/var/lib/mobyle/programs/treealign.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>treealign</name>
<doc>
<title>treealign</title>
<description>
<text lang="en">Phylogenetic alignment of homologous sequences</text>
</description>
<authors>J. Hein</authors>
<reference>Hein, J.: Unified approach to alignment and phylogenies. Meth. Enzymol. 183:626-645 (1990).</reference>
<reference>Hein, J.: A new method that simultaneously aligns and reconstruct ancestral sequences for any number of homologous sequences, when the phylogeny is given. Mol. Biol. Evol. 6:649-668 (1989).</reference>
<reference>Hein, J.: A tree reconstruction method that is economical in the number of pairwise comparisons used. Mol. Biol. Evol. 6:669-684 (1989).</reference>
</doc>
<category>alignment:pairwise</category>
<category>phylogeny:parsimony</category>
<command>treealign</command>
</head>
<parameters>
<parameter ismandatory="1" issimple="1">
<name>fileseq</name>
<prompt lang="en">Sequences File</prompt>
<type>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>NBRF</dataFormat>
</type>
<format>
<code proglang="perl">"$value\\n"</code>
<code proglang="python">str(value)+ "\n"</code>
</format>
<argpos>30</argpos>
<comment>
<text lang="en">The sequences should
be homologous and there should be a history to be found. If you give it a set
of COMPLETELY unrelated sequences, it is possible that it will not be able to
align them, since it cannot allocate enough memory.</text>
<text lang="en">The sequences should not vary in length because they have been sequenced
unequally much. Length differences should be due to evolution. Thus it should
not be used to look for local homologies.</text>
</comment>
<paramfile>par.dat</paramfile>
<example>
>P1;alpha
GDGKMTADKLNFPGNS*
>P1;beta
GDGKNTRDKINFPGNS*
>P1;gamma
GDGKNTADKINFPGNS*
</example>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>seqtype</name>
<prompt lang="en">Sequence type</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>null</value>
</vdef>
<vlist>
<velem undef="1">
<value>null</value>
<label>Choose a sequence type</label>
</velem>
<velem>
<value>1</value>
<label>Protein (1)</label>
</velem>
<velem>
<value>0</value>
<label>DNA (0)</label>
</velem>
</vlist>
<format>
<code proglang="perl">"$value"</code>
<code proglang="python">str(value)</code>
</format>
<argpos>11</argpos>
<paramfile>par.dat</paramfile>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>nuseq</name>
<prompt lang="en">Number of sequences</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">" $value"</code>
<code proglang="python">" "+str(value)</code>
</format>
<argpos>12</argpos>
<paramfile>par.dat</paramfile>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>gap_open</name>
<prompt lang="en">Gap open penalty</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">" $value"</code>
<code proglang="python">" "+str(value)</code>
</format>
<ctrl>
<message>
<text lang="en">Enter a non-negative value</text>
</message>
<code proglang="perl">$value >= 0</code>
<code proglang="python">value >= 0</code>
</ctrl>
<argpos>13</argpos>
<paramfile>par.dat</paramfile>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>gap_ext</name>
<prompt lang="en">Gap extension penalty</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">" $value\\n"</code>
<code proglang="python">" " + str(value) + "\n"</code>
</format>
<argpos>14</argpos>
<paramfile>par.dat</paramfile>
</parameter>
<paragraph>
<name>other_options</name>
<prompt lang="en">Other options</prompt>
<parameters>
<parameter>
<name>ancesterout</name>
<prompt lang="en">Present ancestral sequences</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? "1" : "0"</code>
<code proglang="python">( "0" , "1" )[ value ]</code>
</format>
<argpos>21</argpos>
<paramfile>par.dat</paramfile>
</parameter>
</parameters>
</paragraph>
<parameter isout="1">
<name>filetree</name>
<prompt lang="en">Output tree file</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<format>
<code proglang="perl">"$fileseq.tree\\n"</code>
<code proglang="python">str(fileseq)+ ".tree\n"</code>
</format>
<argpos>40</argpos>
<paramfile>par.dat</paramfile>
<filenames>
<code proglang="perl">"*.tree"</code>
<code proglang="python">"*.tree"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>fileali</name>
<prompt lang="en">Output alignment file</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<format>
<code proglang="perl">"$fileseq.ali\\n"</code>
<code proglang="python">str(fileseq)+".ali\n"</code>
</format>
<argpos>50</argpos>
<paramfile>par.dat</paramfile>
<filenames>
<code proglang="perl">"*.ali"</code>
<code proglang="python">"*.ali"</code>
</filenames>
</parameter>
</parameters>
</program>
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