/var/lib/mobyle/programs/lvb.xml is in mobyle-programs 5.1.1-1.
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>lvb</name>
<version>2.3</version>
<doc>
<title>LVB</title>
<description>
<text lang="en">Reconstructing Evolution With Parsimony And Simulated Annealing</text>
</description>
<authors>D. Barker</authors>
<reference>Barker, D. 2004. LVB: Parsimony and simulated annealing in the search for phylogenetic trees. Bioinformatics, 20, 274-275.</reference>
<doclink>http://biology.st-andrews.ac.uk/cegg/lvb.htm</doclink>
<homepagelink>http://biology.st-andrews.ac.uk/cegg/lvb.htm</homepagelink>
<sourcelink>http://biology.st-andrews.ac.uk/cegg/lvb.htm</sourcelink>
</doc>
<category>phylogeny:parsimony</category>
</head>
<parameters>
<parameter iscommand="1" ishidden="1">
<name>lvb</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">"lvb <lvb.params"</code>
<code proglang="python">"lvb <lvb.params"</code>
</format>
<argpos>0</argpos>
</parameter>
<parameter ismandatory="1">
<name>infile</name>
<prompt lang="en">Alignment File</prompt>
<type>
<datatype>
<class>Alignment</class>
</datatype>
<dataFormat>PHYLIPI</dataFormat>
</type>
<precond>
<code proglang="perl">$infile ne "infile"</code>
<code proglang="python">infile != "infile"</code>
</precond>
<format>
<code proglang="perl">"ln -s $value infile; "</code>
<code proglang="python">"ln -s " + str(value) + " infile; "</code>
</format>
<argpos>-1</argpos>
</parameter>
<parameter ishidden="1">
<name>format</name>
<prompt lang="en">Format is INTERLEAVED or SEQUENTIAL</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>I</value>
</vdef>
<vlist>
<velem>
<value>I</value>
<label>INTERLEAVED (I)</label>
</velem>
<velem>
<value>S</value>
<label>SEQUENTIAL (S)</label>
</velem>
</vlist>
<format>
<code proglang="perl">"$value\\n"</code>
<code proglang="python">str(value) + "\n"</code>
</format>
<argpos>1</argpos>
<paramfile>lvb.params</paramfile>
</parameter>
<parameter>
<name>gaps_treatment</name>
<prompt lang="en">Treatment of gaps represented by '-' </prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>U</value>
</vdef>
<vlist>
<velem>
<value>U</value>
<label>UNKNOWN (U)</label>
</velem>
<velem>
<value>F</value>
<label>FIFTH STATE (F)</label>
</velem>
</vlist>
<format>
<code proglang="perl">"$value\\n"</code>
<code proglang="python">str(value) + "\n"</code>
</format>
<argpos>2</argpos>
<comment>
<text lang="en">A gap represented by the letter 'O' in the data matrix is always treated as a character state in its own right (fifth state). lvb can treat gaps represented by'-' in either of the following ways:</text>
<text lang="en">Fifth state '-' is treated as equivalent to 'O'. </text>
<text lang="en">Unknown '-' is treated as equivalent to '?', i.e., as an ambiguous site that may contain 'A' or 'C' or 'G' or 'T' or 'O'. </text>
<text lang="en">'Fifth state' may give excessive weight to multi-site gaps, since each affected base will be counted as one event.</text>
</comment>
<paramfile>lvb.params</paramfile>
</parameter>
<parameter>
<name>seed</name>
<prompt lang="en">Seed for the random number generator</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value)? "$value\\n" : "\\n"</code>
<code proglang="python">( "\n" , str(value) + "\n" )[ value is not None ]</code>
</format>
<argpos>3</argpos>
<comment>
<text lang="en">When prompted for the random number seed, enter an integer in the range 0 to 900000000 inclusive. The default value is taken from the system clock and hence will vary from one analysis to the next, changing every second. The default is usually appropriate.</text>
</comment>
<paramfile>lvb.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>bootstrap</name>
<prompt lang="en">How many bootstrap replicates required (bootstrap)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">"$value\\n"</code>
<code proglang="python">str(value) + "\n"</code>
</format>
<ctrl>
<message>
<text lang="en">This server allows no more than 1000 replicates</text>
</message>
<code proglang="perl">$bootstrap < 1000</code>
<code proglang="python">bootstrap <= 1000</code>
</ctrl>
<argpos>5</argpos>
<comment>
<text lang="en">Number of bootstrap replicates required as an integer in the range 1 to 1000 inclusive, or 0 for no bootstrapping (this server allows no more than 1000 replicates)</text>
</comment>
<paramfile>lvb.params</paramfile>
</parameter>
<parameter isout="1">
<name>res</name>
<prompt>Tree file</prompt>
<type>
<datatype>
<class>Tree</class>
</datatype>
<dataFormat>NEWICK</dataFormat>
</type>
<filenames>
<code proglang="perl">"outtree"</code>
<code proglang="python">"outtree"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>other_results</name>
<prompt>Results files</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<filenames>
<code proglang="perl">"stat*"</code>
<code proglang="perl">"sum"</code>
<code proglang="perl">"log"</code>
<code proglang="perl">"data"</code>
<code proglang="perl">"ini*"</code>
<code proglang="python">"stat*"</code>
<code proglang="python">"sum"</code>
<code proglang="python">"log"</code>
<code proglang="python">"data"</code>
<code proglang="python">"ini*"</code>
</filenames>
</parameter>
</parameters>
</program>
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