/var/lib/mobyle/programs/msa.xml is in mobyle-programs 5.1.2-1.
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<!-- XML Authors: Corinne Maufrais, Nicolas Joly and Bertrand Neron, -->
<!-- 'Biological Software and Databases' Group, Institut Pasteur, Paris. -->
<!-- Distributed under LGPLv2 License. Please refer to the COPYING.LIB document. -->
<program>
<head>
<name>msa</name>
<version>2.1</version>
<doc>
<title>MSA</title>
<description>
<text lang="en">Multiple sequence alignment</text>
</description>
<authors>S. F. Altschul</authors>
<homepagelink>http://www.ncbi.nlm.nih.gov/CBBresearch/Schaffer/msa.html</homepagelink>
<sourcelink>ftp://fastlink.nih.gov/pub/msa/msa.tar.Z</sourcelink>
</doc>
<category>alignment:multiple</category>
<command>msa</command>
</head>
<parameters>
<parameter ismandatory="1" issimple="1">
<name>seqs</name>
<prompt lang="en">Sequences File</prompt>
<type>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>FASTA</dataFormat>
</type>
<format>
<code proglang="perl">" $value"</code>
<code proglang="python">" "+str(value)</code>
</format>
<argpos>2</argpos>
<comment>
<text lang="en">This is a file containing the sequences to be aligned.</text>
</comment>
</parameter>
<paragraph>
<name>control</name>
<prompt lang="en">Control parameters</prompt>
<argpos>1</argpos>
<parameters>
<parameter>
<name>optimal</name>
<prompt lang="en">Turns off the optimal multiple alignment (-m)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -m":""</code>
<code proglang="python">("" , " -m")[ value ]</code>
</format>
<comment>
<text lang="en">Turns off the optimal multiple alignment segment of the program.This allows the user to see the heuristic alignment and other data produced by the program before the it attempts to produce an optimal multiple alignment.</text>
</comment>
</parameter>
<parameter>
<name>forcedres</name>
<prompt lang="en">User file to force the alignment of certain residues (-f)</prompt>
<type>
<datatype>
<class>ForceAlignmentPattern</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value)? " -f $value" : "" </code>
<code proglang="python">( "" , " -f " + str(value) )[ value is not None ]</code>
</format>
<comment>
<text lang="en">Allows the user to force the alignment of certain residues. The file referred to must have one or more lines of the following format:</text>
<text lang="en">seqs.| "S" precedes block start | "L" precedes block length</text>
<text lang="en">The example would force positions 22 to 31 of sequence 2 to be aligned with positions 21 to 30 of sequence 3 and positions 25 to 34 of sequence 5; it would else force position 35 of sequence 2 to be aligned with position 36 of sequence 3 and position 41 of sequence 5. Needless to say, all positions forced into alignment must be mutually consistent.
</text>
</comment>
<example>2 3 5 S 22 21 25 L 10 S 35 36 41 L 1</example>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>Cost</name>
<prompt lang="en">Cost parameters</prompt>
<argpos>1</argpos>
<parameters>
<parameter>
<name>endgap</name>
<prompt lang="en">Charges terminal gaps the same as internal gaps (-g)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl"> ($value)? " -g":""</code>
<code proglang="python">("" , " -g")[ value ]</code>
</format>
<comment>
<text lang="en">As a default, no charge is made for the existence of a terminal gap.</text>
</comment>
</parameter>
<parameter>
<name>unweight</name>
<prompt lang="en">Cost of a multiple alignment (-b)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl"> ($value)? " -b":""</code>
<code proglang="python">("" , " -b")[ value ]</code>
</format>
<comment>
<text lang="en">The cost of a multiple alignment is taken to be the unweighted sum of all the pairwise alignments. In the absence of this flag, the program estimates an evolutionary tree and uses it to assign weights to each pairwise alignment using either rationale-1 or rational-2 as described in Altschul et al., J. Molec. Biol. 208 (1989).</text>
</comment>
</parameter>
<parameter>
<name>maxscore</name>
<prompt lang="en">Maximum score of an optimal multiple alignment (-d)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl"> (defined $value)? " -d$value" : ""</code>
<code proglang="python">( "" , " -d" + str(value) )[ value is not None ]</code>
</format>
<comment>
<text lang="en">Specifies the maximum score of an optimal multiple alignment. Default is calculated from the scores of the optimal pairwise alignments, the weights, and the epsilons.</text>
</comment>
</parameter>
<parameter>
<name>epsilons</name>
<prompt lang="en">User specified epsilons for each pairwise alignment (-e)</prompt>
<type>
<datatype>
<class>EpsilonFile</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value)? " -e $value" : "" </code>
<code proglang="python">( "" , " -e " + str(value) )[ value is not None ]</code>
</format>
<comment>
<text lang="en">As a default, the program calculates an heuristic multiple alignment and uses it to set epsilons for each pairwise alignment. Frequently the "optimal multiple alignment" will be found to have observed epsilons exceeding those supplied or calculated. When this is the case, it is advisable to rerun the program using suitably augmented epsilons. The file named here should have integers separated by spaces or newlines or both, with one integer for each pair of sequences in the order 1-2, 1-3, ... , 1-N, 2-3, ... , (N-1)-N.</text>
</comment>
</parameter>
<parameter>
<name>costs</name>
<prompt lang="en">User costs file (-c)</prompt>
<type>
<datatype>
<class>Costs</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value)? " -c $value" : "" </code>
<code proglang="python">( "" , " -c " + str(value) )[ value is not None ]</code>
</format>
<comment>
<text lang="en">Allows the user to specify the cost for a gap, as well as the cost for aligning any pair of letters or a letter with a null. The default is PAM-250 costs for protein sequences, using the one-letter code. The format of this file is an integer, followed by all possible pairs of aligned symbols followed by their cost. For example, the file might begin as follows:</text>
<text lang="en"> This would specify a cost of 0 for aligning a null symbol with another null symbol, a cost of 1 for aligning an A with a null symbol, etc., and an additional cost of 3 for the existence of a gap. The program assumes the costs are symmetric, so that there is no need to have a line for C A as well as for A C. All costs must be non-negative integers.</text>
</comment>
<example>
3
- - 0
- A 1
A C 2
</example>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>output</name>
<prompt lang="en">Output parameters</prompt>
<argpos>1</argpos>
<parameters>
<parameter>
<name>quiet</name>
<prompt lang="en">Suppress verbose output (-o)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -o":""</code>
<code proglang="python">("" , " -o")[ value ]</code>
</format>
</parameter>
</parameters>
</paragraph>
</parameters>
</program>
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