/var/lib/mobyle/programs/dca.xml is in mobyle-programs 5.1.2-2.
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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>dca</name>
<version>1.1</version>
<doc>
<title>DCA</title>
<description>
<text lang="en">Divide-and-Conquer Multiple Sequence Alignment</text>
</description>
<authors>J. Stoye</authors>
<reference>A.W.M. Dress, G. Fullen, S.W. Perrey, A Divide and Conquer Approach to Multiple Alignment, Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology (ISMB 95), AAAI Press, Menlo Park, CA, USA, 107-113, 1995.</reference>
<reference>J. Stoye, Multiple Sequence Alignment with the Divide-and-Conquer Method, Gene 211(2), GC45-GC56, 1998. (Gene-COMBIS)</reference>
<comment>
<text lang="en">Divide-and-Conquer Multiple Sequence Alignment (DCA) is a program for producing fast, high quality simultaneous multiple sequence alignments of amino acid, RNA, or DNA sequences. The program is based on the DCA algorithm, a heuristic approach to sum-of-pairs (SP) optimal alignment that has been developed at the FSPM over the years 1995-97.</text>
</comment>
<homepagelink>http://bibiserv.techfak.uni-bielefeld.de/dca/</homepagelink>
<sourcelink>http://bibiserv.techfak.uni-bielefeld.de/download/tools/dca.html</sourcelink>
</doc>
<category>alignment:multiple</category>
<command>dca</command>
</head>
<parameters>
<parameter ismandatory="1" issimple="1">
<name>seq</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>100</argpos>
</parameter>
<paragraph>
<name>control</name>
<prompt lang="en">Control parameters</prompt>
<parameters>
<parameter>
<name>cost</name>
<prompt lang="en">Cost matrix (-c)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>null</value>
</vdef>
<vlist>
<velem undef="1">
<value>null</value>
<label>Default: depends on sequences</label>
</velem>
<velem>
<value>blosum30</value>
<label>BLOSUM30</label>
</velem>
<velem>
<value>blosum45</value>
<label>BLOSUM45</label>
</velem>
<velem>
<value>blosum62</value>
<label>BLOSUM62</label>
</velem>
<velem>
<value>pam160</value>
<label>PAM160</label>
</velem>
<velem>
<value>pam250</value>
<label>PAM250</label>
</velem>
<velem>
<value>unitcost</value>
<label>Unitcost</label>
</velem>
<velem>
<value>dna</value>
<label>DNA</label>
</velem>
<velem>
<value>rna</value>
<label>RNA</label>
</velem>
<velem>
<value>dnarna</value>
<label>DNA/RNA</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef)? " -c $value" : "" </code>
<code proglang="python">( "" , " -c " + str(value) )[ value is not None and value != vdef]</code>
</format>
<argpos>1</argpos>
</parameter>
<parameter>
<name>gaps</name>
<prompt lang="en">Penalize end gaps as internal gaps (-g)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl"> ($value)? " -g ":""</code>
<code proglang="python">("" , " -g ")[ value ]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">Default: free shift</text>
</comment>
</parameter>
<parameter>
<name>approximate</name>
<prompt lang="en">Use approximate cut positions (-a)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl"> ($value)? " -a":""</code>
<code proglang="python">("" , " -a")[ value ]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">On: FastDCA (use approximate cut positions); Off: slower, more accurate algorithm (search for exact cut positions)</text>
</comment>
</parameter>
<parameter>
<name>intensity</name>
<prompt lang="en">Weight intensity (-b)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>0.0</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -b $value" : "" </code>
<code proglang="python">( "" , " -b " + str(value) )[ value is not None and value != vdef]</code>
</format>
<ctrl>
<message>
<text lang="en">Weight intensity must be >= 0.0 and <= 1.0</text>
</message>
<code proglang="perl">$intensity >= 0.0 and $intensity <= 1.0</code>
<code proglang="python">intensity >= 0.0 and intensity <= 1.0</code>
</ctrl>
<argpos>1</argpos>
</parameter>
<parameter>
<name>recursion</name>
<prompt lang="en">Recursion stop size (-l)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>30</value>
</vdef>
<format>
<code proglang="perl"> (defined $value and $value != $vdef)? " -l $value" : "" </code>
<code proglang="python">( "" , " -l " + str(value) )[ value is not None and value != vdef]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">5 ... 100 recommended; small: faster algorithm, maybe worse.</text>
</comment>
</parameter>
<parameter>
<name>window</name>
<prompt lang="en">Window size (-w)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -w $value" : "" </code>
<code proglang="python">( "" , " -w " + str(value) )[ value is not None and value != vdef]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">To correct the alignment in the proximity of division sites, the sequences can be re-aligned inside a window of size w >= 0 placed across each slicing site.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>output</name>
<prompt lang="en">Output parameters</prompt>
<parameters>
<parameter ishidden="1">
<name>quiet</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">" -q"</code>
<code proglang="python">" -q"</code>
</format>
<argpos>1</argpos>
</parameter>
<parameter>
<name>output_format</name>
<prompt lang="en">Output format (-f)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>2</value>
</vdef>
<vlist>
<velem>
<value>1</value>
<label>aln (1)</label>
</velem>
<velem>
<value>2</value>
<label>fasta (2)</label>
</velem>
<velem>
<value>3</value>
<label>nex (3)</label>
</velem>
<velem>
<value>4</value>
<label>dca (4)</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef)? " -f $value" : "" </code>
<code proglang="python">( "" , " -f " + str(value) )[ value is not None and value != vdef]</code>
</format>
<argpos>1</argpos>
</parameter>
<parameter ishidden="1">
<name>suppress_output</name>
<prompt lang="en">Suppress output about progress of the program (-o)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">" -o"</code>
<code proglang="python">" -o"</code>
</format>
<argpos>1</argpos>
</parameter>
</parameters>
</paragraph>
<parameter isstdout="1">
<name>fasta_outfile</name>
<prompt>Alignment file</prompt>
<type>
<datatype>
<class>Alignment</class>
</datatype>
<dataFormat>
<test param="output_format" eq="2">FASTA</test>
<test param="output_format" eq="3">NEXUS</test>
</dataFormat>
</type>
<precond>
<code proglang="perl">$output_format eq "2" or $output_format eq "3"</code>
<code proglang="python">output_format == "2" or output_format == "3"</code>
</precond>
<filenames>
<code proglang="perl">"dca.out"</code>
<code proglang="python">"dca.out"</code>
</filenames>
</parameter>
<parameter isstdout="1">
<name>aln_outfile</name>
<prompt>DCA alignment file</prompt>
<type>
<datatype>
<class>Dcalignment</class>
<superclass>AbstractText</superclass>
</datatype>
<dataFormat>
<test param="output_format" eq="1">CLUSTAL</test>
<test param="output_format" eq="4">DCA</test>
</dataFormat>
</type>
<precond>
<code proglang="perl">$output_format eq "1" or $output_format eq "4"</code>
<code proglang="python">output_format == "1" or output_format == "4"</code>
</precond>
<filenames>
<code proglang="perl">"dca.out"</code>
<code proglang="python">"dca.out"</code>
</filenames>
</parameter>
</parameters>
</program>
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