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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>phyml</name>
<version>20130219.patch</version>
<doc>
<title>PHYML</title>
<description>
<text lang="en">A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood</text>
</description>
<authors>S. Guindon and O. Gascuel</authors>
<reference>Guindon, S. and Gascuel, O. (2003) A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood Systematic Biology, 52(5), 696-704</reference>
<doclink>http://bioweb2.pasteur.fr/docs/phyml/phyml-manual-20122408.pdf</doclink>
<homepagelink>http://code.google.com/p/phyml</homepagelink>
<sourcelink>http://code.google.com/p/phyml</sourcelink>
</doc>
<category>phylogeny:likelihood</category>
<command>phyml</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>inputopt</name>
<prompt lang="en">Input Options</prompt>
<parameters>
<parameter>
<name>datasets</name>
<prompt lang="en">Number of data sets to analyse (-n)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -n $value" : ""</code>
<code proglang="python">("", " -n "+str(value))[value is not None and value != vdef]</code>
</format>
</parameter>
<parameter issimple="1">
<name>bootstrap_sets</name>
<prompt lang="en">Number of bootstraps sets to generate (only works with one data set to analyse) (-b)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">$datasets == 1</code>
<code proglang="python">datasets == 1</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? " -b $value" : ""</code>
<code proglang="python">( "" , " -b " + str(value) )[ value is not None]</code>
</format>
<ctrl>
<message>
<text lang="en">must be an integer >= -5</text>
</message>
<code proglang="python">value >= -5</code>
</ctrl>
<comment>
<div xmlns="http://www.w3.org/1999/xhtml">
<ul>
<li>b > 0: int is the number of bootstrap replicates.</li>
<li>b = 0: neither approximate likelihood ratio test nor bootstrap values are computed.</li>
<li>b = -1: approximate likelihood ratio test returning aLRT statistics.</li>
<li>b = -2: approximate likelihood ratio test returning Chi2-based parametric branch supports.</li>
<li>b = -4: (default) SH-like branch supports alone.</li>
<li>b = -5: approximate Bayes branch supports.</li>
</ul>
</div>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>control_opt</name>
<prompt lang="en">Control Options</prompt>
<parameters>
<parameter>
<name>ntmodel</name>
<prompt lang="en">Nucleotide substitution model (-m)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<precond>
<code proglang="perl">$seqtype eq "nt"</code>
<code proglang="python">seqtype == "nt"</code>
</precond>
<vdef>
<value>HKY85</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>
</vlist>
<format>
<code proglang="perl">($value ne $vdef) ? " -m $value" : ""</code>
<code proglang="python">("", " -m "+str(value))[value != vdef]</code>
</format>
</parameter>
<parameter>
<name>aamodel</name>
<prompt lang="en">Amino-acid substitution model (-m)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<precond>
<code proglang="perl">$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>
<paragraph>
<name>character_frequencies</name>
<prompt>character frequencies</prompt>
<parameters>
<parameter>
<name>predef_char_freq</name>
<prompt lang="en">predefined character frequencies</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>null</value>
</vdef>
<vlist>
<velem undef="1">
<value>null</value>
<label>Choose a character frequencies</label>
</velem>
<velem>
<value>e</value>
<label>e</label>
</velem>
<velem>
<value>m</value>
<label>m</label>
</velem>
</vlist>
<format>
<code proglang="python">("" , " -f " + str(value))[value is not None and value != vdef]</code>
</format>
<comment>
<div xmlns="http://www.w3.org/1999/xhtml">
<ul>
<li>e:<ul>
<li><span style="font-weight:bold">Nucleotide sequences</span>: (Empirical) the equilibrium base frequencies
are estimated by counting the occurence of the different bases in the alignment (default).</li>
<li><span style="font-weight:bold">Amino-acid sequences</span>: (Empirical) the equilibrium amino-acid frequencies are estimated by counting
the occurence of the different amino-acids in the alignment.</li>
</ul>
</li>
<li>m:<ul>
<li><span style="font-weight:bold">Nucleotide sequences</span>: (ML) the equilibrium base frequencies are estimated using maximum likelihood.</li>
<li><span style="font-weight:bold">Amino-acid sequences</span>: (Model) the equilibrium amino-acid frequencies are estimated using
the frequencies defined by the substitution model (default).</li>
</ul>
</li>
</ul>
</div>
</comment>
</parameter>
<parameter>
<name>user_character_frequencies</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<precond>
<code proglang="python">predef_char_freq is None and seqtype == "nt" and (a_freq is not None and c_freq is not None and g_freq is not None and t_freq is not None)</code>
</precond>
<format>
<code proglang="python">("", " -f %f,%f,%f,%f" % (a_freq, c_freq, g_freq, t_freq) )[a_freq is not None or c_freq is not None]</code>
</format>
<interface type="form">
<div xmlns="http://www.w3.org/1999/xhtml">
<label class="parameter" data-issimple="false">User character frequencies</label>
<a class="blindLink commentToggle" title="click to expand/collapse contextual help"
onclick="if (typeof portal=='undefined'){var target=document.getElementById(this.getAttribute('href').substr(1));
target.style.display=(target.style.display=='none') ? '':'none';}" href="#phyml_fake_comment::comment">?</a>
<div id="phyml_fake_comment::comment" class="commentText closed" mode="ajaxTarget" style="overflow: visible; display: none; visibility: hidden;">
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.</div>
</div>
</interface>
</parameter>
<!-- if a value is None the ctrl is not evaluated so I can't display error above the unset frequencies -->
<parameter>
<name>a_freq</name>
<prompt lang="en">A frequencies</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<ctrl>
<message>
<text lang="en">frequencies for a, c, g ,t must be set</text>
</message>
<code proglang="python">a_freq is not None and c_freq is not None and g_freq is not None and t_freq is not None</code>
</ctrl>
</parameter>
<parameter>
<name>c_freq</name>
<prompt lang="en">C frequencies</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<ctrl>
<message>
<text lang="en">frequencies for a, c, g ,t must be set</text>
</message>
<code proglang="python">a_freq is not None and c_freq is not None and g_freq is not None and t_freq is not None</code>
</ctrl>
</parameter>
<parameter>
<name>g_freq</name>
<prompt lang="en">G frequencies</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<ctrl>
<message>
<text lang="en">frequencies for a, c, g ,t must be set</text>
</message>
<code proglang="python">a_freq is not None and c_freq is not None and g_freq is not None and t_freq is not None</code>
</ctrl>
</parameter>
<parameter>
<name>t_freq</name>
<prompt lang="en">T frequencies</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<ctrl>
<message>
<text lang="en">frequencies for a, c, g ,t must be set</text>
</message>
<code proglang="python">a_freq is not None and c_freq is not None and g_freq is not None and t_freq is not None</code>
</ctrl>
</parameter>
</parameters>
<layout>
<vbox>
<box>predef_char_freq</box>
<box>user_character_frequencies</box>
<layout>
<hbox>
<box>a_freq</box>
<box>c_freq</box>
<box>g_freq</box>
<box>t_freq</box>
</hbox>
</layout>
</vbox>
</layout>
</paragraph>
<parameter>
<name>tstvratio1</name>
<prompt lang="en">set transition/transversion ratio to get the maximum likelihood estimate (DNA sequences only)</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">set proportion of invariable sites to get the maximum likelihood estimate. (-v)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<!--
option plante avec -b sur raclette. A fixer avec l'auteur.
<precond>
<code proglang="perl">not $bootstrap_sets</code>
<code proglang="python">bootstrap_sets is None</code>
</precond>
-->
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($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>
<!--
option plante avec -b sur raclette. A fixer avec l'auteur.
<precond>
<code proglang="perl">not $bootstrap_sets and not $propinvar1</code>
<code proglang="python">bootstrap_sets is None and propinvar1</code>
</precond>
-->
<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>
<comment>
<text lang="en">
This option will not be took in account if
"set proportion of invariable sites to get the maximum likelihood estimate"
is switch on.
</text>
</comment>
</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 $value" : ""</code>
<code proglang="python">("", " -c "+str(value))[value is not None and value != vdef]</code>
</format>
</parameter>
<parameter>
<name>gamma1</name>
<prompt lang="en">set distribution of the gamma distribution shape parameter to get the maximum likelihood estimate</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -a e" : ""</code>
<code proglang="python">("", " -a e")[value]</code>
</format>
</parameter>
<parameter>
<name>gamma2</name>
<prompt lang="en">distribution of the gamma distribution shape 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 $value" : ""</code>
<code proglang="python">("", " -a "+str(value))[value is not None]</code>
</format>
<ctrl>
<message>
<text lang="en">Must be a positive value</text>
</message>
<code proglang="python">value > 0</code>
</ctrl>
<comment>
<text lang="en">Can be a fixed positive value.</text>
<text lang="en">This option will not be took into account if
"set distribution of the gamma distribution shape parameter to get the maximum likelihood estimate"
is switch on.
</text>
</comment>
</parameter>
<parameter>
<name>move</name>
<prompt lang="en">Tree topology search operation (-s)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>NNI</value>
</vdef>
<vlist>
<velem>
<value>NNI</value>
<label>NNI</label>
</velem>
<velem>
<value>SPR</value>
<label>SPR (a bit slower than NNI)</label>
</velem>
<velem>
<value>BEST</value>
<label>BEST (best of NNI and SPR search)</label>
</velem>
</vlist>
<format>
<code proglang="perl">($value ne $vdef) ? " -s $value" : ""</code>
<code proglang="python">("", " -s "+str(value))[value != vdef]</code>
</format>
<comment>
<text lang="en">
PhyML proposes three different methods to estimate tree topologies. The default
approach is to use simultaneous NNI. This option corresponds to the original PhyML
algorithm. The second approach relies on subtree pruning and regrafting (SPR).
It generally finds better tree topologies compared to NNI but is also significantly
slower. The third approach, termed BEST, simply estimates the phylogeny using
both methods and returns the best solution among the two.
</text>
</comment>
</parameter>
<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>
<comment>
<text lang="en">The tree must be in Newick format.</text>
</comment>
</parameter>
<parameter>
<name>optimisation</name>
<prompt lang="en">parameter optimisation</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>tlr</value>
</vdef>
<vlist>
<velem>
<value>tlr</value>
<label>tree topology (t), branch length (l) and rate parameters (r) are optimised.</label>
</velem>
<velem>
<value>tl</value>
<label>tree topology and branch length are optimised.</label>
</velem>
<velem>
<value>lr</value>
<label>branch length and rate parameters are optimised.</label>
</velem>
<velem>
<value>l</value>
<label>branch length are optimised.</label>
</velem>
<velem>
<value>r</value>
<label>rate parameters are optimised.</label>
</velem>
<velem>
<value>n</value>
<label>no parameter is optimised.</label>
</velem>
</vlist>
<format>
<code proglang="python">("", " -o " + str(value))[value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">This option focuses on specific parameter optimisation.</text>
</comment>
</parameter>
<parameter>
<name>rand_start</name>
<prompt lang="en">sets the initial tree to random.</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="python">move in ('SPR', 'BEST')</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " --rand_start ")[bool(value)]</code>
</format>
<comment>
<text lang="en">It is only valid if SPR searches are to be performed.</text>
</comment>
</parameter>
<parameter>
<name>n_rand_starts</name>
<prompt>the number of initial random trees to be used.</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="python">move in ('SPR', 'BEST')</code>
</precond>
<format>
<code proglang="python">("", " --n_rand_starts " + str(value))[value is not None]</code>
</format>
<comment>
<text lang="en">It is only valid if SPR searches are to be performed.</text>
</comment>
</parameter>
<parameter>
<name>r_seed</name>
<prompt>the seed used to initiate the random number generator (must be an integer)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="python">( "", " --r_seed " + str(value))[value is not None]</code>
</format>
</parameter>
<parameter>
<name>print_site_lnl</name>
<prompt>Print the likelihood for each site in file.</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">(""," --print_site_lnl ")[bool(value)]</code>
</format>
</parameter>
<parameter>
<name>print_trace</name>
<prompt>Print each phylogeny explored during the tree search process in file.</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">(""," --print_trace ")[bool(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">"*_phyml_stats.txt"</code>
<code proglang="python">"*_phyml_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">"*_phyml_tree.txt"</code>
<code proglang="python">"*_phyml_tree.txt"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>boot_outfile</name>
<prompt lang="en">Bootstrap output file</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<filenames>
<code proglang="perl">"*_phyml_boot_stats.txt"</code>
<code proglang="python">"*_phyml_boot_stats.txt"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>boot_outtree</name>
<prompt lang="en">Bootstrap output trees</prompt>
<type>
<datatype>
<class>Tree</class>
</datatype>
<dataFormat>NEWICK</dataFormat>
</type>
<filenames>
<code proglang="perl">"*_phyml_boot_trees.txt"</code>
<code proglang="python">"*_phyml_boot_trees.txt"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>site_lnl_output</name>
<prompt lang="en">The likelihood for each site.</prompt>
<precond>
<code proglang="perl">$print_site_lnl</code>
<code proglang="python">bool(print_site_lnl)</code>
</precond>
<type>
<datatype>
<class>Report</class>
</datatype>
</type>
<filenames>
<code proglang="perl">"*_phyml_lk.txt"</code>
<code proglang="python">"*_phyml_lk.txt"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>trace_output</name>
<prompt lang="en">trace of each phylogeny explored during the tree search process.</prompt>
<precond>
<code proglang="perl">$print_trace</code>
<code proglang="python">bool(print_trace)</code>
</precond>
<type>
<datatype>
<class>Report</class>
</datatype>
</type>
<filenames>
<code proglang="perl">"*_phyml_trace.txt"</code>
<code proglang="python">"*_phyml_trace.txt"</code>
</filenames>
</parameter>
</parameters>
</program>
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