/var/lib/mobyle/programs/kitsch.xml is in mobyle-programs 5.1.2-2.
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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>kitsch</name>
<xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="Entities/phylip_package.xml"/>
<doc>
<title>kitsch</title>
<description>
<text lang="en">Fitch-Margoliash and Least Squares Methods with Evolutionary Clock</text>
</description>
<doclink>http://bioweb2.pasteur.fr/docs/phylip/doc/kitsch.html</doclink>
<comment>
<text lang="en">This program carries out the Fitch-Margoliash
and Least Squares methods, plus a variety of others of the
same family, with the assumption that all tip species are
contemporaneous, and that there is an evolutionary clock (in
effect, a molecular clock). This means that branches of the
tree cannot be of arbitrary length, but are constrained so
that the total length from the root of the tree to any species
is the same.</text>
</comment>
</doc>
<category>phylogeny:distance</category>
</head>
<parameters>
<parameter iscommand="1" ishidden="1">
<name>kitsch</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">"kitsch <kitsch.params"</code>
<code proglang="python">"kitsch <kitsch.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 $infile infile && "</code>
<code proglang="python">"ln -s " + str(infile) + " infile && "</code>
</format>
<argpos>-5</argpos>
<comment>
<text lang="en">Give a file containing a distance matrix
obtained by distance matrix programs like prodist or
dnadist</text>
</comment>
<example>
5
Alpha 0.000000 0.330447 0.625670 1.032032 1.354086
Beta 0.330447 0.000000 0.375578 1.096290 0.677616
Gamma 0.625670 0.375578 0.000000 0.975798 0.861634
Delta 1.032032 1.096290 0.975798 0.000000 0.226703
Epsilon 1.354086 0.677616 0.861634 0.226703 0.000000
</example>
</parameter>
<paragraph>
<name>fitch_options</name>
<prompt lang="en">Fitch options</prompt>
<parameters>
<parameter>
<name>Method</name>
<prompt lang="en">Program method (D)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>F</value>
</vdef>
<flist>
<felem>
<value>F</value>
<label>Fitch-Margoliash</label>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</felem>
<felem>
<value>M</value>
<label>Minimum Evolution</label>
<code proglang="perl">"D\\n"</code>
<code proglang="python">"D\n"</code>
</felem>
</flist>
<argpos>1</argpos>
<paramfile>kitsch.params</paramfile>
</parameter>
<parameter>
<name>negative_branch</name>
<prompt lang="en">Negative branch lengths allowed (-)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? "-\\n" : ""</code>
<code proglang="python">( "" , "-\n")[ value ]</code>
</format>
<argpos>1</argpos>
<paramfile>kitsch.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 vdef != value ]</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>kitsch.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>kitsch.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">($value) ? "M\\n$numtiple_number\\n$multiple_seed\\n" : ""</code>
<code proglang="python">( "" , "M\n"+str(multiple_number)+"\n"+str(multiple_seed)+"\n")[ value ]</code>
</format>
<argpos>10</argpos>
<paramfile>kitsch.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>multiple_number</name>
<prompt lang="en">How many data sets</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">$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 kitsch.infile && cp kitsch.outtree intree && consense <consense.params && mv outtree consense.outtree && mv outfile consense.outfile" : ""</code>
<code proglang="python">("" , " && cp infile kitsch.infile && cp kitsch.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>
<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>
<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 $jumble )</code>
<code proglang="python">not ( user_tree and jumble )</code>
</ctrl>
<argpos>1</argpos>
<comment>
<text lang="en">The U (User Tree) option requires a bifurcating tree, unlike FITCH, which requires an unrooted tree with a trifurcation at its base.</text>
<text lang="en">If a tree with a trifurcation at the base is by mistake fed into the U option of KITSCH then some of its species (the entire rightmost furc, in fact) will be ignored and too small a tree read in. This should result in an error message and the program should stop.</text>
<text lang="en">It is important to understand the difference between the User Tree formats for KITSCH and FITCH. You may want to use RETREE to convert a user tree that is suitable for FITCH into one suitable for KITSCH or vice versa.</text>
</comment>
<paramfile>kitsch.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>tree_file</name>
<prompt lang="en">User Tree file</prompt>
<type>
<datatype>
<class>Tree</class>
</datatype>
<dataFormat>NEWICK</dataFormat>
</type>
<precond>
<code proglang="perl">$user_tree</code>
<code proglang="python">user_tree</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? "cat $tree_file >> intree && " : ""</code>
<code proglang="python">( "" , "cat "+ str( value ) +" >> intree && " ) [ value is not None ]</code>
</format>
<argpos>-1</argpos>
<comment>
<text lang="en">Note that the User Trees (used by option U) must be rooted trees (with a bifurcation at their base). If you take a user tree from FITCH and try to evaluate it in KITSCH, it must first be rooted. This can be done using RETREE</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>output</name>
<prompt lang="en">Output options</prompt>
<parameters>
<parameter>
<name>print_tree</name>
<prompt lang="en">Print out tree (3)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">($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>kitsch.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">($value) ? "" : "4\\n"</code>
<code proglang="python">( "4\n" , "" )[ value ]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">Tells the program to save the tree in a treefile (a standard representation of trees where the tree is specified by a nested pairs of parentheses, enclosing names and separated by commas).</text>
</comment>
<paramfile>kitsch.params</paramfile>
</parameter>
<parameter>
<name>printdata</name>
<prompt lang="en">Print out the data at start of run (1)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? "1\\n" : ""</code>
<code proglang="python">("", "1\n" )[ value ]</code>
</format>
<argpos>1</argpos>
<paramfile>kitsch.params</paramfile>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>other_options</name>
<prompt lang="en">Other options</prompt>
<parameters>
<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>kitsch.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">($value) ? "S\\n" : ""</code>
<code proglang="python">( "" , "S\n" )[ value ]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">If the S (subreplication) option is in effect, the above degrees of freedom must be modified by noting that N is not n(n-1)/2 but is the sum of the numbers of replicates of all cells in the distance matrix read in, which may be either square or triangular. A further explanation of the statistical test of the clock is given in a paper of mine (Felsenstein, 1986).</text>
</comment>
<paramfile>kitsch.params</paramfile>
</parameter>
</parameters>
</paragraph>
<parameter isout="1">
<name>outfile</name>
<prompt>Kitsch output file</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<format>
<code proglang="perl">" && mv outfile kitsch.outfile"</code>
<code proglang="python">" && mv outfile kitsch.outfile"</code>
</format>
<filenames>
<code proglang="perl">"kitsch.outfile"</code>
<code proglang="python">"kitsch.outfile"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>treefile</name>
<prompt>Kitch tree file</prompt>
<type>
<datatype>
<class>Tree</class>
</datatype>
<dataFormat>NEWICK</dataFormat>
</type>
<precond>
<code proglang="perl">$print_treefile</code>
<code proglang="python">print_treefile</code>
</precond>
<format>
<code proglang="perl">" && mv outtree kitsch.outtree"</code>
<code proglang="python">" && mv outtree kitsch.outtree"</code>
</format>
<filenames>
<code proglang="perl">"kitsch.outtree"</code>
<code proglang="python">"kitsch.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>kitsch.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>kitsch.params</paramfile>
</parameter>
</parameters>
</program>
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