/var/lib/mobyle/programs/neighbor.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>neighbor</name>
<xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="Entities/phylip_package.xml"/>
<doc>
<title>neighbor</title>
<description>
<text lang="en">Neighbor-Joining and UPGMA methods</text>
</description>
<doclink>http://bioweb2.pasteur.fr/docs/phylip/doc/neighbor.html</doclink>
<comment>
<text lang="en">This program implements the Neighbor-Joining
method of Saitou and Nei (1987) and the UPGMA method of
clustering. </text>
<text lang="en">NEIGHBOR constructs a tree by successive
clustering of lineages, setting branch lengths as the
lineages join. The tree is not rearranged thereafter. The
tree does not assume an evolutionary clock, so that it is in
effect an unrooted tree.</text>
</comment>
</doc>
<category>phylogeny:distance</category>
</head>
<parameters>
<parameter iscommand="1" ishidden="1">
<name>neighbor</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">"neighbor <neighbor.params"</code>
<code proglang="python">"neighbor <neighbor.params"</code>
</format>
<argpos>0</argpos>
</parameter>
<parameter ismandatory="1">
<name>distance_method</name>
<prompt lang="en">Distance method</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>neighbor</value>
</vdef>
<vlist>
<velem>
<value>neighbor</value>
<label>Neighbor-joining</label>
</velem>
<velem>
<value>upgma</value>
<label>UPGMA</label>
</velem>
</vlist>
<format>
<code proglang="perl">($value eq "upgma") ? "N\\n" : ""</code>
<code proglang="python">( "" , "N\n")[ value == "upgma" ]</code>
</format>
<argpos>1</argpos>
<paramfile>neighbor.params</paramfile>
</parameter>
<parameter ismandatory="1" issimple="1" ismaininput="1">
<name>infile</name>
<prompt lang="en">Distances matrix File</prompt>
<type>
<datatype>
<class>PhylipDistanceMatrix</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$infile ne "infile"</code>
<code proglang="python">infile != "infile"</code>
</precond>
<format>
<code proglang="perl">"ln -s $infile infile && "</code>
<code proglang="python">"ln -s "+str(infile)+" infile && "</code>
</format>
<ctrl>
<message>
<text lang="en">Distance matrix file cannot be named `outfile'</text>
</message>
<code proglang="perl">$infile ne "outfile"</code>
<code proglang="python">infile != "outfile"</code>
</ctrl>
<argpos>-10</argpos>
<comment>
<text lang="en">Give a file containing a distance matrix
obtained by distance matrix programs like protdist 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>
<paragraph>
<name>jumble_opt</name>
<prompt lang="en">Randomize options</prompt>
<parameters>
<parameter>
<name>jumble</name>
<prompt lang="en">Randomize (jumble) input order (J)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? "J\\n$jumble_seed\\n" : ""</code>
<code proglang="python">( "" , "J\n" + str( jumble_seed ) + "\n" )[ value ]</code>
</format>
<ctrl>
<message>
<text lang="en">you can't use "Jumble options" and "Bootstrap options" at the same time</text>
</message>
<code proglang="perl">not( $multiple and $jumble)</code>
<code proglang="python">not( multiple and jumble)</code>
</ctrl>
<argpos>20</argpos>
<paramfile>neighbor.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>jumble_seed</name>
<prompt lang="en">Random number seed for jumble (must be odd)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">$jumble</code>
<code proglang="python">jumble</code>
</precond>
<format>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</format>
<ctrl>
<message>
<text lang="en">Random number seed must be odd</text>
</message>
<code proglang="perl">$value > 0 and ($value % 2) != 0</code>
<code proglang="python">value > 0 and (value % 2) != 0</code>
</ctrl>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>bootstrap</name>
<prompt lang="en">Bootstrap options</prompt>
<parameters>
<parameter>
<name>multiple</name>
<prompt lang="en">Analyze multiple data sets (M)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? "M\\n$multiple_number\\n$multiple_seed\\n" : ""</code>
<code proglang="python">("", "M\n"+str(multiple_number)+"\n"+str(multiple_seed)+"\n")[ value ]</code>
</format>
<ctrl>
<message>
<text lang="en">you can't use "Jumble options" and "Bootstrap options" at the same time</text>
</message>
<code proglang="perl">not( $multiple and $jumble)</code>
<code proglang="python">not( multiple and jumble)</code>
</ctrl>
<argpos>10</argpos>
<paramfile>neighbor.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>multiple_number</name>
<prompt lang="en">How many data sets</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">$multiple</code>
<code proglang="python">multiple</code>
</precond>
<format>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</format>
<ctrl>
<message>
<text lang="en">There must be no more than 1000 datasets for this server</text>
</message>
<code proglang="perl">$value <= 1000</code>
<code proglang="python">value <= 1000</code>
</ctrl>
<ctrl>
<message>
<text lang="en">Bad data sets number: it must be greater than 1</text>
</message>
<code proglang="perl">$value > 1</code>
<code proglang="python">value > 1</code>
</ctrl>
</parameter>
<parameter ismandatory="1">
<name>multiple_seed</name>
<prompt lang="en">Random number seed for multiple dataset (must be odd)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">$multiple</code>
<code proglang="python">multiple</code>
</precond>
<format>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</format>
<ctrl>
<message>
<text lang="en">Random number seed must be odd</text>
</message>
<code proglang="perl">$value < 0 and ($value % 2) != 0</code>
<code proglang="python">value > 0 and (value % 2) != 0</code>
</ctrl>
<paramfile>neighbor.params</paramfile>
</parameter>
<parameter>
<name>consense</name>
<prompt lang="en">Compute a consensus tree</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">$multiple and $print_treefile</code>
<code proglang="python">multiple and print_treefile</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " && cp infile neighbor.infile && cp neighbor.outtree intree && consense <consense.params && mv outtree consense.outtree && mv outfile consense.outfile" : ""</code>
<code proglang="python">("" , " && cp infile neighbor.infile && cp neighbor.outtree intree && consense <consense.params && mv outtree consense.outtree && mv outfile consense.outfile")[ value ]</code>
</format>
<argpos>10</argpos>
</parameter>
</parameters>
</paragraph>
<parameter ishidden="1">
<name>consense_confirm</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<precond>
<code proglang="perl">$consense</code>
<code proglang="python">consense</code>
</precond>
<format>
<code proglang="perl">"Y\\n"</code>
<code proglang="python">"Y\n"</code>
</format>
<argpos>1000</argpos>
<paramfile>consense.params</paramfile>
</parameter>
<parameter ishidden="1">
<name>consense_terminal_type</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<precond>
<code proglang="perl">$consense</code>
<code proglang="python">consense</code>
</precond>
<format>
<code proglang="perl">"T\\n"</code>
<code proglang="python">"T\n"</code>
</format>
<argpos>-2</argpos>
<paramfile>consense.params</paramfile>
</parameter>
<parameter isout="1">
<name>consense_outfile</name>
<prompt lang="en">Consense output file</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<precond>
<code proglang="perl">$consense</code>
<code proglang="python">consense</code>
</precond>
<filenames>
<code proglang="perl">"consense.outfile"</code>
<code proglang="python">"consense.outfile"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>consense_treefile</name>
<prompt lang="en">Consense output tree</prompt>
<type>
<datatype>
<class>Tree</class>
</datatype>
<dataFormat>NEWICK</dataFormat>
</type>
<precond>
<code proglang="perl">$consense</code>
<code proglang="python">consense</code>
</precond>
<filenames>
<code proglang="perl">"consense.outtree"</code>
<code proglang="python">"consense.outtree"</code>
</filenames>
</parameter>
<paragraph>
<name>output</name>
<prompt lang="en">Output options</prompt>
<parameters>
<parameter>
<name>print_tree</name>
<prompt lang="en">Print out tree (3)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">($value) ? "" : "3\\n"</code>
<code proglang="python">( "3\n" , "" )[ value ]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">Tells the program to print a semi-graphical picture of the tree in the outfile.</text>
</comment>
<paramfile>neighbor.params</paramfile>
</parameter>
<parameter>
<name>print_treefile</name>
<prompt lang="en">Write out trees onto tree file (4)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">($value) ? "" : "4\\n"</code>
<code proglang="python">( "4\n" , "" )[ value ]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">Tells the program to save the tree in a treefile (a standard representation of trees where the tree is specified by a nested pairs of parentheses, enclosing names and separated by commas).</text>
</comment>
<paramfile>neighbor.params</paramfile>
</parameter>
<parameter>
<name>printdata</name>
<prompt lang="en">Print out the data at start of run (1)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? "1\\n" : ""</code>
<code proglang="python">( "" , "1\n" )[ value ]</code>
</format>
<argpos>1</argpos>
<paramfile>neighbor.params</paramfile>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>other_options</name>
<prompt lang="en">Other options</prompt>
<parameters>
<parameter>
<name>outgroup</name>
<prompt lang="en">Outgroup species (default, use as outgroup species 1) (O)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">$distance_method eq "neighbor"</code>
<code proglang="python">distance_method == "neighbor"</code>
</precond>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? "O\\n$value\\n" : ""</code>
<code proglang="python">( "" , "O\n" +str( value )+ "\n" )[ value is not None and value != vdef]</code>
</format>
<ctrl>
<message>
<text lang="en">Please enter a value greater than 0</text>
</message>
<code proglang="perl">$value > 0</code>
<code proglang="python">value > 0</code>
</ctrl>
<argpos>1</argpos>
<comment>
<text lang="en">The O (Outgroup) option specifies which species is to have the root of the tree be on the line leading to it.</text>
<text lang="en">For example, if the outgroup is a species "Mouse" then the root of the tree will be placed in the middle of the branch which is connected to this species, with Mouse branching off on one side of the root and the lineage leading to the rest of the tree on the other.</text>
<text lang="en">This option is toggle on by choosing the number of the outgroup (the species being taken in the numerical order that they occur in the input file).</text>
<text lang="en">Outgroup-rooting will not be attempted if it is a user-defined tree, despite your invoking the option.</text>
<text lang="en">When it is used, the tree as printed out is still listed as being an unrooted tree, though the outgroup is connected to the bottommost node so that it is easy to visually convert the tree into rooted form.</text>
</comment>
<paramfile>neighbor.params</paramfile>
</parameter>
<parameter>
<name>triangular</name>
<prompt lang="en">Matrix format</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>square</value>
</vdef>
<flist>
<felem>
<value>square</value>
<label>Square</label>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</felem>
<felem>
<value>lower</value>
<label>Lower-triangular (L)</label>
<code proglang="perl">"L\\n"</code>
<code proglang="python">"L\n"</code>
</felem>
<felem>
<value>upper</value>
<label>Upper-triangular (R)</label>
<code proglang="perl">"R\\n"</code>
<code proglang="python">"R\n"</code>
</felem>
</flist>
<argpos>1</argpos>
<paramfile>neighbor.params</paramfile>
</parameter>
</parameters>
</paragraph>
<parameter isout="1">
<name>outfile</name>
<prompt lang="en">Neighbor output file</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<format>
<code proglang="perl">" && mv outfile neighbor.outfile"</code>
<code proglang="python">" && mv outfile neighbor.outfile"</code>
</format>
<filenames>
<code proglang="perl">"neighbor.outfile"</code>
<code proglang="python">"neighbor.outfile"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>treefile</name>
<prompt lang="en">Neighbor output tree file</prompt>
<type>
<datatype>
<class>Tree</class>
</datatype>
<dataFormat>NEWICK</dataFormat>
</type>
<precond>
<code proglang="perl">$print_treefile</code>
<code proglang="python">print_treefile</code>
</precond>
<format>
<code proglang="perl">" && mv outtree neighbor.outtree"</code>
<code proglang="python">" && mv outtree neighbor.outtree"</code>
</format>
<filenames>
<code proglang="perl">"neighbor.outtree"</code>
<code proglang="python">"neighbor.outtree"</code>
</filenames>
</parameter>
<parameter ishidden="1">
<name>confirm</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">"Y\\n"</code>
<code proglang="python">"Y\n"</code>
</format>
<argpos>1000</argpos>
<paramfile>neighbor.params</paramfile>
</parameter>
<parameter ishidden="1">
<name>terminal_type</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">"0\\n"</code>
<code proglang="python">"0\n"</code>
</format>
<argpos>-1</argpos>
<paramfile>neighbor.params</paramfile>
</parameter>
</parameters>
</program>
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