/var/lib/mobyle/programs/fitch.xml is in mobyle-programs 5.1.1-1.
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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>fitch</name>
<xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="Entities/phylip_package.xml"/>
<doc>
<title>fitch</title>
<description>
<text lang="en">Fitch-Margoliash and Least-Squares Distance Methods</text>
</description>
<doclink>http://bioweb2.pasteur.fr/docs/phylip/doc/fitch.html</doclink>
<comment>
<text lang="en">This program carries out Fitch-Margoliash,
Least Squares, and a number of similar methods</text>
</comment>
</doc>
<category>phylogeny:distance</category>
</head>
<parameters>
<parameter iscommand="1" ishidden="1">
<name>fitch</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">"fitch <fitch.params"</code>
<code proglang="python">"fitch <fitch.params"</code>
</format>
<argpos>0</argpos>
</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 $infile infile && "</code>
<code proglang="python">"ln -s " + str( value ) + " infile && "</code>
</format>
<argpos>-5</argpos>
<comment>
<text lang="en">Give a file containing a distance matrix
obtained by distance matrix programs like protdist or
dnadist</text>
</comment>
<example>
5
Alpha 0.000000 0.330447 0.625670 1.032032 1.354086
Beta 0.330447 0.000000 0.375578 1.096290 0.677616
Gamma 0.625670 0.375578 0.000000 0.975798 0.861634
Delta 1.032032 1.096290 0.975798 0.000000 0.226703
Epsilon 1.354086 0.677616 0.861634 0.226703 0.000000
</example>
</parameter>
<parameter>
<name>Method</name>
<prompt lang="en">Method (D)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>FM</value>
</vdef>
<flist>
<felem>
<value>FM</value>
<label>Fitch-Margoliash</label>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</felem>
<felem>
<value>ME</value>
<label>Minimum Evolution</label>
<code proglang="perl">"D\\n"</code>
<code proglang="python">"D\n"</code>
</felem>
</flist>
<paramfile>fitch.params</paramfile>
</parameter>
<paragraph>
<name>fitch_options</name>
<prompt lang="en">Fitch options</prompt>
<parameters>
<parameter>
<name>negative_branch</name>
<prompt lang="en">Negative branch lengths allowed (-)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? "-\\n" : ""</code>
<code proglang="python">( "" , "-\n" )[ value ]</code>
</format>
<argpos>1</argpos>
<paramfile>fitch.params</paramfile>
</parameter>
<parameter>
<name>power</name>
<prompt lang="en">Power (P)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>2.0</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? "P\\n$value\\n" : ""</code>
<code proglang="python">( "" , "P\n" + str(value ) + "\n" )[ value is not None and value != vdef ]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">For the Fitch-Margoliash method, which is the default method with this program, P is 2.0. For the Cavalli-Sforza and Edwards least squares method it should be set to 0 (so that the denominator is always 1). An intermediate method is also available in which P is 1.0, and any other value of P, such as 4.0 or -2.3, can also be used. This generates a whole family of methods.</text>
<text lang="en">Please read the documentation (man distance).</text>
</comment>
<paramfile>fitch.params</paramfile>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>jumble_options</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>
<precond>
<code proglang="perl">not $user_tree</code>
<code proglang="python">not user_tree</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? "J\\n$jumble_seed\\n$jumble_number\\n" : ""</code>
<code proglang="python">( "" , "J\n"+str( jumble_seed ) +"\n" + str( jumble_number ) +"\n" )[ value ]</code>
</format>
<argpos>20</argpos>
<paramfile>fitch.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>jumble_seed</name>
<prompt lang="en">Random number seed (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 ($value % 2) != 0</code>
<code proglang="python">value > 0 and (value % 2) != 0</code>
</ctrl>
<argpos>19</argpos>
</parameter>
<parameter>
<name>jumble_number</name>
<prompt lang="en">Number of times to jumble</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">$jumble</code>
<code proglang="python">jumble</code>
</precond>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</format>
<argpos>19</argpos>
</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$multiple_seed\\n" : ""</code>
<code proglang="python">( "", "M\n"+str(multiple_number)+"\n"+str(multiple_seed)+"\n")[value]</code>
</format>
<argpos>10</argpos>
<paramfile>fitch.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>multiple_number</name>
<prompt lang="en">How many data sets</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">$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">$value <= 1000</code>
<code proglang="python">value <= 1000</code>
</ctrl>
<argpos>9</argpos>
</parameter>
<parameter ismandatory="1">
<name>multiple_seed</name>
<prompt lang="en">Random number seed (must be odd)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">$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>
<argpos>19</argpos>
</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 fitch.infile && cp fitch.outtree intree && consense <consense.params && mv outtree consense.outtree && mv outfile consense.outfile" : ""</code>
<code proglang="python">( "" , " && cp infile fitch.infile && cp fitch.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>Consense output file</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<precond>
<code proglang="perl">$consense</code>
<code proglang="python">consense</code>
</precond>
<filenames>
<code proglang="perl">"consense.outfile"</code>
<code proglang="python">"consense.outfile"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>consense_treefile</name>
<prompt>Consense tree file</prompt>
<type>
<datatype>
<class>Tree</class>
</datatype>
<dataFormat>NEWICK</dataFormat>
</type>
<precond>
<code proglang="perl">$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>user_tree_opt</name>
<prompt lang="en">User tree options</prompt>
<parameters>
<parameter ismandatory="1">
<name>user_tree</name>
<prompt lang="en">Use User tree (default: no, search for best tree) (U)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">defined $tree_file</code>
<code proglang="python">tree_file is not None</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? "U\\n" : ""</code>
<code proglang="python">( "" , "U\n")[ value ]</code>
</format>
<ctrl>
<message>
<text lang="en">You cannot randomize (jumble) your dataset and give a user tree at the same time</text>
</message>
<code proglang="perl">not ( $user_tree and $jumble )</code>
<code proglang="python">not ( user_tree and jumble )</code>
</ctrl>
<argpos>1</argpos>
<comment>
<text lang="en">To give your tree to the program, you must normally put it in the alignment file, after the sequences, preceded by a line indicating how many trees you give.</text>
<text lang="en">Here, this will be automatically appended: just give a treefile and the number of trees in it.</text>
</comment>
<paramfile>fitch.params</paramfile>
</parameter>
<parameter>
<name>tree_file</name>
<prompt lang="en">User Tree file</prompt>
<type>
<datatype>
<class>Tree</class>
</datatype>
<dataFormat>NEWICK</dataFormat>
</type>
<precond>
<code proglang="perl">$user_tree</code>
<code proglang="python">user_tree</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? "cat $tree_file >> intree; " : ""</code>
<code proglang="python">("" , "cat "+str( tree_file ) + " >> intree; " )[ value is not None ]</code>
</format>
<argpos>-1</argpos>
</parameter>
<parameter>
<name>use_lengths</name>
<prompt lang="en">Use lengths from user trees (N)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">$user_tree</code>
<code proglang="python">user_tree</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? "N\\n" : ""</code>
<code proglang="python">( "" , "N\n" )[ value ]</code>
</format>
<argpos>2</argpos>
<paramfile>fitch.params</paramfile>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>output</name>
<prompt lang="en">Output options</prompt>
<parameters>
<parameter>
<name>print_tree</name>
<prompt lang="en">Print out tree (3)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">($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>fitch.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">($value) ? "" : "4\\n"</code>
<code proglang="python">( "4\n" , "" )[ value ]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">Tells the program to save the tree in a treefile (a standard representation of trees where the tree is specified by a nested pairs of parentheses, enclosing names and separated by commas).</text>
</comment>
<paramfile>fitch.params</paramfile>
</parameter>
<parameter>
<name>printdata</name>
<prompt lang="en">Print out the data at start of run (1)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? "1\\n" : ""</code>
<code proglang="python">( "" , "1\n" )[ value ]</code>
</format>
<argpos>1</argpos>
<paramfile>fitch.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 root (O)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<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">$value > 0</code>
<code proglang="python">value > 0</code>
</ctrl>
<argpos>1</argpos>
<paramfile>fitch.params</paramfile>
</parameter>
<parameter>
<name>triangular</name>
<prompt lang="en">Matrix format</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>square</value>
</vdef>
<flist>
<felem>
<value>square</value>
<label>Square</label>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</felem>
<felem>
<value>lower</value>
<label>Lower-triangular</label>
<code proglang="perl">"L\\n"</code>
<code proglang="python">"L\n"</code>
</felem>
<felem>
<value>upper</value>
<label>Upper-triangular</label>
<code proglang="perl">"R\\n"</code>
<code proglang="python">"R\n"</code>
</felem>
</flist>
<argpos>1</argpos>
<paramfile>fitch.params</paramfile>
</parameter>
<parameter>
<name>subreplicates</name>
<prompt lang="en">Subreplicates (S)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? "S\\n" : ""</code>
<code proglang="python">( "" , "S\n" )[ value ]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">If the S (subreplication) option is in effect, the above degrees of freedom must be modified by noting that N is not n(n-1)/2 but is the sum of the numbers of replicates of all cells in the distance matrix read in, which may be either square or triangular. A further explanation of the statistical test of the clock is given in a paper of mine (Felsenstein, 1986).</text>
</comment>
<paramfile>fitch.params</paramfile>
</parameter>
<parameter>
<name>global</name>
<prompt lang="en">Global rearrangements (G)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? "G\\n" : ""</code>
<code proglang="python">( "", "G\n")[ value ]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">is the Global search option. This causes, after the last species is added to the tree, each possible group to be removed and re-added. This improves the result, since the position of every species is reconsidered. It approximately triples the run-time of the program. It is not an option in KITSCH because it is the default and is always in force there.</text>
</comment>
<paramfile>fitch.params</paramfile>
</parameter>
</parameters>
</paragraph>
<parameter isout="1">
<name>outfile</name>
<prompt>Fitch output file</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<format>
<code proglang="perl">" && mv outfile fitch.outfile"</code>
<code proglang="python">" && mv outfile fitch.outfile"</code>
</format>
<filenames>
<code proglang="perl">"fitch.outfile"</code>
<code proglang="python">"fitch.outfile"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>treefile</name>
<prompt>Fitch tree file</prompt>
<type>
<datatype>
<class>Tree</class>
</datatype>
<dataFormat>NEWICK</dataFormat>
</type>
<precond>
<code proglang="perl">$print_treefile</code>
<code proglang="python">print_treefile</code>
</precond>
<format>
<code proglang="perl">" && mv outtree fitch.outtree"</code>
<code proglang="python">" && mv outtree fitch.outtree"</code>
</format>
<filenames>
<code proglang="perl">"fitch.outtree"</code>
<code proglang="python">"fitch.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>fitch.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>fitch.params</paramfile>
</parameter>
</parameters>
</program>
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