/var/lib/mobyle/programs/bionj.xml is in mobyle-programs 5.1.2-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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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>bionj</name>
<doc>
<title>BIONJ</title>
<description>
<text lang="en">Neighbor Joining algorithm improved for molecular sequences</text>
</description>
<authors>O. Gascuel</authors>
<reference>Gascuel O., 1997, BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data, Molecular Biology and Evolution 14(7):685-695</reference>
<homepagelink>http://www.lirmm.fr/~w3ifa/MAAS/BIONJ/</homepagelink>
<sourcelink>http://www.lirmm.fr/~w3ifa/MAAS/BIONJ/</sourcelink>
</doc>
<category>phylogeny:distance</category>
<command>bionj</command>
</head>
<parameters>
<parameter ismandatory="1" issimple="1">
<name>infile</name>
<prompt lang="en">Distances matrix File</prompt>
<type>
<datatype>
<class>PhylipDistanceMatrix</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<format>
<code proglang="perl">" $value"</code>
<code proglang="python">" "+str(value)</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">Enter a matrix in Phylip format.</text>
<text lang="en">This algorithm is adapted to evolutive
distances calculated from molecular data sequences (O. Gascuel,
1997, MBE 14(7), 685-695).</text>
<text lang="en">If only one data matrix is given, then BIONJ
returns one tree. When the input file contains several matrices
given one after the other, as obtained when combining PHYLIP's
SEQBOOT and DNADIST to perform a bootstrap, BIONJ returns the
same number of trees, written one after the other in the output
file; this file may be given to PHYLIP's CONSENSE to obtain the
bootstrap tree.</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>
<parameter>
<name>treefile_name</name>
<prompt lang="en">Name of Tree File </prompt>
<type>
<datatype>
<class>Filename</class>
</datatype>
</type>
<vdef>
<value>treefile</value>
</vdef>
<format>
<code proglang="perl">" $value"</code>
<code proglang="python">" " + str(value)</code>
</format>
<argpos>2</argpos>
</parameter>
<parameter isout="1">
<name>treefile</name>
<prompt lang="en">Tree File</prompt>
<type>
<datatype>
<class>Tree</class>
</datatype>
<dataFormat>NEWICK</dataFormat>
</type>
<filenames>
<code proglang="perl">$treefile_name</code>
<code proglang="python">str(treefile_name)</code>
</filenames>
</parameter>
</parameters>
</program>
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