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<?xml version='1.0' encoding='UTF-8'?>
<!-- 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>muscle</name>
<version>3.8.31</version>
<doc>
<title>Muscle</title>
<description>
<text lang="en">MUSCLE is a program for creating multiple alignments of amino acid or nucleotide sequences.</text>
</description>
<authors>Edgar, R.C.</authors>
<reference doi="10.1093/nar/gkh340">Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.</reference>
<doclink>http://www.drive5.com/muscle/</doclink>
<homepagelink>http://www.drive5.com/muscle/</homepagelink>
<sourcelink>http://www.drive5.com/muscle/downloads.htm</sourcelink>
</doc>
<category>alignment:multiple</category>
<command>muscle</command>
</head>
<parameters>
<parameter ishidden="1">
<name>quiet</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">" -quiet"</code>
<code proglang="python">" -quiet"</code>
</format>
</parameter>
<paragraph>
<name>inputs</name>
<prompt lang="en">Inputs options</prompt>
<parameters>
<parameter issimple="1" ismandatory="1">
<name>sequence</name>
<prompt lang="en">Sequences (-in)</prompt>
<type>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>FASTA</dataFormat>
<card>2,n</card>
</type>
<precond>
<code proglang="perl">not defined($profile1) and not defined($profile2)</code>
<code proglang="python">profile1 is None and profile2 is None</code>
</precond>
<format>
<code proglang="perl">"-in $value"</code>
<code proglang="python">" -in " + str(value)</code>
</format>
<argpos>10</argpos>
</parameter>
<parameter>
<name>seqtype</name>
<prompt lang="en">Determining sequence type (-seqtype)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>auto</value>
</vdef>
<vlist>
<velem undef="1">
<value>auto</value>
<label>Automatic</label>
</velem>
<velem>
<value>protein</value>
<label>Protein</label>
</velem>
<velem>
<value>dna</value>
<label>DNA</label>
</velem>
<velem>
<value>rna</value>
<label>RNA</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " -seqtype $value " : ""</code>
<code proglang="python">( "" , " -seqtype " + str(value) )[ value is not None and value != vdef ]</code>
</format>
<comment>
<text lang="en">By default, MUSCLE looks at the first 100 letters in the input sequence data (excluding gaps). If 95% or more of those letters are valid nucleotides (AGCTUN), then the file is treated as nucleotides, otherwise as amino acids.</text>
<text lang="en">This method almost always guesses correctly, but you can make sure by specifying the sequence type on the command line.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>optimization</name>
<prompt lang="en">Optimization parameters</prompt>
<parameters>
<parameter>
<name>maxiters</name>
<prompt lang="en">Maximum number of iterations (-maxiters)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>16</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -maxiters $value" : ""</code>
<code proglang="python">( "" , " -maxiters " + str( value ) )[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">You can control the number of iterations that MUSCLE does by specifying the -maxiters option.</text>
<text lang="en">If you specify 1, 2 or 3, then this is exactly the number of iterations that will be performed.</text>
<text lang="en">If the value is greater than 3, then muscle will continue up to the maximum you specify or until convergence is reached, which ever happens sooner.</text>
<text lang="en">The default is 16. If you have a large number of sequences, refinement may be rather slow.</text>
</comment>
</parameter>
<parameter>
<name>maxtrees</name>
<prompt lang="en">Maximum number of trees (-maxtrees)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? "-maxtrees $value" : ""</code>
<code proglang="python">( "" , " -maxtrees " + str( value ) )[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">Option controls the maximum number of new trees to create in iteration 2.</text>
<text lang="en">experience suggests that a point of diminishing returns is typically reached after the first tree, so the default value is 1.</text>
<text lang="en">If a larger value is given, the process will repeat until convergence or until this number of trees has been created, which ever comes first.</text>
</comment>
</parameter>
<parameter>
<name>maxhours</name>
<prompt lang="en">Maximum time to run in hours (-maxhours)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $maxhours) ? "-maxhours $value" : ""</code>
<code proglang="python">( "" , " -maxhours " + str( value ) )[ maxhours is not None ]</code>
</format>
<comment>
<text lang="en">If you have a large alignment, muscle may take a long time to complete. It is sometimes convenient to say "I want the best alignment I can get in 24 hours" rather than specifying a set of options that will take an unknown length of time.</text>
<text lang="en">This is done by using -maxhours, which specifies a floating-point number of hours. If this time is exceeded, muscle will write out current alignment and stop. For example,</text>
<text lang="en">muscle -in huge.fa -out huge.afa -maxiters 9999 -maxhours 24.0</text>
</comment>
</parameter>
<!--
<parameter ishidden="1">
<name>maxmemory</name>
<prompt lang="en">(-maxmb)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</format>
</parameter>
-->
<parameter>
<name>diags</name>
<prompt lang="en">Find diagonals (faster for similar sequences) (-diags)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -diags " : ""</code>
<code proglang="python">( "" , " -diags " )[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">Creating a pair-wise alignment by dynamic programming requires computing an L1 * L2 matrix, where L1 and L2 are the sequence lengths.</text>
<text lang="en">A trick used in algorithms such as BLAST is to reduce the size of this matrix by using fast methods to find "diagonals", i.e. short regions of high similarity between the two sequences.</text>
<text lang="en">This speeds up the algorithm at the expense of some reduction in accuracy.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<parameter>
<name>scoring</name>
<prompt lang="en">The profile scoring function (for protein only)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<precond>
<code proglang="perl">$seqtype ne "nucleo"</code>
<code proglang="python">seqtype != "nucleo"</code>
</precond>
<vdef>
<value>le</value>
</vdef>
<flist>
<felem>
<value>le</value>
<label>log-expectation (-le)</label>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</felem>
<felem>
<value>sp</value>
<label>sum of pairs score using the PAM200 matrix (-sp)</label>
<code proglang="perl">" -sp "</code>
<code proglang="python">" -sp "</code>
</felem>
<felem>
<value>sv</value>
<label>sum of pairs score using the VTML240 matrix (-sv)</label>
<code proglang="perl">" -sv "</code>
<code proglang="python">" -sv "</code>
</felem>
</flist>
<comment>
<text lang="en">Three different protein profile scoring functions are supported,</text>
<text lang="en">- the log-expectation score (-le option)</text>
<text lang="en">- and a sum of pairs score using either the PAM200 matrix (-sp)</text>
<text lang="en">- or the VTML240 matrix (-sv).</text>
<text lang="en">The log-expectation score is the default as it gives better results on our tests, but is typically somewhere between two or three times slower than the sum-of-pairs score.</text>
<text lang="en">For nucleotides, -spn is currently the only option (which is of course the default for nucleotide data, so you don't need to specify this option).</text>
</comment>
</parameter>
<paragraph>
<name>profile_option</name>
<prompt lang="en">Profile Alignments parameters</prompt>
<comment>
<text lang="en">To align two sequence alignments. Not compatible with Input options.</text>
</comment>
<parameters>
<parameter>
<name>profile1</name>
<prompt lang="en">Profile 1 </prompt>
<type>
<datatype>
<class>Alignment</class>
</datatype>
<dataFormat>FASTA</dataFormat>
</type>
<precond>
<code proglang="perl">not defined($sequence)</code>
<code proglang="python">sequence is None</code>
</precond>
<format>
<code proglang="perl">"-in1 $value"</code>
<code proglang="python">" -in1 " + str(value)</code>
</format>
</parameter>
<parameter>
<name>profile2</name>
<prompt lang="en">Profile 2 </prompt>
<type>
<datatype>
<class>Alignment</class>
</datatype>
<dataFormat>FASTA</dataFormat>
</type>
<precond>
<code proglang="perl">not defined($sequence)</code>
<code proglang="python">sequence is None</code>
</precond>
<format>
<code proglang="perl">"-in2 $value"</code>
<code proglang="python">" -in2 " + str(value)</code>
</format>
</parameter>
<parameter ishidden="1">
<name>profile</name>
<prompt lang="en">(-profile)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">not defined($sequence) and defined($profile1) and defined($profile2)</code>
<code proglang="python">sequence is None and profile1 is not None and profile2 is not None</code>
</precond>
<format>
<code proglang="perl">""</code>
<code proglang="python">" -profile "</code>
</format>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>outpout_options</name>
<prompt lang="en">Output Options</prompt>
<parameters>
<parameter>
<name>outformat</name>
<prompt lang="en">output format</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>fasta</value>
</vdef>
<flist>
<felem>
<value>fasta</value>
<label>fasta</label>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</felem>
<felem>
<value>html</value>
<label>html</label>
<code proglang="perl">" -html "</code>
<code proglang="python">" -html "</code>
</felem>
<felem>
<value>msf</value>
<label>msf</label>
<code proglang="perl">" -msf "</code>
<code proglang="python">" -msf "</code>
</felem>
<felem>
<value>phyi</value>
<label>phylip</label>
<code proglang="perl">" -phyi "</code>
<code proglang="python">" -phyi "</code>
</felem>
<!-- it's a clustalw with a muscle header which is not supported by squizz -->
<felem>
<value>clw</value>
<label>muscle format</label>
<code proglang="perl">" -clw "</code>
<code proglang="python">" -clw "</code>
</felem>
<felem>
<value>clwstrict</value>
<label>clustalw 1.81</label>
<code proglang="perl">" -clwstrict "</code>
<code proglang="python">" -clwstrict "</code>
</felem>
</flist>
<comment>
<text lang="en">fasta : Write output in Fasta format</text>
<text lang="en">html : Write output in HTML format </text>
<text lang="en">msf : Write output in GCG MSF format</text>
<text lang="en">phylip : Write output in Phylip (interleaved) format</text>
<text lang="en">muscle : Write output in CLUSTALW format with muscle header </text>
<text lang="en">clustalw : Write output in CLUSTALW format with CLUSTAL W (1.81)</text>
</comment>
</parameter>
<parameter>
<name>outfile</name>
<prompt lang="en">Filename (-out)</prompt>
<type>
<datatype>
<class>Filename</class>
</datatype>
</type>
<format>
<code proglang="perl">" -out $value"</code>
<code proglang="python">("", " -out " + str(value))[value is not None]</code>
</format>
</parameter>
</parameters>
</paragraph>
<parameter isstdout="1">
<name>alignmentout</name>
<prompt lang="en">Alignment</prompt>
<type>
<datatype>
<class>Alignment</class>
</datatype>
<dataFormat>
<test param="outformat" eq="fasta">FASTA</test>
<test param="outformat" eq="msf">MSF</test>
<test param="outformat" eq="phyi">PHYLIPI</test>
<test param="outformat" eq="clwstrict">CLUSTAL</test>
<test param="outformat" eq="clw">MUSCLE</test>
</dataFormat>
</type>
<precond>
<code proglang="perl">$outformat =~ /^(fasta|msf|phyi|clwstrict|clw)$/ </code>
<code proglang="python">outformat in [ 'fasta' , 'msf' , 'phyi' , 'clwstrict' , 'clw']</code>
</precond>
<filenames>
<code proglang="perl">(defined $outfile) ? "$outfile" : "muscle.out"</code>
<code proglang="python">( outfile , "muscle.out")[outfile is None]</code>
</filenames>
</parameter>
<parameter isstdout="1">
<name>muscleHtmlout</name>
<prompt lang="en">Alignment</prompt>
<type>
<datatype>
<class>MuscleHtmlAlignment</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$outformat == 'html' </code>
<code proglang="python">outformat == 'html'</code>
</precond>
<filenames>
<code proglang="perl">(defined $outfile) ? "$outfile" : "muscle.out"</code>
<code proglang="python">( outfile , "muscle.out")[outfile is None]</code>
</filenames>
</parameter>
</parameters>
</program>
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