in Lsample_lib3.tc_lib,Mlalign_rs_s_pair -domain -start=100 -len=60</span></p>\r
-\r
-</div>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6;margin-left:0mm;margin-right:10.0mm'>\r
-\r
-<p class=examplefilesmallCxSpFirst><span lang=EN-US>TOLB_ECOLI_212_26<span\r
-style='mso-tab-count:3'>                 </span><span\r
-style='mso-spacerun:yes'>    </span>211 SKLAYVTFESGR--SALVIQTLANGAVRQV-ASFPRHNGAPAFSPDGSKLAFA</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US>TOLB_ECOLI_165_218<span\r
-style='mso-spacerun:yes'>    </span>164 TRIAYVVQTNGGQFPYELRVSDYDGYNQFVVHRSPQPLMSPAWSPDGSKLAYV</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US>TOLB_ECOLI_256_306<span\r
-style='mso-spacerun:yes'>    </span>255 SKLAFALSKTGS--LNLYVMDLASGQIRQV-TDGRSNNTEPTWFPDSQNLAFT</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US>TOLB_ECOLI_307_350<span\r
-style='mso-spacerun:yes'>    </span>306 -------DQAGR--PQVYKVNINGGAPQRI-TWEGSQNQDADVSSDGKFMVMV</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US>TOLB_ECOLI_351_393<span\r
-style='mso-spacerun:yes'>    </span>350 -------SNGGQ--QHIAKQDLATGGV-QV-LSSTFLDETPSLAPNGTMVIYS<span\r
-style='mso-spacerun:yes'>  </span></span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><span\r
-style='mso-spacerun:yes'>                        </span>1<span\r
-style='mso-spacerun:yes'>           </span>*<span\r
-style='mso-spacerun:yes'>        </span><span\r
-style='mso-spacerun:yes'>     </span>*<span style='mso-spacerun:yes'>   \r
-</span>:<span style='mso-spacerun:yes'>     </span><span\r
-style='mso-spacerun:yes'>     </span>.<span style='mso-spacerun:yes'>  \r
-</span>.:.<span style='mso-spacerun:yes'>  </span>:<span\r
-style='mso-spacerun:yes'>    </span></span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><span\r
-style='mso-spacerun:yes'>        </span>MENU: Type Letter Flag[number] and\r
-Return: ex |10</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><span\r
-style='mso-spacerun:yes'>        </span>|x<span style='mso-spacerun:yes'>     \r
-</span>--&gt;Set<span style='mso-spacerun:yes'>     </span>the START to x</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><span\r
-style='mso-spacerun:yes'>        </span>&gt;x<span\r
-style='mso-spacerun:yes'>      </span>--&gt;Set<span\r
-style='mso-spacerun:yes'>     </span>the LEN<span style='mso-spacerun:yes'>  \r
-</span>to x</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><span\r
-style='mso-spacerun:yes'>        </span>Cx<span style='mso-spacerun:yes'>     \r
-</span>--&gt;Set<span style='mso-spacerun:yes'>     </span>the sCale to x</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><span\r
-style='mso-spacerun:yes'>        </span>Sname<span style='mso-spacerun:yes'>  \r
-</span>--&gt;Save<span style='mso-spacerun:yes'>    </span>the<span\r
-style='mso-spacerun:yes'>  </span>Alignment </span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><span\r
-style='mso-spacerun:yes'>        </span>Bx<span style='mso-spacerun:yes'>     \r
-</span>--&gt;Save<span style='mso-spacerun:yes'>    </span>Goes back x it </span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><span\r
-style='mso-spacerun:yes'>        </span>return<span style='mso-spacerun:yes'> \r
-</span>--&gt;Compute the<span style='mso-spacerun:yes'>  </span>Alignment</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><span\r
-style='mso-spacerun:yes'>        </span>X<span style='mso-spacerun:yes'>      \r
-</span>--&gt;eXit</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US>[ITERATION<span\r
-style='mso-spacerun:yes'>   </span>1] [START=211] [LEN= 50] [SCALE=-100]<span\r
-style='mso-spacerun:yes'>      </span>YOUR CHOICE:</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US>For instance, to set the\r
-length of the domain to 40, type: </span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US>[ITERATION<span\r
-style='mso-spacerun:yes'>   </span>1] [START=211] [LEN= 50] [SCALE=-100]<span\r
-style='mso-spacerun:yes'>      </span>YOUR CHOICE:&gt;40[return]</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US>[return]</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US>Which will generate:</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US>TOLB_ECOLI_212_252<span\r
-style='mso-spacerun:yes'>    </span>211\r
-SKLAYVTFESGRSALVIQTLANGAVRQVASFPRHNGAPAF<span style='mso-spacerun:yes'> \r
-</span>251</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US>TOLB_ECOLI_256_296<span\r
-style='mso-spacerun:yes'>    </span>255\r
-SKLAFALSKTGSLNLYVMDLASGQIRQVTDGRSNNTEPTW<span style='mso-spacerun:yes'> \r
-</span>295</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US>TOLB_ECOLI_300_340<span\r
-style='mso-spacerun:yes'>    </span>299\r
-QNLAFTSDQAGRPQVYKVNINGGAPQRITWEGSQNQDADV<span style='mso-spacerun:yes'> \r
-</span>339</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US>TOLB_ECOLI_344_383<span\r
-style='mso-spacerun:yes'>    </span>343\r
-KFMVMVSSNGGQQHIAKQDLATGGV-QVLSSTFLDETPSL<span style='mso-spacerun:yes'> \r
-</span>382</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US>TOLB_ECOLI_387_427<span\r
-style='mso-spacerun:yes'>    </span>386\r
-TMVIYSSSQGMGSVLNLVSTDGRFKARLPATDGQVKFPAW<span style='mso-spacerun:yes'> \r
-</span>426</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><span\r
-style='mso-spacerun:yes'>                        </span>1<span\r
-style='mso-spacerun:yes'>   </span>:<span style='mso-spacerun:yes'>    \r
-</span>:<span style='mso-spacerun:yes'>     </span>:<span\r
-style='mso-spacerun:yes'>       </span><span\r
-style='mso-spacerun:yes'>    </span>::<span style='mso-spacerun:yes'>        \r
-</span>.<span style='mso-spacerun:yes'>     </span>40</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><span\r
-style='mso-spacerun:yes'>        </span>MENU: Type Letter Flag[number] and\r
-Return: ex |10</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><span\r
-style='mso-spacerun:yes'>        </span>|x<span style='mso-spacerun:yes'>     \r
-</span>--&gt;Set<span style='mso-spacerun:yes'>     </span>the START to x</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><span\r
-style='mso-spacerun:yes'>        </span>&gt;x<span\r
-style='mso-spacerun:yes'>      </span>--&gt;Set<span\r
-style='mso-spacerun:yes'>     </span>the LEN<span style='mso-spacerun:yes'>  \r
-</span>to x</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><span\r
-style='mso-spacerun:yes'>        </span>Cx<span style='mso-spacerun:yes'>     \r
-</span>--&gt;Set<span style='mso-spacerun:yes'>     </span>the sCale to x</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><span\r
-style='mso-spacerun:yes'>        </span>Sname<span style='mso-spacerun:yes'>  \r
-</span>--&gt;Save<span style='mso-spacerun:yes'>    </span>the<span\r
-style='mso-spacerun:yes'>  </span>Alignment </span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><span\r
-style='mso-spacerun:yes'> </span><span style='mso-spacerun:yes'>      \r
-</span>Bx<span style='mso-spacerun:yes'>      </span>--&gt;Save<span\r
-style='mso-spacerun:yes'>    </span>Goes back x it </span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><span\r
-style='mso-spacerun:yes'>        </span>return<span style='mso-spacerun:yes'> \r
-</span>--&gt;Compute the<span style='mso-spacerun:yes'>  </span>Alignment</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><span\r
-style='mso-spacerun:yes'>        </span>X<span style='mso-spacerun:yes'>      \r
-</span>--&gt;eXit</span></p>\r
-\r
-<p class=examplefilesmallCxSpMiddle><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=examplefilesmallCxSpLast><span lang=EN-US>[ITERATION<span\r
-style='mso-spacerun:yes'>   </span>3] [START=211] [LEN= 40] [SCALE=-100]<span\r
-style='mso-spacerun:yes'>      </span>YOUR CHOICE: </span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>If you want to indicate the\r
-coordinates, relative to a specific sequence, type:</span></p>\r
-\r
-<p class=example2><span lang=EN-US><span style='mso-tab-count:1'>  </span>|&lt;seq_name&gt;:start</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Type S&lt;your name&gt; to save the\r
-current alignment, and extract a new motif. </span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Type X when you are done.</span></p>\r
-\r
-<h2><a name="_Toc235958635"></a><a name="_Toc102494857"></a><a\r
-name="_Toc102494387"></a><a name="_Toc101065323"><span style='mso-bookmark:\r
-_Toc102494387'><span style='mso-bookmark:_Toc102494857'><span style='mso-bookmark:\r
-_Toc235958635'><span lang=EN-US>Output Control</span></span></span></span></a></h2>\r
-\r
-<h3><a name="_Toc235958636"></a><a name="_Toc102494858"></a><a\r
-name="_Toc102494388"></a><a name="_Toc101065324"><span style='mso-bookmark:\r
-_Toc102494388'><span style='mso-bookmark:_Toc102494858'><span style='mso-bookmark:\r
-_Toc235958636'><span lang=EN-US>Generic</span></span></span></span></a></h3>\r
-\r
-<p class=flag><a name="_Toc235958637"></a><a name="_Toc102494859"><span\r
-style='mso-bookmark:_Toc235958637'><span lang=AF>Conventions Regarding\r
-Filenames</span></span></a></p>\r
-\r
-<p class=MyNormal><span lang=AF>stdout, stderr, stdin, no, /dev/null are valid\r
-filenames. They cause the corresponding file to be output in stderr or stdout,\r
-for an input file, stdin causes the program to requests the corresponding file\r
-through pipe. No causes a suppression of the output, as does /dev/null.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958638"></a><a name="_Toc102494860"><span\r
-style='mso-bookmark:_Toc235958638'><span lang=AF>Identifying the Output files\r
-automatically</span></span></a></p>\r
-\r
-<p class=MyNormal><span lang=AF>In the t_coffee output, each output appears in\r
-a line:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefile><span lang=EN-US>##### FILENAME &lt;name&gt; TYPE\r
-&lt;Type&gt; FORMAT &lt;Format&gt;</span></p>\r
-\r
-</div>\r
-\r
-<p class=flag><a name="_Toc102494861"></a><a name="_Toc102494389"></a><a\r
-name="_Toc101065325"></a><a name="_Toc235958639"><span style='mso-bookmark:\r
-_Toc101065325'><span style='mso-bookmark:_Toc102494389'><span style='mso-bookmark:\r
-_Toc102494861'><span lang=AF>-no_warning</span></span></span></span></a><span\r
-style='mso-bookmark:_Toc101065325'><span style='mso-bookmark:_Toc102494389'><span\r
-style='mso-bookmark:_Toc102494861'></span></span></span></p>\r
-\r
-<p class=flagusage><span style='mso-bookmark:_Toc101065325'><span\r
-style='mso-bookmark:_Toc102494389'><span style='mso-bookmark:_Toc102494861'><span\r
-lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-no_warning<o:p></o:p></span></span></span></span></p>\r
-\r
-<p class=instruction><span style='mso-bookmark:_Toc101065325'><span\r
-style='mso-bookmark:_Toc102494389'><span style='mso-bookmark:_Toc102494861'><span\r
-lang=EN-US>Default: Switched off</span></span></span></span></p>\r
-\r
-<p class=flagdescription><span style='mso-bookmark:_Toc101065325'><span\r
-style='mso-bookmark:_Toc102494389'><span style='mso-bookmark:_Toc102494861'><span\r
-lang=EN-US>Suppresseswarning output.<i style='mso-bidi-font-style:normal'><o:p></o:p></i></span></span></span></span></p>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065325'><span style='mso-bookmark:_Toc102494389'><span\r
-style='mso-bookmark:_Toc102494861'><span lang=EN-US><o:p>&nbsp;</o:p></span></span></span></span></h3>\r
-\r
-<h3><span style='mso-bookmark:_Toc101065325'><span style='mso-bookmark:_Toc102494389'><span\r
-style='mso-bookmark:_Toc102494861'><a name="_Toc235958640"><span lang=EN-US>Alignments</span></a></span></span></span></h3>\r
-\r
-<p class=flag><a name="_Toc235958641"></a><a name="_Toc102494862"></a><a\r
-name="_Toc101065326"><span style='mso-bookmark:_Toc102494862'><span\r
-style='mso-bookmark:_Toc235958641'><span lang=AF>-outfile</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-outfile=&lt;out_aln file,default,no&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default:-outfile=default</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Indicates the name of the alignment\r
-output by t_coffee. If the default is used, the alignment is named <i\r
-style='mso-bidi-font-style:normal'>&lt;your sequences&gt;.aln<o:p></o:p></i></span></p>\r
-\r
-<p class=flag><a name="_Toc235958642"></a><a name="_Toc102494863"></a><a\r
-name="_Toc101065327"><span style='mso-bookmark:_Toc102494863'><span\r
-style='mso-bookmark:_Toc235958642'><span lang=AF>-output</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-output=&lt;format1,format2,...&gt; <o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default:-output=clustalw</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Indicates the format used for\r
-outputting the -outfile.</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Supported formats are:</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'>            </span></span></p>\r
-\r
-<p class=flagdescriptionid1><span lang=EN-US>clustalw_aln, clustalw<span\r
-style='mso-tab-count:1'>       </span>: ClustalW format.</span></p>\r
-\r
-<p class=flagdescriptionid1><span lang=EN-US>gcg, msf_aln<span\r
-style='mso-spacerun:yes'>      </span><span style='mso-tab-count:1'>  </span><span\r
-style='mso-tab-count:1'>                </span>: MSF alignment.</span></p>\r
-\r
-<p class=flagdescriptionid1><span lang=EN-US>pir_aln<span style='mso-tab-count:\r
-3'>                                  </span>: pir alignment.</span></p>\r
-\r
-<p class=flagdescriptionid1><span lang=EN-US>fasta_aln<span style='mso-tab-count:\r
-2'>                             </span>: fasta alignment.</span></p>\r
-\r
-<p class=flagdescriptionid1><span lang=EN-US>phylip<span style='mso-tab-count:\r
-3'>                                   </span>: Phylip format.</span></p>\r
-\r
-<p class=flagdescriptionid1><span lang=EN-US>pir_seq<span style='mso-tab-count:\r
-3'>                                  </span>: pir sequences (no gap).</span></p>\r
-\r
-<p class=flagdescriptionid1><span lang=EN-US>fasta_seq<span style='mso-tab-count:\r
-2'>                             </span>: fasta sequences (no gap).</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><span style='mso-tab-count:2'>                            </span></span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>As well as:</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=flagdescriptionid1><span lang=EN-US>score_ascii<span style='mso-tab-count:\r
-1'>           </span>: causes the output of a reliability flag </span></p>\r
-\r
-<p class=flagdescriptionid1><span lang=EN-US>score_html<span style='mso-tab-count:\r
-1'>           </span>: causes the output to be a reliability plot in HTML</span></p>\r
-\r
-<p class=flagdescriptionid1><span lang=EN-US>score_pdf<span style='mso-tab-count:\r
-1'>             </span>: idem in PDF (if ps2pdf is installed on your system).</span></p>\r
-\r
-<p class=flagdescriptionid1><span lang=EN-US>score_ps<span style='mso-tab-count:\r
-1'>               </span><span style='mso-tab-count:1'>                </span>:\r
-idem in postscript.</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>More than one format can be\r
-indicated:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee sample_seq1.fasta -output=clustalw,gcg, score_html </span></p>\r
-\r
-</div>\r
-\r
-<p class=flagdescription><span lang=EN-US>A publication describing the CORE\r
-index is available on:</span></p>\r
-\r
-<p class=MyNormal><span lang=AF><a\r
-href="http://www.tcoffee.org/Publications/Pdf/core.pp.pdf"><span lang=EN-US\r
-style='mso-ansi-language:EN-US'>http://www.tcoffee.org/Publications/Pdf/core.pp.pdf</span></a></span></p>\r
-\r
-<p class=flag><a name="_Toc235958643"></a><a name="_Toc102494864"></a><a\r
-name="_Toc101065328"><span style='mso-bookmark:_Toc102494864'><span\r
-style='mso-bookmark:_Toc235958643'><span lang=AF>-outseqweight</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-outseqweight=&lt;filename&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: not used</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Indicates the name of the file in\r
-which the sequences weights should be saved..</span></p>\r
-\r
-<p class=flag><a name="_Toc235958644"></a><a name="_Toc102494865"></a><a\r
-name="_Toc101065329"><span style='mso-bookmark:_Toc102494865'><span\r
-style='mso-bookmark:_Toc235958644'><span lang=AF>-case</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-case=&lt;keep,upper,lower&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -case=keep</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>Instructs the program on the case to be used in\r
-the output file (Clustalw uses upper case). The default keeps the case and\r
-makes it possible to maintain a mixture of upper and lower case residues.</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>If you need to change the case of your file,\r
-you can use seq_reformat:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee \96other_pg seq_reformat \96in sample_aln1.aln \96action +lower \96output\r
-clustalw </span></p>\r
-\r
-</div>\r
-\r
-<p class=flag><a name="_Toc235958645"></a><a name="_Toc102494866"></a><a\r
-name="_Toc101065330"><span style='mso-bookmark:_Toc102494866'><span\r
-style='mso-bookmark:_Toc235958645'><span lang=AF>-cpu</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>deprecated<o:p></o:p></span></p>\r
-\r
-<p class=flag><a name="_Toc235958646"></a><a name="_Toc102494867"><span\r
-style='mso-bookmark:_Toc235958646'><span lang=AF>-outseqweight</span></span></a></p>\r
-\r
-<p class=MyNormal><span lang=AF>Usage: -outseqweight=&lt;name of the file\r
-containing the weights applied&gt;</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>Default: -outseqweight=no</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>Will cause the program to output the weights\r
-associated with every sequence in the dataset.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958647"></a><a name="_Toc102494868"></a><a\r
-name="_Toc101065331"><span style='mso-bookmark:_Toc102494868'><span\r
-style='mso-bookmark:_Toc235958647'><span lang=AF>-outorder [cw]</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-outorder=&lt;input OR aligned OR\r
-filename&gt; <o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default:-outorder=input</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Sets the order of the sequences in\r
-the output alignment: <b>-outorder=input</b> means the sequences are kept in\r
-the original order. <b>-outorder=aligned</b> means the sequences come in the\r
-order indicated by the tree. This order can be seen as a one-dimensional\r
-projection of the tree distances. <b style='mso-bidi-font-weight:normal'>\96outdorder=&lt;filename&gt;</b>Filename\r
-is a legal fasta file, whose order will be used in the final alignment.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958648"><span lang=AF>-inorder [cw]</span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-inorder=&lt;input OR aligned&gt; <o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default:-inorder=aligned</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Multiple alignments based on dynamic\r
-programming depend slightly on the order in which the incoming sequences are\r
-provided. To prevent this effect sequences are arbitrarily sorted at the\r
-beginning of the program (-inorder=aligned). However, this affects the sequence\r
-order within the library. You can switch this off by ststing \96inorder=input.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958649"></a><a name="_Toc102494869"><span\r
-style='mso-bookmark:_Toc235958649'><span lang=AF>-seqnos</span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-seqnos=&lt;on or off&gt; <o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default:-seqnos=off</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>Causes the output alignment to contain residue\r
-numbers at the end of each line:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span lang=EN-US>T-COFFEE</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>seq1 aaa---aaaa--------aa 9</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>seq2 a-----aa-----------a 4</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>seq1 a-----------------a 11</span></p>\r
-\r
-<p class=examplefileCxSpLast><span lang=EN-US>seq2 aaaaaaaaaaaaaaaaaaa 19</span></p>\r
-\r
-</div>\r
-\r
-<h3><a name="_Toc235958650"></a><a name="_Toc102494870"></a><a\r
-name="_Toc102494390"></a><a name="_Toc101065332"><span style='mso-bookmark:\r
-_Toc102494390'><span style='mso-bookmark:_Toc102494870'><span style='mso-bookmark:\r
-_Toc235958650'><span lang=EN-US>Libraries</span></span></span></span></a></h3>\r
-\r
-<p class=MyNormal><span lang=AF>Although, it does not necessarily do so\r
-explicitly, T-Coffee always end up combining libraries. Libraries are\r
-collections of pairs of residues. Given a set of libraries, T-Coffee makes an\r
-attempt to assemble the alignment with the highest level of consistence. You\r
-can think of the alignment as a timetable. Each library pair would be a request\r
-from students or teachers, and the job of T-Coffee would be to assemble the\r
-time table that makes as many people as possible happy\85</span></p>\r
-\r
-<p class=flag><a name="_Toc235958651"></a><a name="_Toc102494871"><span\r
-style='mso-bookmark:_Toc235958651'><span lang=AF>-out_lib</span></span></a></p>\r
-\r
-<p class=MyNormal><span lang=AF>Usage:<span style='mso-spacerun:yes'> \r
-</span>-out_lib=&lt;name of the library,default,no&gt; </span></p>\r
-\r
-<p class=MyNormal><span lang=AF>Default:-out_lib=default</span></p>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Sets the name of the library output.\r
-Default implies &lt;run_name&gt;.tc_lib</span></p>\r
-\r
-<p class=flag><a name="_Toc235958652"></a><a name="_Toc102494872"></a><a\r
-name="_Toc101065333"><span style='mso-bookmark:_Toc102494872'><span\r
-style='mso-bookmark:_Toc235958652'><span lang=AF>-lib_only</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span\r
-style='mso-spacerun:yes'>  </span>-lib_only<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: unset</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Causes the program to stop once the\r
-library has been computed. Must be used in conjunction with the flag <b\r
-style='mso-bidi-font-weight:normal'>\96out_lib</b></span></p>\r
-\r
-<h3><a name="_Toc235958653"></a><a name="_Toc102494873"></a><a\r
-name="_Toc102494391"></a><a name="_Toc101065334"><span style='mso-bookmark:\r
-_Toc102494391'><span style='mso-bookmark:_Toc102494873'><span style='mso-bookmark:\r
-_Toc235958653'><span lang=EN-US>Trees</span></span></span></span></a></h3>\r
-\r
-<p class=flag><a name="_Toc235958654"></a><a name="_Toc102494874"></a><a\r
-name="_Toc101065335"><span style='mso-bookmark:_Toc102494874'><span\r
-style='mso-bookmark:_Toc235958654'><span lang=AF>-newtree</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--newtree=&lt;tree file&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: No file specified</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Indicates the name of the file into\r
-which the guide tree will be written. The default will be\r
-&lt;sequence_name&gt;.dnd, or &lt;run_name.dnd&gt;. The tree is written in the\r
-parenthesis format known as newick or <st1:place w:st="on"><st1:State w:st="on">New\r
-  Hampshire</st1:State></st1:place> and used by Phylips (see the format\r
-section).</span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.5pt;\r
-padding:0mm 0mm 0mm 0mm;background:#F7CBB7'>\r
-\r
-<p class=Warning><span lang=EN-US>Do NOT confuse this guide tree with a\r
-phylogenetic tree.</span></p>\r
-\r
-</div>\r
-\r
-<h2><a name="_Toc235958655"></a><a name="_Toc102494875"></a><a\r
-name="_Toc102494392"></a><a name="_Toc101065336"><span style='mso-bookmark:\r
-_Toc102494392'><span style='mso-bookmark:_Toc102494875'><span style='mso-bookmark:\r
-_Toc235958655'><span lang=EN-US>Reliability Estimation</span></span></span></span></a></h2>\r
-\r
-<h3><a name="_Toc235958656"></a><a name="_Toc102494876"></a><a\r
-name="_Toc102494393"></a><a name="_Toc101065337"><span style='mso-bookmark:\r
-_Toc102494393'><span style='mso-bookmark:_Toc102494876'><span style='mso-bookmark:\r
-_Toc235958656'><span lang=EN-US>CORE Computation</span></span></span></span></a></h3>\r
-\r
-<p class=MyNormal><span lang=AF>The CORE is an index that indicates the\r
-consistency between the library of piarwise alignments and the final multiple\r
-alignment. Our experiment indicate that the higher this consistency, the more\r
-reliable the alignment. A publication describing the CORE index can be found\r
-on:</span></p>\r
-\r
-<p class=MyNormal><a name="_Toc102494877"></a><a name="_Toc101065338"><span\r
-style='mso-bookmark:_Toc102494877'></span></a><a\r
-href="http://www.tcoffee.org/Publications/Pdf/core.pp.pdf"><span\r
-style='mso-bookmark:_Toc101065338'><span style='mso-bookmark:_Toc102494877'><span\r
-lang=EN-US style='mso-ansi-language:EN-US'>http://www.tcoffee.org/Publications/Pdf/core.pp.pdf</span></span></span><span\r
-style='mso-bookmark:_Toc101065338'><span style='mso-bookmark:_Toc102494877'></span></span></a><span\r
-style='mso-bookmark:_Toc101065338'><span style='mso-bookmark:_Toc102494877'></span></span></p>\r
-\r
-<p class=flag><span style='mso-bookmark:_Toc101065338'><span style='mso-bookmark:\r
-_Toc102494877'><a name="_Toc235958657"><span lang=AF>-evaluate_mode</span></a></span></span></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--evaluate_mode=&lt;t_coffee_fast,t_coffee_slow,t_coffee_non_extended &gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: -evaluate_mode=t_coffee_fast</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>This flag indicates the mode used to\r
-normalize the t_coffee score when computing the reliability score. </span></p>\r
-\r
-<p class=flagdescription><i style='mso-bidi-font-style:normal'><span\r
-lang=EN-US>t_coffee_fast</span></i><span lang=EN-US>: Normalization is made\r
-using the highest score in the MSA. This evaluation mode was validated and in\r
-our hands, pairs of residues with a score of 5 or higher have 90 % chances to\r
-be correctly aligned to one another. </span></p>\r
-\r
-<p class=flagdescription><i style='mso-bidi-font-style:normal'><span\r
-lang=EN-US>t_coffee_slow:</span></i><span lang=EN-US> Normalization is made\r
-using the library. This usually results in lower score and a scoring scheme\r
-more sensitive to the number of sequences in the dataset. Note that this\r
-scoring scheme is not any more slower, thanks to the implementation of a faster\r
-heuristic algorithm. </span></p>\r
-\r
-<p class=flagdescription><i style='mso-bidi-font-style:normal'><span\r
-lang=EN-US>t_coffee_non_extended:</span></i><span lang=EN-US> the score of each\r
-residue is the ratio between the sum of its non extended scores with the column\r
-and the sum of all its possible non extended scores.</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>These modes will be useful when\r
-generating colored version of the output, with the <b style='mso-bidi-font-weight:\r
-normal'>\96output</b> flag:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee sample_seq1.fasta \96evaluate_mode t_coffee_slow \96output score_ascii,\r
-score_html </span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee sample_seq1.fasta \96evaluate_mode t_coffee_fast \96output score_ascii,\r
-score_html </span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee sample_seq1.fasta \96evaluate_mode t_coffee_non_extended \96output\r
-score_ascii, score_html </span></p>\r
-\r
-</div>\r
-\r
-<h2><a name="_Toc235958658"></a><a name="_Toc102494878"></a><a\r
-name="_Toc102494394"></a><a name="_Toc101065339"><span style='mso-bookmark:\r
-_Toc102494394'><span style='mso-bookmark:_Toc102494878'><span style='mso-bookmark:\r
-_Toc235958658'><span lang=EN-US>Generic Output</span></span></span></span></a></h2>\r
-\r
-<p class=flag><a name="_Toc235958659"></a><a name="_Toc102494879"><span\r
-style='mso-bookmark:_Toc235958659'><span lang=AF>-run_name</span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--run_name=&lt;your run name&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default: no default set</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>This flag causes the prefix &lt;your\r
-sequences&gt; to be replaced by &lt;your run name&gt; when renaming the default\r
-output files.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958660"></a><a name="_Toc102494880"></a><a\r
-name="_Toc101065340"><span style='mso-bookmark:_Toc102494880'><span\r
-style='mso-bookmark:_Toc235958660'><span lang=AF>-quiet</span></span></span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--quiet=&lt;stderr,stdout,file name OR nothing&gt;.<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default:-quiet=stderr</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Redirects the standard output to\r
-either a file. <b>-quiet</b> on its own redirect the output to /dev/null.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958661"></a><a name="_Toc102494881"><span\r
-style='mso-bookmark:_Toc235958661'><span lang=AF>-align [CW]</span></span></a></p>\r
-\r
-<p class=MyNormal><span lang=AF>This flag indicates that the program must\r
-produce the alignment. It is here for compatibility with ClustalW.</span></p>\r
-\r
-<h2><a name="_Toc235958662"><span lang=EN-US>APDB, iRMSD and tRMSD Parameters</span></a></h2>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.5pt;\r
-padding:0mm 0mm 0mm 0mm;background:#F7CBB7'>\r
-\r
-<p class=Warning><span lang=EN-US>Warning: These flags will only work within\r
-the APDB package that can be invoked via the \96other_pg parameter of T-Coffee:</span></p>\r
-\r
-<p class=Warning><span lang=EN-US><span style='mso-tab-count:2'>                               </span><span\r
-style='mso-spacerun:yes'> </span>t_coffee \96other_pg apdb \96aln &lt;your aln&gt;</span></p>\r
-\r
-<p class=Warning><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-</div>\r
-\r
-<p class=flag><a name="_Toc235958663"><span lang=AF>-quiet [Same as T-Coffee]</span></a></p>\r
-\r
-<p class=flag><a name="_Toc235958664"><span lang=AF>-run_name [Same as\r
-T-Coffee]</span></a></p>\r
-\r
-<p class=flag><a name="_Toc235958665"><span lang=AF>-aln</span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--aln=&lt;file_name&gt;.<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default:none</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Indicates the name of the file\r
-containing the sequences that need to be evaluated. The sequences whose\r
-structure is meant to be used must be named according to their PDB identifier. </span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>The format can be FASTA, CLUSTAL or\r
-any of the formats supported by T-Coffee. APDB only evaluates residues in\r
-capital and ignores those in lower case. If your sequences are in lower case,\r
-you can upper case them using seq_reformat:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee \96other_pg seq_reformat \96in 3d_sample4.aln \96action +upper \96output\r
-clustalw &gt; 3d_sample4.cw_aln</span></p>\r
-\r
-</div>\r
-\r
-<p class=flagdescription><span lang=EN-US>The alignment can then be evaluated\r
-using the defaultr of APDB:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee \96other_pg apdb \96aln 3d_sample4.aln</span></p>\r
-\r
-</div>\r
-\r
-<p class=flagdescription><span lang=EN-US>The alignment can contain as many\r
-structures as you wish.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958666"><span lang=AF>-n_excluded_nb</span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--n_excluded_nb=&lt;integer&gt;.<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default:1</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>When evaluating the local score of a\r
-pair of aligned residues, the residues immediately next to that column should\r
-not contribute to the measure. By default the first to the left and first to\r
-the right are excluded.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958667"><span lang=AF>-maximum_distance</span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--maximum_distance=&lt;float&gt;.<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default:10</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Size of the neighborhood considered\r
-around every residue. If .-local_mode is set to sphere, -maximum_distance is\r
-the radius of a sphere centered around each residue. If \96local_mode is set to\r
-window, then \96maximum_distance is the size of the half window (i.e.\r
-window_size=-maximum_distance*2+1).</span></p>\r
-\r
-<p class=flag><a name="_Toc235958668"><span lang=AF>-similarity_threshold</span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--similarity_threshold=&lt;integer&gt;.<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default:70</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Fraction of the neighborhood that\r
-must be supportive for a pair of residue to be considered correct in APDB. The\r
-neighborhood is a sphere defined by \96maximum_distance, and the support is\r
-defined by \96md_threshold.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958669"><span lang=AF>-local_mode</span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--local_mode=&lt;sphere,window&gt;.<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default:sphere</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Defines the shape of a neighborhood,\r
-either as a sphere or as a window.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958670"><span lang=AF>-filter</span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--filter=&lt;0.00-1.00&gt;.<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default:1.00</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>Defines the centiles that should be\r
-kept when making the local measure. Foir instance, -filter=0.90 means that the\r
-the 10 last centiles will be removed from the evaluation. The filtration is\r
-carried out on the iRMSD values.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958671"><span lang=AF>-print_rapdb [Unsupported]</span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--print_rapdb (FLAG)<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default:off</span></p>\r
-\r
-<p class=flagdescription><span lang=EN-US>This causes the prints out of the\r
-exact neighborhood of every considered pair of residues.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958672"><span lang=AF>-outfile [Same as T-Coffee]</span></a></p>\r
-\r
-<p class=MyNormal><span lang=AF>This flag is meant to control the output name\r
-of the colored APDB output. This file will either display the local APDB score\r
-or the local iRMD, depending on the value of \96color_mode. The default format is\r
-defined by \96ouptut and is score_html.</span></p>\r
-\r
-<p class=flag><a name="_Toc235958673"><span lang=AF>-color_mode</span></a></p>\r
-\r
-<p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:\r
--color_mode=&lt;apdb, irmsd&gt;<o:p></o:p></span></p>\r
-\r
-<p class=instruction><span lang=EN-US>Default:apdb</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>This flag is meant to control the colored APDB\r
-output (local score). This file will either display the local APDB score or the\r
-local iRMD.</span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 3.0pt;\r
-padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0mm;margin-right:\r
-4.25pt'>\r
-\r
-<p class=ChapterTitle><a name="_Toc235958674"><span lang=EN-US>Building a\r
-Server</span></a></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF>We maintain a T-Coffee server (www.tcoffee.org).\r
-We will be pleased to provide anyone who wants to set up a similar service with\r
-the sources</span></p>\r
-\r
-<h3><a name="_Toc102494884"></a><a name="_Toc102494396"></a><a\r
-name="_Toc235958675"><span style='mso-bookmark:_Toc102494396'><span\r
-style='mso-bookmark:_Toc102494884'><span lang=EN-US>Environment Variables</span></span></span></a><span\r
-style='mso-bookmark:_Toc102494396'><span style='mso-bookmark:_Toc102494884'></span></span></h3>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc102494396'><span\r
-style='mso-bookmark:_Toc102494884'><span lang=AF>T-Coffee stores a lots of\r
-information in locations that may be unsuitable when running a server. </span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc102494396'><span\r
-style='mso-bookmark:_Toc102494884'><span lang=AF>By default, T-Coffee will\r
-generate and rely on the follwing directory structure:</span></span></span></p>\r
-\r
-<p class=example><span style='mso-bookmark:_Toc102494396'><span\r
-style='mso-bookmark:_Toc102494884'><span lang=EN-US>/home/youraccount/<span\r
-style='mso-tab-count:2'>         </span>#HOME_4_TCOFFEE</span></span></span></p>\r
-\r
-<p class=example><span style='mso-bookmark:_Toc102494396'><span\r
-style='mso-bookmark:_Toc102494884'><span lang=EN-US>HOME_4_TCOFFEE/.t_coffee/ <span\r
-style='mso-tab-count:1'> </span>#DIR_4_TCOFFEE</span></span></span></p>\r
-\r
-<p class=example><span style='mso-bookmark:_Toc102494396'><span\r
-style='mso-bookmark:_Toc102494884'><span lang=EN-US>DIR_4_TCOFFEE/cache<span\r
-style='mso-tab-count:2'>        </span>#CACHE_4_TCOFFEE</span></span></span></p>\r
-\r
-<p class=example><span style='mso-bookmark:_Toc102494396'><span\r
-style='mso-bookmark:_Toc102494884'><span lang=EN-US>DIR_4_TCOFFEE/tmp<span\r
-style='mso-tab-count:2'>          </span>#TMP_4_TCOFFEE</span></span></span></p>\r
-\r
-<p class=example><span style='mso-bookmark:_Toc102494396'><span\r
-style='mso-bookmark:_Toc102494884'><span lang=EN-US>DIR_4_TCOFFEE/methods<span\r
-style='mso-tab-count:2'>            </span>#METHOS_4_TCOFFEE</span></span></span></p>\r
-\r
-<p class=example><span style='mso-bookmark:_Toc102494396'><span\r
-style='mso-bookmark:_Toc102494884'><span lang=EN-US>DIR_4_TCOFFEE/mcoffee<span\r
-style='mso-tab-count:2'>            </span>#MCOFFEE_4_TCOFFEE</span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc102494396'><span\r
-style='mso-bookmark:_Toc102494884'><span lang=AF><o:p>&nbsp;</o:p></span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc102494396'><span\r
-style='mso-bookmark:_Toc102494884'><span lang=AF>By default, all these\r
-directories are automatically created, following the dependencies suggested\r
-here. </span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc102494396'><span\r
-style='mso-bookmark:_Toc102494884'><span lang=AF>The first step is the\r
-determination of the HOME. By default the program tries to use HOME_4_TCOFFEE,\r
-then the HOME variable and TMP or TEMP if HOME is not set on your system or\r
-your account. It is your responsibility to make sure that one of these\r
-variables is set to some valid location where the T-Coffee process is allowed\r
-to read and write.</span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc102494396'><span\r
-style='mso-bookmark:_Toc102494884'><span lang=AF>If no valid location can be\r
-found for HOME_4_TCOFFEE, the program exits. If you are running T-Coffee on a\r
-server, we recommend to hard set the following locations, where your scratch is\r
-a valid location. </span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc102494396'><span\r
-style='mso-bookmark:_Toc102494884'><span lang=AF><o:p>&nbsp;</o:p></span></span></span></p>\r
-\r
-<p class=example><span style='mso-bookmark:_Toc102494396'><span\r
-style='mso-bookmark:_Toc102494884'><span lang=EN-US>HOME_4_TCOFFEE=\94your scratch\94</span></span></span></p>\r
-\r
-<p class=example><span style='mso-bookmark:_Toc102494396'><span\r
-style='mso-bookmark:_Toc102494884'><span lang=EN-US>TMP_4_TCOFFEE=\94your\r
-scratch\94</span></span></span></p>\r
-\r
-<p class=example><span style='mso-bookmark:_Toc102494396'><span\r
-style='mso-bookmark:_Toc102494884'><span lang=EN-US>DIR_4_TCOFFEE=\94your\r
-scratch\94</span></span></span></p>\r
-\r
-<p class=example><span style='mso-bookmark:_Toc102494396'><span\r
-style='mso-bookmark:_Toc102494884'><span lang=EN-US>CACHE_4_TCOFFEE=\94your\r
-scratch\94</span></span></span></p>\r
-\r
-<p class=example><span style='mso-bookmark:_Toc102494396'><span\r
-style='mso-bookmark:_Toc102494884'><span lang=EN-US>NO_ERROR_REPORT_4_TCOFFEE=1</span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc102494396'><span\r
-style='mso-bookmark:_Toc102494884'><span lang=AF>Note that<span\r
-style='mso-spacerun:yes'>  </span>it is a good idea to have a cron job that\r
-cleans up this scratch area, once in a while. </span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc102494396'><span\r
-style='mso-bookmark:_Toc102494884'><span lang=AF><o:p>&nbsp;</o:p></span></span></span></p>\r
-\r
-<h3><span style='mso-bookmark:_Toc102494396'><span style='mso-bookmark:_Toc102494884'><a\r
-name="_Toc235958676"><span lang=EN-US>Output of the .dnd file.</span></a></span></span></h3>\r
-\r
-<p class=MyNormal><span lang=AF>A common source of error when running a server:\r
-T-Coffee MUST output the .dnd file because it re-reads it to carry out the\r
-progressive alignment. By default T-Coffee outputs this file in the directory\r
-where the process is running. If the T-Coffee process does not have permission\r
-to write in that directory, the computation will abort...</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>To avoid this, simply specify the name of the\r
-output tree: </span></p>\r
-\r
-<p class=MyNormal><span lang=AF><span style='mso-tab-count:1'>         </span>-newtree=&lt;writable\r
-file (usually in /tmp)&gt;</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>Chose the name so that two processes may not\r
-over-write each other dnd file. </span></p>\r
-\r
-<h3><a name="_Toc235958677"></a><a name="_Toc102494885"></a><a\r
-name="_Toc102494397"><span style='mso-bookmark:_Toc102494885'><span\r
-style='mso-bookmark:_Toc235958677'><span lang=EN-US>Permissions</span></span></span></a></h3>\r
-\r
-<p class=MyNormal><span lang=AF>The t_coffee process MUST be allowed to write\r
-in some scratch area, even when it is ran by Mr nobody... Make sure the /tmp/\r
-partition is not protected.</span></p>\r
-\r
-<h3><a name="_Toc235958678"></a><a name="_Toc102494886"></a><a\r
-name="_Toc102494398"><span style='mso-bookmark:_Toc102494886'><span\r
-style='mso-bookmark:_Toc235958678'><span lang=EN-US>Other Programs</span></span></span></a></h3>\r
-\r
-<p class=MyNormal><span lang=AF>T-Coffee may call various programs while it\r
-runs (lalign2list by defaults). Make sure your process knows where to find\r
-these executables.</span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 3.0pt;\r
-padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0mm;margin-right:\r
-4.25pt'>\r
-\r
-<p class=ChapterTitle><a name="_Toc235958679"></a><a name="_Toc102494887"></a><a\r
-name="_Toc101065353"><span style='mso-bookmark:_Toc102494887'><span\r
-style='mso-bookmark:_Toc235958679'><span lang=EN-US>F</span></span></span></a><span\r
-style='mso-bookmark:_Toc235958679'><span lang=EN-US>ormats</span></span></p>\r
-\r
-</div>\r
-\r
-<h2><a name="_Toc235958680"></a><a name="_Toc102494888"></a><a\r
-name="_Toc102494399"></a><a name="_Toc101065354"><span style='mso-bookmark:\r
-_Toc102494399'><span style='mso-bookmark:_Toc102494888'><span style='mso-bookmark:\r
-_Toc235958680'><span lang=EN-US>Parameter files</span></span></span></span></a></h2>\r
-\r
-<p class=MyNormal><span lang=AF>Parameter files used with -parameters,\r
--t_coffee_defaults, -dali_defaults... Must contain a valid parameter string\r
-where line breaks are allowed. These files cannot contain any comment, the\r
-recommended format is one parameter per line:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span lang=EN-US><span style='mso-tab-count:1'>      </span>&lt;parameter\r
-name&gt;=&lt;value1&gt;,&lt;value2&gt;....</span></p>\r
-\r
-<p class=examplefileCxSpLast><span lang=EN-US><span style='mso-tab-count:1'>      </span>&lt;parameter\r
-name&gt;=.....</span></p>\r
-\r
-</div>\r
-\r
-<h2><a name="_Toc235958681"></a><a name="_Toc102494889"></a><a\r
-name="_Toc102494400"></a><a name="_Toc101065355"><span style='mso-bookmark:\r
-_Toc102494400'><span style='mso-bookmark:_Toc102494889'><span style='mso-bookmark:\r
-_Toc235958681'><span lang=EN-US>Sequence Name Handling</span></span></span></span></a></h2>\r
-\r
-<p class=MyNormal><span lang=AF>Sequence name handling is meant to be fully\r
-consistent with ClustalW (Version 1.75). This implies that in some cases the\r
-names of your sequences may be edited when coming out of the program. Five\r
-rules apply:</span></p>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 1.0pt 1.0pt 1.0pt'>\r
-\r
-<p class=Noteboxtitle style='border:none;mso-border-alt:solid windowtext .5pt;\r
-padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US>Naming\r
-Your Sequences the <st1:Street w:st="on"><st1:address w:st="on">Right Way</st1:address></st1:Street></span></p>\r
-\r
-<p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;\r
-padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US>1-No\r
-Space</span></p>\r
-\r
-<p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;\r
-padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US>Names\r
-that do contain spaces, for instance:</span></p>\r
-\r
-<p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;\r
-padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US><span\r
-style='mso-tab-count:1'>            </span>&gt;seq1 human_myc</span></p>\r
-\r
-<p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;\r
-padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US>will be\r
-turned into</span></p>\r
-\r
-<p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;\r
-padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US><span\r
-style='mso-tab-count:1'>            </span>&gt;seq1</span></p>\r
-\r
-<p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;\r
-padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US>It is\r
-your responsibility to make sure that the names you provide are not ambiguous\r
-after such an editing. This editing is consistent with Clustalw (Version 1.75)</span></p>\r
-\r
-<p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;\r
-padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;\r
-padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US>2-No\r
-Strange Character</span></p>\r
-\r
-<p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;\r
-padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US>Some non\r
-alphabetical characters are replaced with underscores. These are: ';:()'</span></p>\r
-\r
-<p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;\r
-padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US>Other\r
-characters are legal and will be kept unchanged. This editing is meant to keep\r
-in line with Clustalw (Version 1.75).</span></p>\r
-\r
-<p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;\r
-padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;\r
-padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US>3-&gt; is\r
-NEVER legal (except as a header token in a FASTA file)</span></p>\r
-\r
-<p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;\r
-padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;\r
-padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US>4-Name\r
-length must be below 100 characters, although 15 is recommended for\r
-compatibility with other programs.</span></p>\r
-\r
-<p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;\r
-padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US>5-Duplicated\r
-sequences will be renamed (i.e. sequences with the same name in the same\r
-dataset) are allowed but will be renamed according to their original order.\r
-When sequences come from multiple sources via the \96in flag, consistency of the\r
-renaming is not guaranteed. You should avoid duplicated sequences as they will\r
-cause your input to differ from your output thus making it difficult to track\r
-data.</span></p>\r
-\r
-</div>\r
-\r
-<h2><a name="_Toc235958682"></a><a name="_Toc102494890"></a><a\r
-name="_Toc102494401"></a><a name="_Toc101065356"><span style='mso-bookmark:\r
-_Toc102494401'><span style='mso-bookmark:_Toc102494890'><span style='mso-bookmark:\r
-_Toc235958682'><span lang=EN-US>Automatic Format Recognition</span></span></span></span></a></h2>\r
-\r
-<p class=MyNormal><span lang=AF>Most common formats are automatically\r
-recognized by t_coffee. See -in and the next section for more details. If your\r
-format is not recognized, use readseq or clustalw to switch to another format.\r
-We recommend Fasta.</span></p>\r
-\r
-<h2><a name="_Toc235958683"></a><a name="_Toc102494891"></a><a\r
-name="_Toc102494402"></a><a name="_Toc101065357"><span style='mso-bookmark:\r
-_Toc102494402'><span style='mso-bookmark:_Toc102494891'><span style='mso-bookmark:\r
-_Toc235958683'><span lang=EN-US>Structures</span></span></span></span></a></h2>\r
-\r
-<p class=MyNormal><span lang=AF>PDB format is recognized by T-Coffee. T-Coffee\r
-uses extract_from_pdb (cf \96other_pg flag). extract_from_pdb is a small embeded\r
-module that can be used on its own to extract information from pdb files.</span></p>\r
-\r
-<h2><a name="_Toc235958684"><span lang=EN-US>RNA Structures</span></a></h2>\r
-\r
-<p class=MyNormal><span lang=AF>RNA structures can either be coded as T-Coffee\r
-libraries, with each line indicating two paired residues, or as alifold output.\r
-The selex format is also partly supported (see the seq_reformat tutorial on RNA\r
-sequences handling).</span></p>\r
-\r
-<h2><a name="_Toc235958685"></a><a name="_Toc102494892"></a><a\r
-name="_Toc102494403"></a><a name="_Toc101065358"><span style='mso-bookmark:\r
-_Toc102494403'><span style='mso-bookmark:_Toc102494892'><span style='mso-bookmark:\r
-_Toc235958685'><span lang=EN-US>Sequences</span></span></span></span></a></h2>\r
-\r
-<p class=MyNormal><span lang=AF>Sequences can come in the following formats:\r
-fasta, pir, swiss-prot, clustal aln, msf aln and t_coffee aln. These formats\r
-are the one automatically recognized. Please replace the '*' sign sometimes\r
-used for stop codons with an X.</span></p>\r
-\r
-<h2><a name="_Toc235958686"></a><a name="_Toc102494893"></a><a\r
-name="_Toc102494404"></a><a name="_Toc101065359"><span style='mso-bookmark:\r
-_Toc102494404'><span style='mso-bookmark:_Toc102494893'><span style='mso-bookmark:\r
-_Toc235958686'><span lang=EN-US>Alignments</span></span></span></span></a></h2>\r
-\r
-<p class=MyNormal><span lang=AF>Alignments can come in the following formats:\r
-msf, ClustalW, Fasta, Pir and t_coffee. The t_coffee format is very similar to\r
-the ClustalW format, but slightly more flexible. Any interleaved format with\r
-sequence name on each line will be correctly parsed:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span lang=EN-US>&lt;empy line&gt; <span\r
-style='mso-tab-count:1'>      </span>[Facultative]n</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>&lt;line of text&gt; <span\r
-style='mso-tab-count:1'>   </span>[Required]</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>&lt;line of text&gt;<span\r
-style='mso-tab-count:3'>               </span>[Facultative]n</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>&lt;empty line&gt;<span\r
-style='mso-tab-count:3'>                 </span>[Required]</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>&lt;empty line&gt;<span\r
-style='mso-tab-count:3'>                 </span>[Facultative]n</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>&lt;seq1\r
-name&gt;&lt;space&gt;&lt;seq1&gt;</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>&lt;seq2\r
-name&gt;&lt;space&gt;&lt;seq2&gt;</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>&lt;seq3\r
-name&gt;&lt;space&gt;&lt;seq3&gt;</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>&lt;empty line&gt;<span\r
-style='mso-tab-count:3'>                 </span>[Required]</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>&lt;empty line&gt;<span\r
-style='mso-tab-count:3'>                 </span>[Facultative]n</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>&lt;seq1\r
-name&gt;&lt;space&gt;&lt;seq1&gt;</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>&lt;seq2\r
-name&gt;&lt;space&gt;&lt;seq2&gt;</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>&lt;seq3\r
-name&gt;&lt;space&gt;&lt;seq3&gt;</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>&lt;empty line&gt;<span\r
-style='mso-tab-count:3'>                 </span>[Required]</span></p>\r
-\r
-<p class=examplefileCxSpLast><span lang=EN-US>&lt;empty line&gt;<span\r
-style='mso-tab-count:3'>                 </span>[Facultative]n</span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF>An empty line is a line that does NOT contain\r
-amino-acid. A line that contains the ClustalW annotation (.:*) is empty.</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>Spaces are forbidden in the name. When the\r
-alignment is being read, non character signs are ignored in the sequence field\r
-(such as numbers, annotation\85).</span></p>\r
-\r
-<p class=Note><span lang=EN-US style='mso-ansi-language:EN-US'>Note: a\r
-different number of lines in the different blocks will cause the program to\r
-crash or hang.<o:p></o:p></span></p>\r
-\r
-<h2><a name="_Toc235958687"></a><a name="_Toc102494894"></a><a\r
-name="_Toc102494405"></a><a name="_Toc101065360"><span style='mso-bookmark:\r
-_Toc102494405'><span style='mso-bookmark:_Toc102494894'><span style='mso-bookmark:\r
-_Toc235958687'><span lang=EN-US>Libraries</span></span></span></span></a></h2>\r
-\r
-<h3><a name="_Toc235958688"></a><a name="_Toc102494895"></a><a\r
-name="_Toc102494406"><span style='mso-bookmark:_Toc102494895'><span\r
-style='mso-bookmark:_Toc235958688'><span lang=EN-US>T-COFFEE_LIB_FORMAT_01</span></span></span></a></h3>\r
-\r
-<p class=MyNormal><span lang=AF>This is currently the only supported format.</span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span lang=EN-US>!&lt;space&gt; TC_LIB_FORMAT_01</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>&lt;nseq&gt;</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>&lt;seq1 name&gt; &lt;seq1\r
-length&gt; &lt;seq1&gt;</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>&lt;seq2 name&gt; &lt;seq2\r
-length&gt; &lt;seq2&gt;</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>&lt;seq3 name&gt; &lt;seq3\r
-length&gt; &lt;seq3&gt;</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>!Comment</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>(!Comment)n</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>#Si1 Si2</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>Ri1 Ri2 V1 (V2, V3)</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>#1 2</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>12 13 99 (12/0 vs 13/1, weight\r
-99)</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>12 14 70</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>15 16 56</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>#1 3</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>12 13 99 </span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>12 14 70</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>15 16 56</span></p>\r
-\r
-<p class=examplefileCxSpLast><span lang=EN-US>!&lt;space&gt;SEQ_1_TO_N </span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF>Si1: index of Sequence 1</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>Ri1: index of residue 1 in seq1</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>V1: Integer Value: Weight</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>V2, V3: optional values</span></p>\r
-\r
-<p class=Note><span lang=EN-US style='mso-ansi-language:EN-US'>Note 1: There is\r
-a space between the ! And SEQ_1_TO_N<o:p></o:p></span></p>\r
-\r
-<p class=Note><span lang=EN-US style='mso-ansi-language:EN-US'>Note 2: The last\r
-line (! SEQ_1_TO_N) indicates that:<o:p></o:p></span></p>\r
-\r
-<p class=MyNormal><span lang=AF>Sequences and residues are numbered from 1 to\r
-N, unless the token SEQ_1_TO_N is omitted, in which case the sequences are\r
-numbered from 0 to N-1, and residues are from 1 to N.</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>Residues do not need to be sorted, and neither\r
-do the sequences. The same pair can appear several times in the library. For\r
-instance, the following file would be legal:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span lang=EN-US>#1 2</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>12 13 99</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>#1 2</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>15 16 99 </span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>#1 1</span></p>\r
-\r
-<p class=examplefileCxSpLast><span lang=EN-US>12 14 70</span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><a name="_Toc102494896"></a><a name="_Toc102494407"><span\r
-style='mso-bookmark:_Toc102494896'><span lang=AF>It is also poosible to declare\r
-ranges of resdues rather than single pairs. For instance, the following:</span></span></a></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc102494407'><span\r
-style='mso-bookmark:_Toc102494896'><span lang=EN-US>#0 1</span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494407'><span\r
-style='mso-bookmark:_Toc102494896'><span lang=EN-US>+BLOCK+<span\r
-style='mso-spacerun:yes'>  </span>10 12 14 99</span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494407'><span\r
-style='mso-bookmark:_Toc102494896'><span lang=EN-US>+BLOCK+<span\r
-style='mso-spacerun:yes'>  </span>15 30 40 99</span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494407'><span\r
-style='mso-bookmark:_Toc102494896'><span lang=EN-US>#0 2</span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494407'><span\r
-style='mso-bookmark:_Toc102494896'><span lang=EN-US>15 16 99 </span></span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494407'><span\r
-style='mso-bookmark:_Toc102494896'><span lang=EN-US>#0 1</span></span></span></p>\r
-\r
-<p class=examplefileCxSpLast><span style='mso-bookmark:_Toc102494407'><span\r
-style='mso-bookmark:_Toc102494896'><span lang=EN-US>12 14 70</span></span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc102494407'><span\r
-style='mso-bookmark:_Toc102494896'><span lang=AF>The first statement BLOCK\r
-declares a BLOCK of length 10, that starts on position 12 of sequence 1 and\r
-position 14 of sequence 2 and where each pair of residues within the block has\r
-a score of 99. The second BLOCK starts on residue 30 of 1, residue 40 of 2 and\r
-extends for 15 residues.</span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc102494407'><span\r
-style='mso-bookmark:_Toc102494896'><span lang=AF>Blocks can overalp and be\r
-incompatible with one another, just like single constraints.</span></span></span></p>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc102494407'><span\r
-style='mso-bookmark:_Toc102494896'><span lang=AF><span\r
-style='mso-spacerun:yes'>  </span></span></span></span></p>\r
-\r
-<h3><span style='mso-bookmark:_Toc102494407'><span style='mso-bookmark:_Toc102494896'><a\r
-name="_Toc235958689"><span lang=EN-US>T-COFFEE_LIB_FORMAT_02</span></a></span></span></h3>\r
-\r
-<p class=MyNormal><span lang=AF>A simpler format is being developed, however it\r
-is not yet fully supported and is only mentioned here for development purpose.</span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span lang=EN-US>! TC_LIB_FORMAT_02</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>#S1 SEQ1 [OPTIONAL]</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>#S2 SEQ2 [OPTIONAL]</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>...</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>!comment [OPTIONAL]</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>S1 R1 Ri1 S2 R2 Ri2 V1 (V2 V3)</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>=&gt; <st1:place w:st="on">N R1</st1:place>\r
-Ri1 S2 R2 Ri2 V1 (V2 V3)</span></p>\r
-\r
-<p class=examplefileCxSpLast><span lang=EN-US>...</span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF>S1, S2: name of sequence 1 and 2</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>SEQ1: sequence of S1</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>Ri1, Ri2: index of the residues in their\r
-respective sequence</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>R1, R2: Residue type</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>V1, V2, V3: integer Values (V2 and V3 are\r
-optional)</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>Value1, Value 2 and Value3 are optional.</span></p>\r
-\r
-<h2><a name="_Toc101065361"></a><a name="_Toc235958690"></a><a\r
-name="_Toc102494897"></a><a name="_Toc102494408"><span style='mso-bookmark:\r
-_Toc102494897'><span style='mso-bookmark:_Toc235958690'><span style='mso-bookmark:\r
-_Toc101065361'><span lang=EN-US>Library List</span></span></span></span></a><span\r
-style='mso-bookmark:_Toc101065361'></span></h2>\r
-\r
-<p class=MyNormal><span style='mso-bookmark:_Toc101065361'><span lang=AF>These\r
-are lists of pairs of sequences that must be used to compute a library. The\r
-format is:</span></span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc101065361'><span\r
-lang=EN-US>&lt;nseq&gt; &lt;S1&gt; &lt;S2&gt;</span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065361'><span\r
-lang=EN-US>2 hamg2 globav</span></span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065361'><span\r
-lang=EN-US>3 hamgw hemog singa</span></span></p>\r
-\r
-<p class=examplefileCxSpLast><span style='mso-bookmark:_Toc101065361'><span\r
-lang=EN-US>...</span></span></p>\r
-\r
-</div>\r
-\r
-<h2><span style='mso-bookmark:_Toc101065361'><a name="_Toc235958691"></a><a\r
-name="_Toc102494898"></a><a name="_Toc102494409"><span style='mso-bookmark:\r
-_Toc102494898'><span style='mso-bookmark:_Toc235958691'><span lang=EN-US>Substitution\r
-matrices.</span></span></span></a></span></h2>\r
-\r
-<p class=MyNormal><span lang=AF>If the required substitution matrix is not available,\r
-write your own in a file using the following format:</span></p>\r
-\r
-<h3><a name="_Toc235958692"></a><a name="_Toc102494899"></a><a\r
-name="_Toc102494410"></a><a name="_Toc101065362"><span style='mso-bookmark:\r
-_Toc102494410'><span style='mso-bookmark:_Toc102494899'><span style='mso-bookmark:\r
-_Toc235958692'><span lang=EN-US>ClustalW Style</span></span></span></span></a><span\r
-style='mso-bookmark:_Toc102494410'><span style='mso-bookmark:_Toc102494899'><span\r
-style='mso-bookmark:_Toc235958692'><span lang=EN-US> [Deprecated]</span></span></span></span></h3>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span lang=EN-US># CLUSTALW_MATRIX FORMAT</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>$</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>v1</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>v2 v3</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>v4 v5 v6</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>...</span></p>\r
-\r
-<p class=examplefileCxSpLast><span lang=EN-US>$</span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF>v1, v2... are integers, possibly negatives.</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>The order of the amino acids is:\r
-ABCDEFGHIKLMNQRSTVWXYZ, which means that v1 is the substitution value for A vs\r
-A, v2 for A vs B, v3 for B vs B, v4 for A vs C and so on.</span></p>\r
-\r
-<h3><a name="_Toc235958693"></a><a name="_Toc102494900"></a><a\r
-name="_Toc102494411"></a><a name="_Toc101065363"><span style='mso-bookmark:\r
-_Toc102494411'><span style='mso-bookmark:_Toc102494900'><span style='mso-bookmark:\r
-_Toc235958693'><span lang=EN-US>BLAST Format [Recommended]</span></span></span></span></a></h3>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span lang=EN-US># BLAST_MATRIX FORMAT</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US># ALPHABET=AGCT</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US><span\r
-style='mso-spacerun:yes'> </span>A G C T</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>A 0 1 2 3</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>G 0 2 3 4</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>C 1 1 2 3</span></p>\r
-\r
-<p class=examplefileCxSpLast><span lang=EN-US>...</span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF>The alphabet can be freely defined</span></p>\r
-\r
-<h2><a name="_Toc235958694"></a><a name="_Toc102494901"></a><a\r
-name="_Toc102494412"></a><a name="_Toc101065364"><span style='mso-bookmark:\r
-_Toc102494412'><span style='mso-bookmark:_Toc102494901'><span style='mso-bookmark:\r
-_Toc235958694'><span lang=EN-US>Sequences Weights</span></span></span></span></a></h2>\r
-\r
-<p class=MyNormal><span lang=AF>Create your own weight file, using the\r
--seq_weight flag:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;\r
-mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;\r
-background:#E6E6E6'>\r
-\r
-<p class=examplefileCxSpFirst><span lang=EN-US># SINGLE_SEQ_WEIGHT_FORMAT_01</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>seq_name1 v1</span></p>\r
-\r
-<p class=examplefileCxSpMiddle><span lang=EN-US>seq_name2 v2</span></p>\r
-\r
-<p class=examplefileCxSpLast><span lang=EN-US>...</span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF>No duplicate allowed. Sequences not included in\r
-the set of sequences provided to t_coffee will be ignored. Order is free. V1 is\r
-a float. Un-weighted sequences will see their weight set to 1.</span></p>\r
-\r
-<span lang=AF style='font-size:11.0pt;font-family:"Times New Roman";mso-fareast-font-family:\r
-"Times New Roman";mso-bidi-font-family:"Courier New";mso-ansi-language:AF;\r
-mso-fareast-language:EN-US;mso-bidi-language:AR-SA'><br clear=all\r
-style='page-break-before:always'>\r
-</span>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 3.0pt;\r
-padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0mm;margin-right:\r
-4.25pt'>\r
-\r
-<p class=ChapterTitle><a name="_Toc235958695"><span lang=EN-US>Known Problems</span></a></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF>1-Sensitivity to sequence order: It is\r
-difficult to implement a MSA algorithm totally insensitive to the order of\r
-input of the sequences. In t_coffee, robustness is increased by sorting the\r
-sequences alphabetically before aligning them. Beware that this can result in\r
-confusing output where sequences with similar name are unexpectedly close to\r
-one another in the final alignment.</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>2-Nucleotides sequences with long stretches of\r
-Ns will cause problems to lalign, especially when using Mocca. To avoid any\r
-problem, filter out these nucleotides before running mocca.</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>3-Stop codons are sometimes coded with '*' in\r
-protein sequences. This will cause the program to crash or hang. Please replace\r
-the '*' signs with an X.</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>4-Results can differ from one architecture to\r
-another, due rounding differences. This is caused by the tree estimation\r
-procedcure. If you want to make sure an alignment is reproducible, you should\r
-keep the associated dendrogram.</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>5-Deploying the program on a </span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 3.0pt;\r
-padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0mm;margin-right:\r
-4.25pt'>\r
-\r
-<p class=ChapterTitle><a name="_Toc235958696"><span lang=EN-US>Technical Notes</span></a></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF>These notes are only meant for internal\r
-development.</span></p>\r
-\r
-<h2><a name="_Toc235958697"></a><a name="_Toc102494904"></a><a\r
-name="_Toc102494413"><span style='mso-bookmark:_Toc102494904'><span\r
-style='mso-bookmark:_Toc235958697'><span lang=EN-US>Development</span></span></span></a></h2>\r
-\r
-<p class=MyNormal><span lang=AF>The following examples are only meant for\r
-internal development, and are used to insure stability from release to release</span></p>\r
-\r
-<h4><span lang=AF>profile2list</span></h4>\r
-\r
-<p class=MyNormal><span lang=AF>prf1: profile containing one structure</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>prf2: profile containing one structure</span></p>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee<span style='mso-spacerun:yes'> \r
-</span>Rsample_profile1.aln,Rsample_profile2.aln -mode=3dcoffee\r
--outfile=aligned_prf.aln</span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-</div>\r
-\r
-<h3><a name="_Toc235958698"></a><a name="_Toc102494905"></a><a\r
-name="_Toc102494414"><span style='mso-bookmark:_Toc102494905'><span\r
-style='mso-bookmark:_Toc235958698'><span lang=EN-US>Command Line List</span></span></span></a></h3>\r
-\r
-<p class=MyNormal><span lang=AF>These command lines have been checked before\r
-every release (along with the other CL in this documentation:</span></p>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MyNormal><span lang=AF>-external methods;</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US><span\r
-style='mso-tab-count:1'>   </span>PROMPT: t_coffee sample_seq1.fasta \96in=Mclustalw_pair,Mclustalw_msa,Mslow_pair\r
-\96outfile=clustal_text</span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF>-fugue_client</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee \96in Ssample_seq5.fasta Pstruc4.pdb Mfugue_pair</span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF>-A list of command lines kindly provided by\r
-James Watson (used to crash the pg before version 3.40)</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee -in Sseq.fas P2PTC Mfugue_pair</span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee -in S2seqs.fas Mfugue_pair -template_file SELF_P_</span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee -mode 3dcoffee -in Sseq.fas P2PTC</span></p>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee -mode 3dcoffee -in S2seqs.fas -template_file SELF_P_</span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF>-A list of command lines that crashed the\r
-program before 3.81</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee sample_seq6.fasta \96in Mfast_pair Msap_pair Mfugue_pair \96template_file\r
-template_file6.template </span></p>\r
-\r
-</div>\r
-\r
-<p class=MsoBodyText><span lang=EN-US><span style='mso-tab-count:1'>            </span>-A\r
-command line to read \93relaxed\94 pdb files...</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee \96in Msap_pair Ssample_seq7.fasta \96template_file\r
-template_file7.template \96weight 1001 \96out_lib test_lib7.tc_lib \96lib_only </span></p>\r
-\r
-</div>\r
-\r
-<p class=MsoBodyText><span lang=EN-US><span style='mso-tab-count:1'>            </span>-Parsing\r
-of MARNA libraries</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee \96in Lmarna.tc_lib \96outfile maran.test</span></p>\r
-\r
-</div>\r
-\r
-<p class=MsoBodyText><span lang=EN-US><span style='mso-tab-count:1'>            </span>-Parsing\r
-of long sequence lines:</span></p>\r
-\r
-<div style='mso-element:para-border-div;border-top:solid black 1.0pt;\r
-border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:\r
-solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;\r
-background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>\r
-\r
-<p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:\r
-t_coffee \96in Asample_aln5.aln \96outfile test.aln</span></p>\r
-\r
-</div>\r
-\r
-<p class=MsoBodyText><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<div style='mso-element:para-border-div;border:solid windowtext 3.0pt;\r
-padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0mm;margin-right:\r
-4.25pt'>\r
-\r
-<p class=ChapterTitle><a name="_Toc235958699"></a><a name="_Toc102494906"><span\r
-style='mso-bookmark:_Toc235958699'><span lang=EN-US>To D</span></span></a><span\r
-style='mso-bookmark:_Toc235958699'><span lang=EN-US>o\85</span></span></p>\r
-\r
-</div>\r
-\r
-<p class=MyNormal><span lang=AF>-implement UPGMA tree computation</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>-implement seq2dpa_tree</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>-debug dpa</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>-Reconciliate sequences and template when\r
-reading the template</span></p>\r
-\r
-<p class=MyNormal><span lang=AF>-Add the server command lines to the checking\r
-procedure</span></p>\r
-\r
-<p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-<p class=MsoBodyText><span lang=EN-US><o:p>&nbsp;</o:p></span></p>\r
-\r
-</div>\r
-\r
-</body>\r
-\r
-</html>\r