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<?xml version='1.0' encoding='UTF-8'?>
<!-- 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>comalign</name>
<doc>
<title>ComAlign</title>
<description>
<text lang="en">is a program, that given a number of sequences generates a number of heuristic alignments and combines these best possible.</text>
</description>
<authors>O. Caprani, K. Bucka-Lassen</authors>
<homepagelink>http://www.daimi.au.dk/~ocaprani/ComAlign/ComAlign.html</homepagelink>
<sourcelink>http://www.daimi.au.dk/~ocaprani/ComAlign/programs/</sourcelink>
<doclink>http://www.daimi.au.dk/~ocaprani/ComAlign/HowTo.html</doclink>
</doc>
<category>alignment:multiple</category>
<command>ComAlign</command>
</head>
<parameters>
<parameter ismandatory="1" issimple="1">
<name>seq</name>
<prompt lang="en">Sequences File (-f)</prompt>
<type>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>GenAl</dataFormat>
</type>
<format>
<code proglang="perl">" -f$value"</code>
<code proglang="python">" -f" + str(value)</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">the sequences must be in the GenAl format</text>
</comment>
<example>
>Test1
ATGAAA
*
*
>Test2
ATCAAA
*
*
</example>
</parameter>
<parameter>
<name>seed</name>
<prompt lang="en">Random seed number (-s)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -s$value" : ""</code>
<code proglang="python">( "" , " -s" + str(value) )[ value is not None and value != vdef]</code>
</format>
<argpos>1</argpos>
</parameter>
<parameter>
<name>seqnb</name>
<prompt lang="en">Number of sequences that are to be aligned (-n)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>2</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -n$value" : ""</code>
<code proglang="python">( "" , " -n" + str(value) )[ value is not None and value != vdef]</code>
</format>
<argpos>1</argpos>
</parameter>
<parameter>
<name>iterations</name>
<prompt lang="en">Number of iterations (-i)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>10</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -i$value" : ""</code>
<code proglang="python">( "" , " -i" + str(value) )[ value is not None and value != vdef]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">On each iteration a new alignment is added to the pool of alignments ComAlign is working on</text>
</comment>
</parameter>
<parameter>
<name>score</name>
<prompt lang="en">Score: ComAlign records the time it took to find a solution as good as this score (-l)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -l$value" : ""</code>
<code proglang="python">( "" , " -l" + str(value) )[ value is not None]</code>
</format>
<argpos>1</argpos>
</parameter>
<parameter>
<name>time</name>
<prompt lang="en">ComAlign marks the best solution found after this number of 1/100 seconds (-t)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -t$value" : ""</code>
<code proglang="python">( "" , " -t" + str(value) )[ value is not None ]</code>
</format>
<argpos>1</argpos>
</parameter>
<parameter>
<name>last_iterations</name>
<prompt lang="en">Makes ComAlign terminate if the score hasn't changed within the last this number of iterations (-c)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>20</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -c$value" : ""</code>
<code proglang="python">( "" , " -c" + str(value) )[ value is not None and value != vdef]</code>
</format>
<argpos>1</argpos>
</parameter>
<parameter>
<name>print_best</name>
<prompt lang="en">Print the best found alignment on termination (-a)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -a" : ""</code>
<code proglang="python">( "" , " -a" )[ value ]</code>
</format>
<argpos>1</argpos>
</parameter>
</parameters>
</program>
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