/var/lib/mobyle/programs/seq-gen.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>seq-gen</name>
<version>1.3.2</version>
<doc>
<title>SeqGen</title>
<description>
<text lang="en">Sequence-Generator</text>
</description>
<authors>A. Rambaut, N. C. Grassly</authors>
<reference>Rambaut, A. and Grassly, N. C. (1996) Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci.</reference>
<doclink>http://bioweb2.pasteur.fr/docs/seq-gen/index.html</doclink>
<comment>
<text lang="en">Seq-Gen is a program that will simulate the evolution of nucleotide or amino acid sequences along a phylogeny, using common models of the substitution process.</text>
</comment>
<homepagelink>http://tree.bio.ed.ac.uk/software/seqgen/</homepagelink>
<sourcelink>http://tree.bio.ed.ac.uk/download.html?name=seqgen&version=v1.3.2&id=41&num=1</sourcelink>
</doc>
<category>phylogeny:likelihood</category>
</head>
<parameters>
<parameter iscommand="1" ishidden="1">
<name>seqgen</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">"seq-gen"</code>
<code proglang="python">"seq-gen"</code>
</format>
<argpos>0</argpos>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>intree</name>
<prompt lang="en">Input tree file</prompt>
<type>
<datatype>
<class>Tree</class>
</datatype>
<dataFormat>NEWICK</dataFormat>
<dataFormat>NEXUS</dataFormat>
</type>
<format>
<code proglang="perl">"< $value"</code>
<code proglang="python">"< " + str(value)</code>
</format>
<argpos>0</argpos>
</parameter>
<paragraph>
<name>input</name>
<prompt lang="en">Input parameters</prompt>
<argpos>1</argpos>
<parameters>
<parameter>
<name>Length</name>
<prompt lang="en">Sequence length (-l)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>1000</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -l $value":""</code>
<code proglang="python">("" , " -l " + str(value))[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">This option allows the user to set the length in nucleotides that each simulated sequence should be.</text>
</comment>
</parameter>
<parameter>
<name>datasets</name>
<prompt lang="en">Number of simulated datasets per tree (-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>
<comment>
<text lang="en">This option specifies how many separate datasets should be simulated for each tree in the tree file.</text>
</comment>
</parameter>
<parameter>
<name>partition_numb</name>
<prompt lang="en">Number of partitions for each dataset (-p)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -p $value":""</code>
<code proglang="python">("" , " -p " + str(value))[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">Number of partion specifies how many partitions of each data set should be simulated. each partition must have its own tree and number specifying how many sites are in partition. Multiple sets of trees are being inputed with varying numbers of partitions, then this should specify the maximum number of partitions that will be required</text>
</comment>
</parameter>
<parameter>
<name>scale_branch</name>
<prompt lang="en">Scale branch lengths (number greater > 0) (-s)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">not defined $scale_tree</code>
<code proglang="python">scale_tree is None</code>
</precond>
<vdef>
<value>1.0</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -s $value":""</code>
<code proglang="python">("" , " -s " + str(value))[ value is not None and value != vdef]</code>
</format>
<ctrl>
<message>
<text lang="en">Value greater than 0 is required</text>
</message>
<code proglang="perl">$value > 0</code>
<code proglang="python">value > 0</code>
</ctrl>
<comment>
<text lang="en">This option allows the user to set a value with which to scale the branch lengths in order to make them equal the expected number of substitutions per site for each branch. Basically Seq-Gen multiplies each branch length by this value.</text>
<text lang="en">For example if you give an value of 0.5 then each branch length would be halved before using it to simulate the sequences.</text>
</comment>
</parameter>
<parameter>
<name>scale_tree</name>
<prompt lang="en">Total tree scale (a decimal number greater > 0) (-d)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">$scale_branch != 1.0</code>
<code proglang="python">scale_branch != 1.0 </code>
</precond>
<format>
<code proglang="perl">(defined $value)? " -d $value":""</code>
<code proglang="python">("" , " -d " + str(value))[ value is not None ]</code>
</format>
<ctrl>
<message>
<text lang="en">Value greater than 0 is required</text>
</message>
<code proglang="perl">$value > 0</code>
<code proglang="python">value > 0</code>
</ctrl>
<comment>
<text lang="en">This option allows the user to set a value which is the desired length of each tree in units of substitutions per site. The term 'tree length' here is the distance from the root to any one of the tips in units of mean number of substitutions per site. This option can only be used when the input trees are rooted and ultrametric (no difference in rate amongst the lineages). This has the effect of making all the trees in the input file of the same length before simulating data.</text>
<text lang="en"> The option multiplies each branch length by a value equal to SCALE divided by the actual length of the tree.</text>
</comment>
</parameter>
<parameter>
<name>input_seq</name>
<prompt lang="en">Ancestral Sequence number (-k)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value)? " -k $value":""</code>
<code proglang="python">("" , " -k " + str(value))[ value is not None ]</code>
</format>
<comment>
<text lang="en">This option allows the user to use a supplied sequence as the ancestral sequence at the root (otherwise a random sequence is used). The value is an integer number greater than zero which refers to one of the sequences supplied as input with the tree.</text>
<text lang="en">Method: The user can supply a sequence alignment as input, as well as the trees. This should be in relaxed PHYLIP format. The trees can then be placed in this file at the end, after a line stating how many trees there are. The file may look like this: </text>
<text lang="en">4 50</text>
<text lang="en">Taxon1 ATCTTTGTAGTCATCGCCGTATTAGCATTCTTAGATCTAA</text>
<text lang="en">Taxon2 ATCCTAGTAGTCGCTTGCGCACTAGCCTTCCGAAATCTAG</text>
<text lang="en">Taxon3 ACTTCTGTGTTTACTGAGCTACTAGCTTCCCTAAATCTAG</text>
<text lang="en">Taxon4 ATTCCTATATTCGCTAATTTCTTAGCTTTCCTGAATCTGG</text>
<text lang="en">1</text>
<text lang="en">(((Taxon1:0.2,Taxon2:0.2):0.1,Taxon3:0.3):0.1,Taxon4:0.4);</text>
<text lang="en">Note that the labels in the alignment do not have to match those in the tree (the ones in the tree will be used for output) there doesn't even have to be the same number of taxa in the alignment as in the trees. The sequence length supplied by the alignment will be used to obtain the simulated sequence length (unless the l option is set). The k option also refers to one of the sequences to specify the ancestral sequence. (see Appendix A)</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>substitution</name>
<prompt lang="en">Substitution model options</prompt>
<argpos>1</argpos>
<parameters>
<parameter>
<name>model</name>
<prompt lang="en">Model of substitution (-m)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>JTT</value>
</vdef>
<vlist>
<velem>
<value>JTT</value>
<label>JTT</label>
</velem>
<velem>
<value>WAG</value>
<label>WAG</label>
</velem>
<velem>
<value>PAM</value>
<label>PAM</label>
</velem>
<velem>
<value>BLOSUM</value>
<label>BLOSUM</label>
</velem>
<velem>
<value>MTREV</value>
<label>MTREV</label>
</velem>
<velem>
<value>GENERAL</value>
<label>GENERAL</label>
</velem>
<velem>
<value>F84</value>
<label>F84 (nucleic)</label>
</velem>
<velem>
<value>HKY</value>
<label>HKY (nucleic)</label>
</velem>
<velem>
<value>GTR</value>
<label>GTR (nucleic)</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value )? " -m $value" : "" </code>
<code proglang="python">( "" , " -m " + str(value) )[ value is not None ]</code>
</format>
</parameter>
<parameter>
<name>shape</name>
<prompt lang="en">Shape of the gamma distribution to use with gamma rate heterogeneity (-a)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value)? " -a $value":""</code>
<code proglang="python">("" , " -a " + str(value))[ value is not None ]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">Using this option the user may specify a shape for the gamma rate heterogeneity. The default is no site-specific rate heterogeneity. Enter a decimal number.</text>
</comment>
</parameter>
<parameter>
<name>categories</name>
<prompt lang="en">Number of categories for the discrete gamma rate heterogeneity model (-g)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value)? " -g $value":""</code>
<code proglang="python">("" , " -g " + str(value))[ value is not None ]</code>
</format>
<ctrl>
<message>
<text lang="en">Enter an integer number between 2 and 32</text>
</message>
<code proglang="perl">$value >= 2 and $value <= 32</code>
<code proglang="python">value >= 2 and value <= 32 </code>
</ctrl>
<argpos>1</argpos>
<comment>
<text lang="en">Using this option the user may specify the number of categories for the discrete gamma rate heterogeneity model. The default is no site-specific rate heterogeneity (or the continuous model if only the -a option is specified. Enter an integer number between 2 and 32</text>
</comment>
</parameter>
<parameter>
<name>invar_site</name>
<prompt lang="en">Proportion of sites that should be invariable (-i)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>0.0</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -i $value":""</code>
<code proglang="python">("" , " -i " + str(value))[ value is not None and value != vdef]</code>
</format>
<ctrl>
<message>
<text lang="en">Enter a real number between 0.0 and 1.0 </text>
</message>
<code proglang="perl">$value >= 0.0 and $value <= 1.0</code>
<code proglang="python">value >= 0.0 and value <= 1.0</code>
</ctrl>
<argpos>1</argpos>
<comment>
<text lang="en">Specify the proportion of sites that should be invariable. These sites will be chosen randomly with this expected frequency. The default is no invariable sites. Invariable sites are sites thar cannot change as opposed to sites which don't exhibit any changes due to chance (and perhaps a low rate). Enter a real number between 0.0 and 1.0</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>nucleotide_opt</name>
<prompt lang="en">Nucleotid model specific options</prompt>
<argpos>1</argpos>
<parameters>
<paragraph>
<name>rate</name>
<prompt lang="en">Rates for codon position heterogeneity (-c)</prompt>
<comment>
<text lang="en">Using this option the user may specify the relative rates for each codon position. This allows codon-specific rate heterogeneity to be simulated. The default is no site-specific rate heterogeneity.</text>
<text lang="en">You can only have codon rates when using nucleotide models of substitution.</text>
</comment>
<parameters>
<parameter>
<name>rate1</name>
<prompt lang="en">First position</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</format>
<comment>
<text lang="en">Enter a decimal number</text>
<text lang="en">You can only have codon rates when using nucleotide models of substitution.</text>
</comment>
</parameter>
<parameter>
<name>rate2</name>
<prompt lang="en">Second position </prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</format>
<comment>
<text lang="en">Enter a decimal number</text>
</comment>
</parameter>
<parameter>
<name>rate3</name>
<prompt lang="en">Third position (enter a decimal number)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</format>
<comment>
<text lang="en">Enter a decimal number</text>
</comment>
</parameter>
<parameter ishidden="1">
<name>rateAll</name>
<prompt lang="en">Rates</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">defined $rate1 and defined $rate2 and defined $rate3</code>
<code proglang="python">rate1 is not None and rate2 is not None and rate3 is not None</code>
</precond>
<format>
<code proglang="perl">" -c $rate1 $rate2 $rate3"</code>
<code proglang="python">" -c %f %f %f " %(rate1,rate2,rate3)</code>
</format>
</parameter>
</parameters>
</paragraph>
<parameter>
<name>transratio</name>
<prompt lang="en">Transition transversion ratio (TS/TV) for HKY or F84 model (-t)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">$model eq 'HKY' or $model eq 'F84'</code>
<code proglang="python">model =='HKY' or model == 'F84'</code>
</precond>
<format>
<code proglang="perl">(defined $value)? " -t $value":""</code>
<code proglang="python">("" , " -t " + str(value))[ value is not None ]</code>
</format>
<comment>
<text lang="en">This option allows the user to set a value for the transition transversion ratio (TS/TV). This is only valid when either the HKY or F84 model has been selected.</text>
</comment>
</parameter>
<parameter>
<name>matrix</name>
<prompt lang="en">6 values for the general reversable model's rate matrix (ACTG x ACTG) separated by one space (-r)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<vdef>
<value>1.0,1.0,1.0,1.0,1.0,1.0</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value ne $vdef)? " -r $value":""</code>
<code proglang="python">("" , " -r " + str(value))[ value is not None and value != vdef]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">This option allows the user to set 6 values for the general reversable model's rate matrix. This is only valid when either the REV model has been selected.</text>
<text lang="en">The values are six decimal numbers for the rates of transition from A to C, A to G, A to T, C to G, C to T and G to T respectively, separated by spaces or commas. The matrix is symmetrical so the reverse transitions equal the ones set (e.g. C to A equals A to C) and therefore only six values need be set. These values will be scaled such that the last value (G to T) is 1.0 and the others are set relative to this.</text>
</comment>
</parameter>
<paragraph>
<name>frequencies</name>
<prompt lang="en">Relative frequencies of nucleotides (-f)</prompt>
<argpos>1</argpos>
<comment>
<text lang="en">This option is used to specify the relative frequencies of the four nucleotides. By default, Seq-Gen will assume these to be equal. If the given values don't sum to 1.0 then they will be scaled so that they do.</text>
<text lang="en">You must give the frequencies for the 4 nucleotides</text>
</comment>
<parameters>
<parameter>
<name>freqA</name>
<prompt lang="en">Frequencies of the A nucleotide</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</format>
</parameter>
<parameter>
<name>freqC</name>
<prompt lang="en">Frequencies of the C nucleotide </prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</format>
</parameter>
<parameter>
<name>freqG</name>
<prompt lang="en">Frequencies of the G nucleotide</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</format>
</parameter>
<parameter>
<name>freqT</name>
<prompt lang="en">Frequencies of the T nucleotide</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</format>
</parameter>
<parameter ishidden="1">
<name>freqAll</name>
<prompt lang="en">Frequencies</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<precond>
<code proglang="perl">defined $freqA and defined $freqC and defined $freqG and defined $freqT</code>
<code proglang="python">freqA is not None and freqC is not None and freqG is not None and freqT is not None</code>
</precond>
<format>
<code proglang="perl">" -f $freqA,$freqC,$freqG,$freqT"</code>
<code proglang="python">" -f " + str(freqA) + "," + str(freqC) + "," + str(freqG) + "," + str(freqT)</code>
</format>
</parameter>
</parameters>
</paragraph>
</parameters>
</paragraph>
<paragraph>
<name>miscellaneous_opt</name>
<prompt lang="en">Miscellaneous options</prompt>
<argpos>1</argpos>
<parameters>
<parameter>
<name>random_seed</name>
<prompt lang="en">Random number seed (-z)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value)? "-z $value":""</code>
<code proglang="python">("" , "-z " + str(value))[ value is not None ]</code>
</format>
<comment>
<text lang="en">This option allows to specify a seed for the random number generator. Using the same seed (with the same input) will result in identical simulated datasets. This is useful because you can recreate a set of simulations, you must use exactly the same model options</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>output</name>
<prompt lang="en">Output parameters</prompt>
<argpos>1</argpos>
<parameters>
<parameter>
<name>output_format</name>
<prompt lang="en">Output file format (-o)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>p</value>
</vdef>
<vlist>
<velem>
<value>p</value>
<label>PHYLIP (p)</label>
</velem>
<velem>
<value>r</value>
<label>Relaxed PHYLIP (r)</label>
</velem>
<velem>
<value>n</value>
<label>NEXUS (n)</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef)? " -o$value":""</code>
<code proglang="python">("" , " -o" + str(value))[ value is not None and value != vdef]</code>
</format>
</parameter>
<parameter>
<name>quiet</name>
<prompt lang="en">Non verbose output (-q)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -q":""</code>
<code proglang="python">("" , " -q")[ value ]</code>
</format>
<argpos>1</argpos>
</parameter>
<parameter>
<name>write_ancest</name>
<prompt lang="en">Write the ancestral sequences (-wa)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -wa":""</code>
<code proglang="python">("" , " -wa")[ value ]</code>
</format>
<comment>
<text lang="en">This option allows to obtain the sequences for each of the internal nodes in the tree. The sequences are written out along with the sequences for the tips of the tree in relaxed PHYLIP format.</text>
</comment>
</parameter>
<parameter>
<name>write_sites</name>
<prompt lang="en">Write the sites rates (-wr)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -wr":""</code>
<code proglang="python">("" , " -wr")[ value ]</code>
</format>
<comment>
<text lang="en">This option allows to obtain the relative
rate of substitution for each sites as used in each
simulation. This will go to stderr and will be produced
for each replicate simulation.</text>
</comment>
</parameter>
<parameter isstdout="1">
<name>outfile</name>
<prompt lang="en">Output alignment file</prompt>
<type>
<datatype>
<class>Alignment</class>
</datatype>
<dataFormat>
<test param="output_format" eq="p">PHYLIPI</test>
<test param="output_format" eq="r">RPHYLIP</test>
<test param="output_format" eq="n">NEXUS</test>
</dataFormat>
</type>
<filenames>
<code proglang="perl">"seqgen.out"</code>
<code proglang="python">"seqgen.out"</code>
</filenames>
</parameter>
</parameters>
</paragraph>
</parameters>
</program>
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