/var/lib/mobyle/programs/morePhyML.xml is in mobyle-programs 5.1.2-1.
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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>morePhyML</name>
<version>1.14</version>
<doc>
<title>morePhyML</title>
<description>
<text lang="en">Improving ML tree searching with PhyML 3</text>
</description>
<authors>Alexis Criscuolo</authors>
<reference>Criscuolo A (2011) morePhyML: improving the phylogenetic tree space
exploration with PhyML 3. Molecular Phylogenetics and Evolution.</reference>
<reference>Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O
(2010) New algorithms and methods to estimate maximum-likelihood
phylogenies: assessing the performance of PhyML 3.0. Syst Biol
59:307-321.</reference>
<reference>Guindon, S. and Gascuel, O. (2003) A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood Syst. Biol., 52, 696-704</reference>
<sourcelink>ftp://ftp.pasteur.fr/pub/gensoft/projects/morePhyML/</sourcelink>
<doclink>http://bioweb2.pasteur.fr/docs/morePhyML/morePhyML_doc.pdf</doclink>
</doc>
<category>phylogeny:likelihood</category>
<command>morePhyML</command>
</head>
<parameters>
<parameter ismandatory="1" issimple="1">
<name>alignment</name>
<prompt lang="en">Sequence Alignment</prompt>
<type>
<datatype>
<class>Alignment</class>
</datatype>
<dataFormat>PHYLIP-RELAXED</dataFormat>
</type>
<format>
<code proglang="perl">"-i $value"</code>
<code proglang="python">" -i "+str(value)</code>
</format>
</parameter>
<parameter issimple="1">
<name>seqtype</name>
<prompt lang="en">Data type (-d)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>nt</value>
</vdef>
<vlist>
<velem>
<value>nt</value>
<label>DNA (nt)</label>
</velem>
<velem>
<value>aa</value>
<label>Amino-Acids (aa)</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value) ? " -d $value" : ""</code>
<code proglang="python">( "" , " -d " + str(value) )[ value is not None ]</code>
</format>
</parameter>
<paragraph>
<name>control_opt</name>
<prompt lang="en">Control Options</prompt>
<parameters>
<parameter issimple="1">
<name>ntmodel</name>
<prompt lang="en">Nucleotide substitution model (-m)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<precond>
<code proglang="perl">$seqtype eq "nt"</code>
<code proglang="python">seqtype == "nt"</code>
</precond>
<vdef>
<value>GTR</value>
</vdef>
<vlist>
<velem>
<value>HKY85</value>
<label>HKY85</label>
</velem>
<velem>
<value>JC69</value>
<label>JC69</label>
</velem>
<velem>
<value>K80</value>
<label>K80</label>
</velem>
<velem>
<value>F81</value>
<label>F81</label>
</velem>
<velem>
<value>F84</value>
<label>F84</label>
</velem>
<velem>
<value>TN93</value>
<label>TN93</label>
</velem>
<velem>
<value>GTR</value>
<label>GTR</label>
</velem>
<velem>
<value>TN93e</value>
<label>TN93e</label>
</velem>
<velem>
<value>TPM1e</value>
<label>TPM1e</label>
</velem>
<velem>
<value>TPM1u</value>
<label>TPM1u</label>
</velem>
<velem>
<value>TPM2e</value>
<label>TPM2e</label>
</velem>
<velem>
<value>TPM2u</value>
<label>TPM2u</label>
</velem>
<velem>
<value>TPM3e</value>
<label>TPM3e</label>
</velem>
<velem>
<value>TPM3u</value>
<label>TPM3u</label>
</velem>
<velem>
<value>TIM1e</value>
<label>TIM1e</label>
</velem>
<velem>
<value>TIM1u</value>
<label>TIM1u</label>
</velem>
<velem>
<value>TIM2e</value>
<label>TIM2e</label>
</velem>
<velem>
<value>TIM2u</value>
<label>TIM2u</label>
</velem>
<velem>
<value>TIM3e</value>
<label>TIM3e</label>
</velem>
<velem>
<value>TIM3u</value>
<label>TIM3u</label>
</velem>
<velem>
<value>TVMe</value>
<label>TVMe</label>
</velem>
<velem>
<value>TVMu</value>
<label>TVMu</label>
</velem>
<velem>
<value>SYM</value>
<label>SYM</label>
</velem>
</vlist>
<format>
<code proglang="perl">($value ne $vdef) ? " -m $value" : ""</code>
<code proglang="python">("", " -m "+str(value))[value != vdef]</code>
</format>
</parameter>
<parameter issimple="1">
<name>aamodel</name>
<prompt lang="en">Amino-acid substitution model (-m)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<precond>
<code proglang="perl">$seqtype eq "aa"</code>
<code proglang="python">seqtype == "aa"</code>
</precond>
<vdef>
<value>LG</value>
</vdef>
<vlist>
<velem>
<value>LG</value>
<label>LG</label>
</velem>
<velem>
<value>WAG</value>
<label>WAG</label>
</velem>
<velem>
<value>JTT</value>
<label>JTT</label>
</velem>
<velem>
<value>MtREV</value>
<label>MtREV</label>
</velem>
<velem>
<value>Dayhoff</value>
<label>Dayhoff</label>
</velem>
<velem>
<value>DCMut</value>
<label>DCMut</label>
</velem>
<velem>
<value>RtREV</value>
<label>RtREV</label>
</velem>
<velem>
<value>CpREV</value>
<label>CpREV</label>
</velem>
<velem>
<value>VT</value>
<label>VT</label>
</velem>
<velem>
<value>Blosum62</value>
<label>Blosum62</label>
</velem>
<velem>
<value>MtMam</value>
<label>MtMam</label>
</velem>
<velem>
<value>MtArt</value>
<label>MtArt</label>
</velem>
<velem>
<value>HIVw</value>
<label>HIVw</label>
</velem>
<velem>
<value>HIVb</value>
<label>HIVb</label>
</velem>
</vlist>
<format>
<code proglang="perl">($value ne $vdef) ? " -m $value" : ""</code>
<code proglang="python">("", " -m "+str(value))[value != vdef]</code>
</format>
</parameter>
<!-- ** FIXME: Character frequencies ** -->
<parameter>
<name>tstvratio1</name>
<prompt lang="en">Estimated transition/transversion ratio for DNA sequences? (-t)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">$seqtype eq "nt"</code>
<code proglang="python">seqtype == "nt"</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -t e" : ""</code>
<code proglang="python">( "" , " -t e")[ value ]</code>
</format>
</parameter>
<parameter>
<name>tstvratio2</name>
<prompt lang="en">User transition/transversion ratio for DNA sequences? (-t)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">$seqtype eq "nt" and not $tstvratio1</code>
<code proglang="python">seqtype == "nt" and not tstvratio1</code>
</precond>
<format>
<code proglang="perl">(defined $value ) ? " -t $value" : ""</code>
<code proglang="python">( "" , " -t "+str(value))[ value is not None ]</code>
</format>
</parameter>
<parameter>
<name>propinvar1</name>
<prompt lang="en">Estimated proportion of invariable sites? (-v)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -v e" : ""</code>
<code proglang="python">( "" , " -v e")[ value ]</code>
</format>
</parameter>
<parameter>
<name>propinvar2</name>
<prompt lang="en">User proportion of invariable sites? (-v)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">not $propinvar1</code>
<code proglang="python">not propinvar1</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? " -v $value" : ""</code>
<code proglang="python">( "" , " -v "+str(value))[value is not None]</code>
</format>
<ctrl>
<message>
<text lang="en">Value must be >= 0 and < 1</text>
</message>
<code proglang="perl">$value >= 0 and $value < 1</code>
<code proglang="python">value >= 0 and value < 1</code>
</ctrl>
</parameter>
<parameter>
<name>nbsubstcat</name>
<prompt lang="en">Number of relative substitution rate categories (-c)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -c $value" : ""</code>
<code proglang="python">("", " -c "+str(value))[value is not None and value != vdef]</code>
</format>
</parameter>
<parameter>
<name>gamma1</name>
<prompt lang="en">Estimated Gamma distribution parameter? (-a)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -a e" : ""</code>
<code proglang="python">("", " -a e")[value]</code>
</format>
</parameter>
<parameter>
<name>gamma2</name>
<prompt lang="en">User gamma distribution parameter? (-a)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">not $gamma1</code>
<code proglang="python">not gamma1</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? " -a $value" : ""</code>
<code proglang="python">("", " -a "+str(value))[value is not None]</code>
</format>
</parameter>
<parameter issimple="1">
<name>frequencies</name>
<prompt lang="en">Equilibrium character frequencies (-f)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<!--<precond>
<code proglang="perl">not ($fA and $fT and $fG and $fC)</code>
<code proglang="python">not (fA and fT and fG and fC)</code>
</precond>
--><vdef>
<value>m</value>
</vdef>
<vlist>
<velem>
<value>m</value>
<label>m: equilibrium frequency estimated by ML for nucleotides or defined by the substitution model for amino acids.
</label>
</velem>
<velem>
<value>e</value>
<label>e: equilibrium frequency estimated by counting the occurence of each character state in the alignment.
</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value) ? " -f $value" : ""</code>
<code proglang="python">("", " -f "+str(value))[value is not None]</code>
</format>
</parameter>
<!--
<paragraph>
<name>user_freq</name>
<prompt lang="en">User bases frequencies (instead of empirical frequencies)</prompt>
<precond>
<code proglang="perl">not $frequencies and seqtype eq 'nt'</code>
<code proglang="python">not frequencies and seqtype == 'nt' </code>
</precond>
<comment>
<text lang="en">"fA fC fG fT" : only valid for nucleotide-based models. fA, fC, fG and fT are floating numbers that
correspond to the frequencies of A, C, G and T respectively.</text>
</comment>
<parameters>
<parameter ismandatory="1">
<name>fA</name>
<prompt lang="en">A frequency</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
</parameter>
<parameter ismandatory="1">
<name>fC</name>
<prompt lang="en">C frequency</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
</parameter>
<parameter ismandatory="1">
<name>fG</name>
<prompt lang="en">G frequency</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
</parameter>
<parameter ismandatory="1">
<name>fT</name>
<prompt lang="en">T frequency</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
</parameter>
<parameter ishidden="1" >
<name>userfrequencies</name>
<prompt lang="en">User bases frequencies (-f)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">$fA and $fT and $fG and $fC</code>
<code proglang="python">fA and fT and fG and fC</code>
</precond>
<format>
<code proglang="perl">($fA and $fC and $fG and $fT) ? "": " -f $fA $fC $fG $fT "</code>
<code proglang="python">( "" ," -f " + str(fA) + " " + str(fC) + " " + str(fG) + " " + str(fT) )[ fA is not None and fC is not None and fG is not None and fT is not None ]</code>
</format>
<argpos>2</argpos>
</parameter>
</parameters>
</paragraph>
-->
<parameter>
<name>usertreefile</name>
<prompt lang="en">Starting tree filename (u)</prompt>
<type>
<datatype>
<class>Tree</class>
</datatype>
<dataFormat>NEWICK</dataFormat>
</type>
<format>
<code proglang="perl">(defined $value) ? " -u $value" : ""</code>
<code proglang="python">("", " -u "+str(value))[value is not None]</code>
</format>
</parameter>
<parameter>
<name>parsimoniousTree</name>
<prompt lang="en">Most parsimonious starting tree (-p)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">(defined $value) ? " -p" : ""</code>
<code proglang="python">("", " -p")[value]</code>
</format>
</parameter>
<parameter>
<name>randomNumber</name>
<prompt lang="en">Number of random starting trees to be used (-n)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -n $value" : ""</code>
<code proglang="python">("", " -n " + str(value))[value is not None]</code>
</format>
<ctrl>
<message>
<text lang="en">Value must be > 0</text>
</message>
<code proglang="perl">$value > 0</code>
<code proglang="python">value > 0 </code>
</ctrl>
</parameter>
<parameter>
<name>tree_swapping</name>
<prompt lang="en">First tree swapping (-s)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>SPR</value>
</vdef>
<vlist>
<velem>
<value>SPR</value>
<label>SPR </label>
</velem>
<velem>
<value>NNI</value>
<label>NNI</label>
</velem>
<velem>
<value>both</value>
<label>both</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " -s $value" : ""</code>
<code proglang="python">("", " -s "+str(value))[value is not None and value !=vdef]</code>
</format>
</parameter>
<parameter>
<name>branch_support</name>
<prompt lang="en">Branch support (-b)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>null</value>
</vdef>
<vlist>
<velem undef="1">
<value>null</value>
<label>SH-like branch support</label>
</velem>
<velem>
<value>-2</value>
<label>-2: khi2-based parametric support</label>
</velem>
<velem>
<value>0</value>
<label>0: none support</label>
</velem>
<velem>
<value>-1</value>
<label>-1: aLRT support</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " -b $value" : ""</code>
<code proglang="python">("", " -b "+str(value))[value is not None and value !=vdef]</code>
</format>
</parameter>
<parameter>
<name>likelihoodCar</name>
<prompt lang="en">Write the likelihood for each character (-l)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">(defined $value) ? " -l" : ""</code>
<code proglang="python">("", " -l")[value]</code>
</format>
</parameter>
<parameter>
<name>firstRun</name>
<prompt lang="en">Write the results outputed by the first run of phyml (-x)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">(defined $value) ? " -x" : ""</code>
<code proglang="python">("", " -x")[value]</code>
</format>
</parameter>
</parameters>
</paragraph>
<parameter isout="1">
<name>outfile</name>
<prompt lang="en">Output file</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<filenames>
<code proglang="perl">"*_morephyml_stats.txt"</code>
<code proglang="python">"*_morephyml_stats.txt"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>outtree</name>
<prompt lang="en">Output tree</prompt>
<type>
<datatype>
<class>Tree</class>
</datatype>
<dataFormat>NEWICK</dataFormat>
</type>
<filenames>
<code proglang="perl">"*_morephyml_tree.txt"</code>
<code proglang="python">"*_morephyml_tree.txt"</code>
</filenames>
</parameter>
</parameters>
</program>
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