/var/lib/mobyle/programs/puzzle.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>puzzle</name>
<version>5.2</version>
<doc>
<title>Tree-Puzzle</title>
<description>
<text lang="en">Maximum likelihood analysis for nucleotide, amino-acid and two state data</text>
</description>
<authors>Heiko A. Schmidt, Korbinian Strimmer and Arndt von Haeseler</authors>
<reference>Strimmer, K., and A. von Haeseler. 1996. Quartet puzzling:A quartet maximum likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13: 964-969.</reference>
<doclink>http://bioweb2.pasteur.fr/docs/puzzle/tree-puzzle.pdf</doclink>
<homepagelink>http://www.tree-puzzle.de/</homepagelink>
<sourcelink>http://www.tree-puzzle.de/</sourcelink>
</doc>
<category>phylogeny:likelihood</category>
<command>puzzle</command>
</head>
<parameters>
<parameter ishidden="1">
<name>stdinput</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">" < puzzle.params"</code>
<code proglang="python">" < puzzle.params"</code>
</format>
<argpos>2</argpos>
</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>puzzle.params</paramfile>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>infile</name>
<prompt lang="en">Alignment File</prompt>
<type>
<datatype>
<class>Alignment</class>
</datatype>
<dataFormat>PHYLIPI</dataFormat>
</type>
<format>
<code proglang="perl">" $infile"</code>
<code proglang="python">" " + str(value)</code>
</format>
<argpos>1</argpos>
</parameter>
<paragraph>
<name>general_options</name>
<prompt lang="en">General options</prompt>
<argpos>1</argpos>
<parameters>
<parameter issimple="1">
<name>analysis_type</name>
<prompt lang="en">Type of analysis? (b)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<flist>
<felem>
<value>1</value>
<label>Tree reconstruction</label>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</felem>
<felem>
<value>2</value>
<label>Likelihood mapping</label>
<code proglang="perl">"b\\n"</code>
<code proglang="python">"b\n"</code>
</felem>
</flist>
<comment>
<text lang="en">Allows to switch between tree reconstruction/analysis by maximum likelihood and likelihood mapping.</text>
</comment>
<paramfile>puzzle.params</paramfile>
</parameter>
<paragraph>
<name>both_options</name>
<prompt lang="en">Both Tree reconstruction and Likelihood mapping options</prompt>
<parameters>
<parameter issimple="1">
<name>parameter_estimates</name>
<prompt lang="en">Parameter estimates? (e)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<flist>
<felem>
<value>1</value>
<label>Approximate (faster)</label>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</felem>
<felem>
<value>2</value>
<label>Exact (slow)</label>
<code proglang="perl">"e\\n"</code>
<code proglang="python">"e\n"</code>
</felem>
</flist>
<comment>
<text lang="en">Determines whether an approximate or the exact likelihood function is used to estimate parameters of the models of sequence evolution. The approximate likelihood function is in most cases sufficient and is faster.</text>
</comment>
<paramfile>puzzle.params</paramfile>
</parameter>
<parameter issimple="1">
<name>parameter_estimation</name>
<prompt lang="en">Parameter estimation uses? (x)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<flist>
<felem>
<value>1</value>
<label>Neighbor-joining tree</label>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</felem>
<felem>
<value>2</value>
<label>Quartet sampling + NJ tree</label>
<code proglang="perl">"x\\n"</code>
<code proglang="python">"x\n"</code>
</felem>
</flist>
<comment>
<text lang="en">Selects the methods used in the estimation of the model parameters. Neighbor-joining tree means that a NJ tree is used to estimate the parameters. Quartet sampling means that a number of random sets of four sequences are selected to estimate parameters. </text>
</comment>
<paramfile>puzzle.params</paramfile>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>likelihood_options</name>
<prompt lang="en">Likelihood mapping options</prompt>
<precond>
<code proglang="perl">$analysis_type eq "2"</code>
<code proglang="python">analysis_type == "2"</code>
</precond>
<parameters>
<parameter>
<name>quartet</name>
<prompt lang="en">Number of quartets? (n)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>10000</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? "n\\n$value\\n" : ""</code>
<code proglang="python">( "" , "n\n" + str(value) + "\n" )[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">If tree reconstruction is selected: number of puzzling steps. Parameter of the quartet puzzling tree search. Generally, the more sequences are used the more puzzling steps are advised. The default value varies depending on the number of sequences (at least 1000).If likelihood mapping is selected: number of qua rtets in a likelihood mapping analysis. Equal to the number of dots in the likelihood mapping diagram. By default 10000 dots/quartets are assumed. To use all possible quartets in clustered likelihood mapping you have to specify a value of n=0.</text>
</comment>
<paramfile>puzzle.params</paramfile>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>reconstruction_options</name>
<prompt lang="en">Tree reconstruction options</prompt>
<precond>
<code proglang="perl">$analysis_type eq "1"</code>
<code proglang="python">analysis_type == "1"</code>
</precond>
<parameters>
<parameter>
<name>tree_search</name>
<prompt lang="en">Tree search procedure? (k)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<flist>
<felem>
<value>1</value>
<label>Quartet puzzling</label>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</felem>
<felem>
<value>2</value>
<label>Evaluate user defined trees</label>
<code proglang="perl">"k\\n"</code>
<code proglang="python">"k\n"</code>
</felem>
<felem>
<value>3</value>
<label>Consensus of user defined trees</label>
<code proglang="perl">"k\\nk\\n"</code>
<code proglang="python">"k\nk\n"</code>
</felem>
<felem>
<value>4</value>
<label>Pairwise distances only (no tree)</label>
<code proglang="perl">"k\\nk\\nk\\n"</code>
<code proglang="python">"k\nk\nk\n"</code>
</felem>
</flist>
<comment>
<text lang="en">Determines how the overall tree is obtained. The topology is either computed with the quartet puzzling algorithm or a set of trees is provided by the user. If there are more than two trees in such a set, maximum likelihood branch lengths will be computed for this tree and a number of tests (KH-test, SH-test, and ELW) will be performed on the trees by default. Instead of the evaluation a consensus can be computed for all the trees for which ML branch lengths and ML value are estimated. Alternatively, a maximum likelihood distance matrix only can also be computed (no overall tree).</text>
</comment>
<paramfile>puzzle.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>tree_file</name>
<prompt lang="en">User Tree file</prompt>
<type>
<datatype>
<class>Tree</class>
</datatype>
<dataFormat>NEWICK</dataFormat>
</type>
<precond>
<code proglang="perl">$tree_search eq "3" or $tree_search eq "2"</code>
<code proglang="python">tree_search == "3" or tree_search == "2"</code>
</precond>
<format>
<code proglang="perl">(defined $value)? "$tree_file\\n" : ""</code>
<code proglang="python">( "" , str(value) +"\n" )[ value is not None ]</code>
</format>
<argpos>2000</argpos>
<paramfile>puzzle.params</paramfile>
</parameter>
<parameter>
<name>clocklike</name>
<prompt lang="en">Compute clocklike branch lengths? (z)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">$tree_search ne "4"</code>
<code proglang="python">tree_search != "4"</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? "z\\n" : ""</code>
<code proglang="python">( "" , "z\n" )[ value ]</code>
</format>
<comment>
<text lang="en">Computation of clock-like maximum likelihood branch lengths. This option also invokes the likelihood ratio clock test.</text>
</comment>
<paramfile>puzzle.params</paramfile>
</parameter>
<parameter>
<name>invalid</name>
<prompt lang="en">Enter an invalid branch number to search for the best location despite of automatic search (l)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">$tree_search ne "4" and $clocklike </code>
<code proglang="python">tree_search != "4" and clocklike </code>
</precond>
<format>
<code proglang="perl">(defined $value)? "l\\n$value\\n" : ""</code>
<code proglang="python">( "" , "l\n" + str(value) + "\n" )[ value is not None]</code>
</format>
<comment>
<text lang="en"> Location of root. Only for computation of clock-like maximum likelihood branch lengths. Allows to specify the branch where the root should be placed in an unrooted tree topology. For example, in the tree (a,b,(c,d)) l = 1 places the root at the branch leading to sequence a whereas l=5 places the root at the internal branch.</text>
</comment>
<paramfile>puzzle.params</paramfile>
</parameter>
<paragraph>
<name>quartet_options</name>
<prompt lang="en">Quartet puzzling options</prompt>
<parameters>
<parameter>
<name>approximate</name>
<prompt lang="en">Approximate quartet likelihood (v)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">($value)? "" : "v\\n"</code>
<code proglang="python">( "v\n" , "" )[ value ]</code>
</format>
<comment>
<text lang="en">For the quartet puzzling tree search only. Only for very small data sets it is necessary to compute an exact maximum likelihood. For larger data sets this option should always be turned on. </text>
</comment>
<paramfile>puzzle.params</paramfile>
</parameter>
<parameter>
<name>unresolved</name>
<prompt lang="en">List unresolved quartets? (u)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? "u\\n" : ""</code>
<code proglang="python">( "" , "u\n" )[ value ]</code>
</format>
<comment>
<text lang="en">Show unresolved quartets. During the quartet puzzling tree search TREE-PUZZLE counts the number of unresolved quartet trees. An unresolved quartet is a quartet where the maximum likelihood values for each of the three possible quartet topologies are so similar that it is not possible to prefer one of them (Strimmer et al., 1997). If this option is selected you will get a detailed list of all star-like quartets. Note, for some data sets there may be a lot of unresolved quartets. In this case a list of all unresolved quartets is probably not very useful and also needs a lot of disk space. </text>
</comment>
<paramfile>puzzle.params</paramfile>
</parameter>
<parameter>
<name>puzzling_step</name>
<prompt lang="en">Number of puzzling steps (n)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>1000</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? "n\\n$value\\n" : ""</code>
<code proglang="python">( "" , "n\n" + str(value) + "\n" )[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">If tree reconstruction is selected: number of puzzling steps. Parameter of the quartet puzzling tree search. Generally, the more sequences are used the more puzzling steps are advised. The default value varies depending on the number of sequences (at least 1000).If likelihood mapping is selected: number of quartets in a likelihood mapping analysis. Equal to the number of dots in the likelihood mapping diagram. By default 10000 dots/quartets are assumed. To use all possible quartets in clustered likelihood mapping you have to specify a value of n=0. </text>
</comment>
<paramfile>puzzle.params</paramfile>
</parameter>
<parameter>
<name>list_puzzling</name>
<prompt lang="en">List puzzling step trees? (j)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<flist>
<felem>
<value>1</value>
<label>No</label>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</felem>
<felem>
<value>2</value>
<label>Unique topologies</label>
<code proglang="perl">"j\\n"</code>
<code proglang="python">"j\n"</code>
</felem>
<felem>
<value>3</value>
<label>Unique topologies & Chronological list</label>
<code proglang="perl">"j\\nj\\n"</code>
<code proglang="python">"j\nj\n"</code>
</felem>
<felem>
<value>4</value>
<label>Chronological list only</label>
<code proglang="perl">"j\\nj\\nj\\n"</code>
<code proglang="python">"j\nj\nj\n"</code>
</felem>
</flist>
<comment>
<text lang="en">Writes all intermediate trees (puzzling step trees) used to compute the quartet puzzling tree into a file, either as a list of topologies ordered by number of occurrences (*.ptorder), or as list about the chronological occurrence of the topologies (*.pstep), or both.</text>
</comment>
<paramfile>puzzle.params</paramfile>
</parameter>
<parameter>
<name>output</name>
<prompt lang="en">Display as outgroup? (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>
<comment>
<text lang="en">For displaying purposes of the unrooted quartet puzzling tree only. The default outgroup is the first sequence of the data set.</text>
</comment>
<paramfile>puzzle.params</paramfile>
</parameter>
</parameters>
</paragraph>
</parameters>
</paragraph>
</parameters>
</paragraph>
<paragraph>
<name>substitution_options</name>
<prompt lang="en">Substitution process options</prompt>
<argpos>1</argpos>
<parameters>
<parameter ismandatory="1">
<name>seqtype</name>
<prompt lang="en">Type of sequence input data? (d)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<flist>
<felem>
<value>1</value>
<label>Nucleotides</label>
<code proglang="perl">"d\\n"</code>
<code proglang="python">"d\n"</code>
</felem>
<felem>
<value>2</value>
<label>Amino acids</label>
<code proglang="perl">"d\\nd\\n"</code>
<code proglang="python">"d\nd\n"</code>
</felem>
</flist>
<argpos>-10</argpos>
<comment>
<text lang="en">Specifies whether nucleotide, amino acid sequences, or twostate data serve as input. The default is automatically set by inspection of the input data. After TREE-PUZZLE has selected an appropriate data type (marked by ?Auto:?) the ?d?-option changes the type in the following order: automatically selected type ! Nucleotides ! Amino acids ! automatically selected type.</text>
</comment>
<paramfile>puzzle.params</paramfile>
</parameter>
<paragraph>
<name>protein_options</name>
<prompt lang="en">Amino acids options</prompt>
<precond>
<code proglang="perl">$seqtype == "2" </code>
<code proglang="python">seqtype == "2" </code>
</precond>
<parameters>
<parameter>
<name>protein_model</name>
<prompt lang="en">Model of substitution for protein (m)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<flist>
<felem>
<value>1</value>
<label>Dayhoff (Dayhoff et al. 1978)</label>
<code proglang="perl">"m\\n"</code>
<code proglang="python">"m\n"</code>
</felem>
<felem>
<value>2</value>
<label>JTT (Jones et al. 1992)</label>
<code proglang="perl">"m\\nm\\n"</code>
<code proglang="python">"m\nm\n"</code>
</felem>
<felem>
<value>3</value>
<label>mtREV24 (Adachi-Hasegawa 1996)</label>
<code proglang="perl">"m\\nm\\nm\\n"</code>
<code proglang="python">"m\nm\nm\n"</code>
</felem>
<felem>
<value>4</value>
<label>BLOSUM 62 (Henikoff-Henikoff 1992)</label>
<code proglang="perl">"m\\nm\\nm\\nm\\n"</code>
<code proglang="python">"m\nm\nm\nm\n"</code>
</felem>
<felem>
<value>5</value>
<label>VT (Mueller-Vingron 2000)</label>
<code proglang="perl">"m\\nm\\nm\\nm\\nm\\n"</code>
<code proglang="python">"m\nm\nm\nm\nm\n"</code>
</felem>
<felem>
<value>6</value>
<label>WAG (Whelan-Goldman 2000)</label>
<code proglang="perl">"m\\nm\\nm\\nm\\nm\\nm\\n"</code>
<code proglang="python">"m\nm\nm\nm\nm\nm\n"</code>
</felem>
</flist>
<comment>
<text lang="en">For amino acid sequence data the Dayhoff et al. (Dayhoff) model, the Jones et al. (JTT) model, the Adachi and Hasegawa (mtREV24) model, the Henikoff and Henikoff (BLOSUM 62), the Muller and Vingron (VT), and theWhelan and Goldman (WAG) substitution model are implemented in TREE-PUZZLE. </text>
<text lang="en">The mtREV24 model describes the evolution of amino acids encoded on mtDNA, and BLOSUM 62 is for distantly related amino acid sequences, as well as the VT model. </text>
</comment>
<paramfile>puzzle.params</paramfile>
</parameter>
<parameter>
<name>prot_freq</name>
<prompt lang="en">Use specified Amino acid frequencies (in %) (f)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? "f\\n" : "" </code>
<code proglang="python">( "" , "f\n" )[ value ]</code>
</format>
<argpos>50</argpos>
<comment>
<text lang="en">The maximum likelihood calculation needs the frequency of each nucleotide (amino acid, doublet) as input. TREE-PUZZLE estimates these values from the sequence input data. This option allows specification of other values.</text>
</comment>
<paramfile>puzzle.params</paramfile>
</parameter>
<paragraph>
<name>specified_prot_freq</name>
<prompt lang="en">Values of specified amino acid frequencies (in %)</prompt>
<precond>
<code proglang="perl">$prot_freq </code>
<code proglang="python">prot_freq </code>
</precond>
<parameters>
<parameter ismandatory="1">
<name>a_freq</name>
<prompt lang="en">pi (A)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">"$value\\n"</code>
<code proglang="python">str(value) + "\n"</code>
</format>
<argpos>51</argpos>
<paramfile>puzzle.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>r_freq</name>
<prompt lang="en">pi (R)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">"$value\\n"</code>
<code proglang="python">str(value) + "\n"</code>
</format>
<argpos>51</argpos>
<paramfile>puzzle.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>n_freq</name>
<prompt lang="en">pi (N)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">"$value\\n"</code>
<code proglang="python">str(value) + "\n"</code>
</format>
<argpos>51</argpos>
<paramfile>puzzle.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>d_freq</name>
<prompt lang="en">pi (D)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">"$value\\n"</code>
<code proglang="python">str(value) + "\n"</code>
</format>
<argpos>51</argpos>
<paramfile>puzzle.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>c_freq</name>
<prompt lang="en">pi (C)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">"$value\\n"</code>
<code proglang="python">str(value) + "\n"</code>
</format>
<argpos>51</argpos>
<paramfile>puzzle.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>q_freq</name>
<prompt lang="en">pi (Q)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">"$value\\n"</code>
<code proglang="python">str(value) + "\n"</code>
</format>
<argpos>51</argpos>
<paramfile>puzzle.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>e_freq</name>
<prompt lang="en">pi (E)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">"$value\\n"</code>
<code proglang="python">str(value) + "\n"</code>
</format>
<argpos>51</argpos>
<paramfile>puzzle.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>g_freq</name>
<prompt lang="en">pi (G)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">"$value\\n"</code>
<code proglang="python">str(value) + "\n"</code>
</format>
<argpos>51</argpos>
<paramfile>puzzle.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>h_freq</name>
<prompt lang="en">pi (H)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">"$value\\n"</code>
<code proglang="python">str(value) + "\n"</code>
</format>
<argpos>51</argpos>
<paramfile>puzzle.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>i_freq</name>
<prompt lang="en">pi (I)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">"$value\\n"</code>
<code proglang="python">str(value) + "\n"</code>
</format>
<argpos>51</argpos>
<paramfile>puzzle.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>l_freq</name>
<prompt lang="en">pi (L)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">"$value\\n"</code>
<code proglang="python">str(value) + "\n"</code>
</format>
<argpos>51</argpos>
<paramfile>puzzle.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>k_freq</name>
<prompt lang="en">pi (K)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">"$value\\n"</code>
<code proglang="python">str(value) + "\n"</code>
</format>
<argpos>51</argpos>
<paramfile>puzzle.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>m_freq</name>
<prompt lang="en">pi (M)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">"$value\\n"</code>
<code proglang="python">str(value) + "\n"</code>
</format>
<argpos>51</argpos>
<paramfile>puzzle.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>f_freq</name>
<prompt lang="en">pi (F)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">"$value\\n"</code>
<code proglang="python">str(value) + "\n"</code>
</format>
<argpos>51</argpos>
<paramfile>puzzle.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>p_freq</name>
<prompt lang="en">pi (P)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">"$value\\n"</code>
<code proglang="python">str(value) + "\n"</code>
</format>
<argpos>51</argpos>
<paramfile>puzzle.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>s_freq</name>
<prompt lang="en">pi (S)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">"$value\\n"</code>
<code proglang="python">str(value) + "\n"</code>
</format>
<argpos>51</argpos>
<paramfile>puzzle.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>t_freq</name>
<prompt lang="en">pi (T)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">"$value\\n"</code>
<code proglang="python">str(value) + "\n"</code>
</format>
<argpos>51</argpos>
<paramfile>puzzle.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>w_freq</name>
<prompt lang="en">pi (W)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">"$value\\n"</code>
<code proglang="python">str(value) + "\n"</code>
</format>
<argpos>51</argpos>
<paramfile>puzzle.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>y_freq</name>
<prompt lang="en">pi (Y)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">"$value\\n"</code>
<code proglang="python">str(value) + "\n"</code>
</format>
<argpos>51</argpos>
<paramfile>puzzle.params</paramfile>
</parameter>
</parameters>
</paragraph>
</parameters>
</paragraph>
<paragraph>
<name>dna_options</name>
<prompt lang="en">DNA options</prompt>
<precond>
<code proglang="perl">$seqtype eq "1"</code>
<code proglang="python">seqtype == "1"</code>
</precond>
<argpos>1</argpos>
<parameters>
<parameter>
<name>dna_model</name>
<prompt lang="en">Model of substitution for DNA (m)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<flist>
<felem>
<value>1</value>
<label>HKY (Hasegawa et al. 1985)</label>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</felem>
<felem>
<value>2</value>
<label>TN (Tamura-Nei 1993)</label>
<code proglang="perl">"m\\n"</code>
<code proglang="python">"m\n"</code>
</felem>
<felem>
<value>3</value>
<label>GTR (e.g. Lanave et al. 1980)</label>
<code proglang="perl">"m\\nm\\n"</code>
<code proglang="python">"m\nm\n"</code>
</felem>
<felem>
<value>4</value>
<label>SH (e.g. Schoeniger-von Haeseler 1994)</label>
<code proglang="perl">"m\\nm\\nm\\n"</code>
<code proglang="python">"m\nm\nm\n"</code>
</felem>
</flist>
<argpos>10</argpos>
<comment>
<text lang="en">The following models are implemented for nucleotides: the general time reversible model (Tavaree, 1986, GTR, e.g.,) model, the Tamura and Nei (TN) model, the Hasegawa et al. (HKY) model, and the Schroniger and von Haeseler (SH) model.</text>
<text lang="en">The SH model describes the evolution of pairs of dependent nucleotides (pairs are the first and the second nucleotide, the third and the fourth nucleotide and so on). It allows for specification of the transition-transversion ratio. </text>
<text lang="en">The original model (Schroniger and von Haeseler, 1994) is obtained by setting the transition-transversion parameter to 0.5. </text>
<text lang="en">The Jukes and Cantor (1969), the Felsenstein (1981), and the Kimura (1980) model are all special cases of the HKY model. </text>
</comment>
<paramfile>puzzle.params</paramfile>
</parameter>
<paragraph>
<name>GTR_options</name>
<prompt lang="en">GTR model rates</prompt>
<precond>
<code proglang="perl">$dna_model eq "4"</code>
<code proglang="python">dna_model == "4"</code>
</precond>
<argpos>11</argpos>
<parameters>
<parameter>
<name>GTR_acrate</name>
<prompt lang="en">A-C rate (1)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>1.00</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? "1\\n$value\\n" : ""</code>
<code proglang="python">( "" , "1\n"+ str(value) + "\n" )[ value is not None and value != vdef]</code>
</format>
<argpos>11</argpos>
<paramfile>puzzle.params</paramfile>
</parameter>
<parameter>
<name>GTR_agrate</name>
<prompt lang="en">A-G rate (2)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>1.00</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? "2\\n$value\\n" : ""</code>
<code proglang="python">( "" , "2\n"+ str(value) + "\n" )[ value is not None and value != vdef]</code>
</format>
<paramfile>puzzle.params</paramfile>
</parameter>
<parameter>
<name>GTR_atrate</name>
<prompt lang="en">A-T rate (3)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>1.00</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? "3\\n$value\\n" : ""</code>
<code proglang="python">( "" , "3\n"+ str(value) + "\n" )[ value is not None and value != vdef]</code>
</format>
<paramfile>puzzle.params</paramfile>
</parameter>
<parameter>
<name>GTR_cgrate</name>
<prompt lang="en">C-G rate (4)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>1.00</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? "4\\n$value\\n" : ""</code>
<code proglang="python">( "" , "4\n"+ str(value) + "\n" )[ value is not None and value != vdef]</code>
</format>
<paramfile>puzzle.params</paramfile>
</parameter>
<parameter>
<name>GTR_ctrate</name>
<prompt lang="en">C-T rate (5)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>1.00</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? "5\\n$value\\n" : ""</code>
<code proglang="python">( "" , "5\n" + str(value) +"\n" )[ value is not None and value != vdef]</code>
</format>
<paramfile>puzzle.params</paramfile>
</parameter>
<parameter>
<name>GTR_gtrate</name>
<prompt lang="en">G-T rate (6)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>1.00</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? "6\\n$value\\n" : ""</code>
<code proglang="python">( "" , "6\n" + str(value) +"\n" )[ value is not None and value != vdef]</code>
</format>
<paramfile>puzzle.params</paramfile>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>SH_options</name>
<prompt lang="en">SH model rates</prompt>
<precond>
<code proglang="perl">$dna_model eq "4"</code>
<code proglang="python">dna_model == "4"</code>
</precond>
<argpos>11</argpos>
<parameters>
<parameter>
<name>symmetrize_frequencies</name>
<prompt lang="en">Symmetrize doublet frequencies (s)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? "s\\n" : ""</code>
<code proglang="python">( "" , "s\n" )[ value ]</code>
</format>
<argpos>11</argpos>
<comment>
<text lang="en">This option is only available for the SH model. With this option the doublet frequencies are symmetrized. For example, the frequencies of ?AT? and ?TA? are then set to the average of both frequencies.</text>
</comment>
<paramfile>puzzle.params</paramfile>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>TN_options</name>
<prompt lang="en">TN model options</prompt>
<precond>
<code proglang="perl">$dna_model eq "2"</code>
<code proglang="python">dna_model == "2"</code>
</precond>
<argpos>11</argpos>
<parameters>
<parameter ismandatory="1">
<name>constrain_TN</name>
<prompt lang="en">Constrain TN model to F84 model (p)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? "p\\n" : ""</code>
<code proglang="python">( "" , "p\n" )[ value ]</code>
</format>
<argpos>11</argpos>
<comment>
<text lang="en">This option is only available for the Tamura-Nei model. With this option the expected (!) transition-transversion ratio for the F84 model have to be entered and TREE-PUZZLE computes the corresponding parameters of the TN model (this depends on base frequencies of the data). This allows to compare the results of TREE-PUZZLE and the PHYLIP maximum likelihood programs which use the F84 model.</text>
</comment>
<paramfile>puzzle.params</paramfile>
</parameter>
<parameter>
<name>f84_ratio</name>
<prompt lang="en">Expected F84 Transition/transversion ratio</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">$constrain_TN </code>
<code proglang="python">constrain_TN </code>
</precond>
<format>
<code proglang="perl">(defined $value)? "$value\\n" : ""</code>
<code proglang="python">( "" , str(value) + "\n" )[ value is not None]</code>
</format>
<argpos>12</argpos>
<paramfile>puzzle.params</paramfile>
</parameter>
<parameter>
<name>y_r</name>
<prompt lang="en">Y/R transition parameter (r)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value)? "r\\n$value\\n" : ""</code>
<code proglang="python">( "" , "r\n" + str(value) +"\n" )[ value is not None ]</code>
</format>
<argpos>13</argpos>
<comment>
<text lang="en">This option is only available for the TN model. This parameter is the ratio of the rates for pyrimidine transitions and purine transitions. You do not need to specify this parameter as TREE-PUZZLE estimates it from the data. For precise definition please read the section in this manual about models of sequence evolution.</text>
</comment>
<paramfile>puzzle.params</paramfile>
</parameter>
</parameters>
</paragraph>
<parameter>
<name>ratio</name>
<prompt lang="en">Transition/transversion ratio (t)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">$dna_model ne "3"</code>
<code proglang="python">dna_model != "3"</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? "t\\n$value\\n" : ""</code>
<code proglang="python">( "" , "t\n" + str(value) + "\n" )[ value is not None ]</code>
</format>
<comment>
<text lang="en">For nucleotide data only. You do not need to specify this parameter as TREE-PUZZLE estimates it from the data. The precise definition of this parameter is given in the section on models of sequence evolution in this manual.</text>
</comment>
<paramfile>puzzle.params</paramfile>
</parameter>
<paragraph>
<name>nuc_freq</name>
<prompt lang="en">Base frequencies (in %) (f)</prompt>
<parameters>
<parameter>
<name>use_specified_nuc</name>
<prompt lang="en">Use specified values?</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? "f\\n" : "" </code>
<code proglang="python">( "" , "f\n" )[ value ]</code>
</format>
<argpos>50</argpos>
<comment>
<text lang="en">The maximum likelihood calculation needs the frequency of each nucleotide (amino acid, doublet) as input. TREE-PUZZLE estimates these values from the sequence input data. This option allows specification of other values.</text>
</comment>
<paramfile>puzzle.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>a_nuc_freq</name>
<prompt lang="en">pi (A)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">$use_specified_nuc </code>
<code proglang="python">use_specified_nuc </code>
</precond>
<format>
<code proglang="perl">"$value\\n"</code>
<code proglang="python">str(value) + "\n"</code>
</format>
<argpos>51</argpos>
<paramfile>puzzle.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>c_nuc_freq</name>
<prompt lang="en">pi (C)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">$use_specified_nuc </code>
<code proglang="python">use_specified_nuc </code>
</precond>
<format>
<code proglang="perl">"$value\\n"</code>
<code proglang="python">str(value) + "\n"</code>
</format>
<argpos>52</argpos>
<paramfile>puzzle.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>g_nuc_freq</name>
<prompt lang="en">pi (G)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">$use_specified_nuc </code>
<code proglang="python">use_specified_nuc </code>
</precond>
<format>
<code proglang="perl">"$value\\n"</code>
<code proglang="python">str(value) + "\n"</code>
</format>
<argpos>53</argpos>
<paramfile>puzzle.params</paramfile>
</parameter>
</parameters>
</paragraph>
</parameters>
</paragraph>
</parameters>
</paragraph>
<paragraph>
<name>rate_options</name>
<prompt lang="en">Rate heterogeneity options</prompt>
<argpos>1</argpos>
<parameters>
<parameter>
<name>rate_heterogeneity</name>
<prompt lang="en">Model of rate heterogeneity (w)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<flist>
<felem>
<value>1</value>
<label>Uniform rate</label>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</felem>
<felem>
<value>2</value>
<label>Gamma distributed rates</label>
<code proglang="perl">"w\\n"</code>
<code proglang="python">"w\n"</code>
</felem>
<felem>
<value>3</value>
<label>Two rates (1 invariable + 1 variable)</label>
<code proglang="perl">"w\\nw\\n"</code>
<code proglang="python">"w\nw\n"</code>
</felem>
<felem>
<value>4</value>
<label>Mixed (1 invariable + n Gamma rates)</label>
<code proglang="perl">"w\\nw\\nw\\n"</code>
<code proglang="python">"w\nw\nw\n"</code>
</felem>
</flist>
<argpos>20</argpos>
<comment>
<text lang="en">TREE-PUZZLE provides several different models of rate heterogeneity: uniform rate over all sites (rate homogeneity), Gamma distributed rates, two rates (1 invariable + 1 variable), and a mixed model (1 invariable rate + Gamma distributed rates). All necessary parameters can be estimated by TREE-PUZZLE. Note that whenever invariable sites are taken into account the parameter estimation will invoke the ?e? option to use an exact likelihood function. For more detailed information please read the section in this manual about models of sequence evolution. See also option ?m? (model of substitution). </text>
</comment>
<paramfile>puzzle.params</paramfile>
</parameter>
<parameter>
<name>alpha</name>
<prompt lang="en">Gamma rate heterogeneity parameter alpha (a)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">$rate_heterogeneity eq "2" or $rate_heterogeneity eq "4" </code>
<code proglang="python">rate_heterogeneity == "2" or rate_heterogeneity == "4" </code>
</precond>
<format>
<code proglang="perl">(defined $value)? "a\\n$value\\n" : ""</code>
<code proglang="python">( "" , "a\n" + str(value) +"\n" )[ value is not None ]</code>
</format>
<argpos>21</argpos>
<comment>
<text lang="en">This is the so-called shape parameter of the Gamma distribution.</text>
</comment>
<paramfile>puzzle.params</paramfile>
</parameter>
<parameter>
<name>gamma_number</name>
<prompt lang="en">Number of Gamma rate categories (c)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">$rate_heterogeneity eq "2" or $rate_heterogeneity eq "4" </code>
<code proglang="python">rate_heterogeneity == "2" or rate_heterogeneity == "4" </code>
</precond>
<vdef>
<value>8</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? "c\\n$value\\n" : ""</code>
<code proglang="python">( "" , "c\n" + str(value) +"\n" )[ value is not None and value != vdef]</code>
</format>
<argpos>21</argpos>
<comment>
<text lang="en">Number of rate categories (4-16) for the discrete Gamma distribution (rate heterogeneity).</text>
</comment>
<paramfile>puzzle.params</paramfile>
</parameter>
<parameter>
<name>invariable</name>
<prompt lang="en">Fraction of invariable sites (i)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">$rate_heterogeneity eq "3" or $rate_heterogeneity eq "4" </code>
<code proglang="python">rate_heterogeneity == "3" or rate_heterogeneity == "4" </code>
</precond>
<format>
<code proglang="perl">(defined $value)? "i\\n$value\\n" : ""</code>
<code proglang="python">( "" , "i\n" + str(value) +"\n" )[ value is not None ]</code>
</format>
<argpos>21</argpos>
<comment>
<text lang="en">Probability of a site to be invariable. This parameter can be estimated from the data by TREE-PUZZLE (only if the approximation option for the likelihood function is turned off). </text>
</comment>
<paramfile>puzzle.params</paramfile>
</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">"$infile.puzzle"</code>
<code proglang="python">str(infile) + ".puzzle"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>outtree</name>
<prompt lang="en">Output tree</prompt>
<type>
<datatype>
<class>Tree</class>
</datatype>
<dataFormat>NEWICK</dataFormat>
</type>
<filenames>
<code proglang="perl">"$infile.tree"</code>
<code proglang="python">str(infile) + ".tree"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>outdist</name>
<prompt lang="en">Output distance</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<filenames>
<code proglang="perl">"$infile.dist"</code>
<code proglang="python">str(infile) + ".dist"</code>
</filenames>
</parameter>
</parameters>
</program>
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