/var/lib/mobyle/programs/quicktree.xml is in mobyle-programs 5.1.2-2.
This file is owned by root:root, with mode 0o644.
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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>quicktree</name>
<version>1.1</version>
<doc>
<title>QuickTree</title>
<description>
<text lang="en">Rapid reconstruction of phylogenies by the Neighbor-Joining method</text>
</description>
<authors>Kevin Howe, Alex Bateman, Richard Durbin</authors>
<reference>Kevin Howe, Alex Bateman and Richard Durbin (2002).
QuickTree: building huge Neighbour-Joining trees of protein
sequences. Bioinformatics 18(11):1546-1547.</reference>
<comment>
<text lang="en">QuickTree is an efficient implementation of
the Neighbor-Joining algorithm, capable of reconstructing
phylogenies from huge alignments in time less than the age of
the universe.</text>
</comment>
<homepagelink>http://www.sanger.ac.uk/Software/analysis/quicktree/</homepagelink>
<sourcelink>http://www.sanger.ac.uk/Software/analysis/quicktree/</sourcelink>
</doc>
<category>phylogeny:distance</category>
<command>quicktree</command>
</head>
<parameters>
<paragraph>
<name>inpufile</name>
<prompt lang="en">Input file</prompt>
<comment>
<text lang="en">You must enter either a distance matrix or a alignment.</text>
</comment>
<parameters>
<parameter ismandatory="1">
<name>aligfile</name>
<prompt lang="en">Alignment file (-in a)</prompt>
<type>
<datatype>
<class>Alignment</class>
</datatype>
<dataFormat>STOCKHOLM</dataFormat>
</type>
<precond>
<code proglang="perl">not defined $distfile or (defined $aligfile and defined $distfile)</code>
<code proglang="python">distfile is None or (distfile and aligfile)</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? " -in a $value" : ""</code>
<code proglang="python">( "" , " -in a " + str(value) )[ value is not None ]</code>
</format>
<ctrl>
<message>
<text lang="en">You must enter either a distance matrix or a alignment.</text>
</message>
<code proglang="perl">not $distfile</code>
<code proglang="python">distfile is None</code>
</ctrl>
<argpos>10</argpos>
</parameter>
<parameter ismandatory="1">
<name>distfile</name>
<prompt lang="en">or Distance matrix (-in m)</prompt>
<type>
<datatype>
<class>PhylipDistanceMatrix</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">not defined $aligfile</code>
<code proglang="python">aligfile is None</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? " -in m $value" : ""</code>
<code proglang="python">( "" , " -in m " + str(value) )[ value is not None ]</code>
</format>
<ctrl>
<message>
<text lang="en">You must enter either a distance matrix or a alignment.</text>
</message>
<code proglang="perl">not defined $aligfile</code>
<code proglang="python">aligfile is None</code>
</ctrl>
<argpos>10</argpos>
<comment>
<text lang="en">Give a file containing a distance matrix
obtained by distance matrix programs like prodist or
dnadist, ...</text>
</comment>
<example>
5
Alpha 0.000000 0.330447 0.625670 1.032032 1.354086
Beta 0.330447 0.000000 0.375578 1.096290 0.677616
Gamma 0.625670 0.375578 0.000000 0.975798 0.861634
Delta 1.032032 1.096290 0.975798 0.000000 0.226703
Epsilon 1.354086 0.677616 0.861634 0.226703 0.000000
</example>
</parameter>
</parameters>
</paragraph>
<parameter>
<name>out</name>
<prompt lang="en">Output (-out)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>t</value>
</vdef>
<vlist>
<velem>
<value>m</value>
<label>Distance matrix in Phylip format(m)</label>
</velem>
<velem>
<value>t</value>
<label>Tree in New Hampshire format (t)</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " -out $value" : ""</code>
<code proglang="python">( "" , " -out " + str(value) )[ value is not None and value != vdef]</code>
</format>
<argpos>3</argpos>
</parameter>
<paragraph>
<name>treeopt</name>
<prompt lang="en">Tree output options</prompt>
<precond>
<code proglang="perl">$out ne "m"</code>
<code proglang="python">out != "m"</code>
</precond>
<parameters>
<parameter>
<name>upgma</name>
<prompt lang="en">Use the UPGMA method to construct the tree (-upgma)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -upgma" : ""</code>
<code proglang="python">( "" , " -upgma" )[ value ]</code>
</format>
<argpos>3</argpos>
<comment>
<text lang="en">Bootstrapping is not available for a matrix output</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>aligopt</name>
<prompt lang="en">Alignment options</prompt>
<parameters>
<parameter>
<name>boot</name>
<prompt lang="en">Calculate bootstrap values with n iterations (-boot)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">not defined $distfile and $out ne "m"</code>
<code proglang="python">distfile is None and out != "m"</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? " -boot $value" : ""</code>
<code proglang="python">( "" , " -boot " + str(value))[ value is not None ]</code>
</format>
<argpos>3</argpos>
<comment>
<text lang="en">Bootstrapping is not available for a matrix output</text>
</comment>
</parameter>
<parameter>
<name>kimura</name>
<prompt lang="en">Use the kimura translation for pairwise distances (-kimura)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">defined $aligfile</code>
<code proglang="python">aligfile is not None</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -kimura" : ""</code>
<code proglang="python">( "" , " -kimura" )[ value ]</code>
</format>
<argpos>3</argpos>
</parameter>
</parameters>
</paragraph>
<parameter isstdout="1">
<name>treefile</name>
<prompt>Tree file</prompt>
<type>
<datatype>
<class>Tree</class>
</datatype>
<dataFormat>NEWICK</dataFormat>
</type>
<precond>
<code proglang="perl">$out ne "m"</code>
<code proglang="python">out != "m"</code>
</precond>
<filenames>
<code proglang="perl">"quicktree.out"</code>
<code proglang="python">"quicktree.out"</code>
</filenames>
</parameter>
<parameter isstdout="1">
<name>distoutfile</name>
<prompt>Distance matrix</prompt>
<type>
<datatype>
<class>PhylipDistanceMatrix</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$out eq "m"</code>
<code proglang="python">out == "m"</code>
</precond>
<filenames>
<code proglang="perl">"quicktree.out"</code>
<code proglang="python">"quicktree.out"</code>
</filenames>
</parameter>
</parameters>
</program>
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