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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>rnaalifold</name>
<xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="Entities/ViennaRNA_package.xml"/>
<doc>
<title>RNAalifold</title>
<description>
<text lang="en">Calculate secondary structures for a set of aligned RNAs</text>
</description>
<reference>D.H. Mathews, J. Sabina, M. Zuker and H. Turner "Expanded Sequence Dependence of Thermodynamic Parameters Provides Robust Prediction of RNA Secondary Structure" JMB, 288, pp 911-940, 1999</reference>
<reference>vo L. Hofacker, Martin Fekete, and Peter F. Stadler "Secondary Structure Prediction for Aligned RNA Sequences" J.Mol.Biol. 319: 1059-1066 (2002).</reference>
<doclink>http://www.tbi.univie.ac.at/RNA/RNAalifold.html</doclink>
<comment>
<text lang="en">RNAalifold reads aligned RNA sequences from file and calculates
their minimum free energy (mfe) structure, partition function (pf) and base pairing probability matrix.
Currently, the input alignment has to be in CLUSTAL format.
It returns the mfe structure in bracket notation, its energy,
the free energy of the thermodynamic ensemble and the frequency of the mfe structure
in the ensemble to outfile. It also produces Postscript files with plots of the resulting
secondary structure graph ("alirna.ps") and a "dot plot" of the base pairing matrix ("alidot.ps").
The file "alifold.out" will contain a list of likely pairs sorted by credibility. </text>
<text lang="en">
CAVEATS: Since gaps are not removed for the evaluation of energies,
it may be of advantage to remove any columns with more than, say,
75% gaps from the alignment before folding with RNAalifold.
</text>
<text lang="en">Sequences are not weighted. If possible, do not mix very similar and dissimilar sequences.
Duplicate sequences, for example, can distort the prediction.
</text>
</comment>
</doc>
<category>alignment:multiple:display</category>
<category>structure:2D_structure</category>
<command>RNAalifold</command>
</head>
<parameters>
<parameter ismandatory="1" issimple="1">
<name>seq</name>
<prompt lang="en">Aligned RNA Sequences File</prompt>
<type>
<biotype>Nucleic</biotype>
<datatype>
<class>Alignment</class>
</datatype>
<dataFormat>CLUSTAL</dataFormat>
</type>
<format>
<code proglang="perl">" $value" </code>
<code proglang="python">" "+str( value ) </code>
</format>
<argpos>1000</argpos>
</parameter>
<paragraph>
<name>control</name>
<prompt lang="en">Control options</prompt>
<argpos>2</argpos>
<parameters>
<parameter>
<name>covariance</name>
<prompt lang="en">Weight of the covariance (-cv)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -cv $value" : ""</code>
<code proglang="python">( "" , " -cv " + str(value) )[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">Set the weight of the covariance term in the energy function to factor. Default is 1.
</text>
</comment>
</parameter>
<parameter>
<name>non_compatible</name>
<prompt lang="en">Penalty for non-compatible sequences in the covariance (-nc)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -nc $value" : ""</code>
<code proglang="python">( "" , " -nc " + str(value) )[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">Set the penalty for non-compatible sequences in the covariance term of the energy function to factor. Default is 1.</text>
</comment>
</parameter>
<parameter>
<name>endgaps</name>
<prompt lang="en">Score pairs with endgaps (-E)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -E" : ""</code>
<code proglang="python">( "" , " -E" )[ value ]</code>
</format>
<comment>
<text lang="en">Score pairs with endgaps same as gap-gap pairs.</text>
</comment>
</parameter>
<parameter>
<name>partition</name>
<prompt lang="en">Calculate the partition function and base pairing probability matrix (-p)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -p" : ""</code>
<code proglang="python">( "" , " -p" )[ value ]</code>
</format>
<comment>
<text lang="en">Calculate the partition function and base pairing probability matrix in addition to the mfe structure. Default is calculation of mfe structure only.</text>
</comment>
</parameter>
<parameter>
<name>temperature</name>
<prompt lang="en">Rescale energy parameters to a temperature of temp C. (-T)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>37</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -T $value" : ""</code>
<code proglang="python">( "" , " -T " + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
<parameter>
<name>tetraloops</name>
<prompt lang="en">Do not include special stabilizing energies for certain tetraloops (-4)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -4" : ""</code>
<code proglang="python">( "" , " -4" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>dangling</name>
<prompt lang="en">How to treat dangling end energies for bases adjacent to helices in free ends and multiloops (-d)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>-d1</value>
</vdef>
<vlist>
<velem>
<value>-d1</value>
<label>Only unpaired bases can participate in at most one dangling end (-d1)</label>
</velem>
<velem>
<value>-d</value>
<label>Ignores dangling ends altogether (-d)</label>
</velem>
<velem>
<value>-d2</value>
<label>The check is ignored, this is the default for partition function folding (-d2)</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef)? " $value" : ""</code>
<code proglang="python">( "" , " " + str(value) )[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">How to treat 'dangling end' energies for bases adjacent to helices in free ends and multiloops: Normally only unpaired bases can participate in at most one dangling end.
With -d2 this check is ignored, this is the default for partition function folding (-p).
-d ignores dangling ends altogether. Note that by default pf and mfe folding treat dangling ends differently,
use -d2 (or -d) in addition to -p to ensure that both algorithms use the same energy model.
The -d2 options is available for RNAfold, RNAeval, and RNAinverse only.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>input</name>
<prompt lang="en">Input parameters</prompt>
<argpos>2</argpos>
<parameters>
<parameter>
<name>circ</name>
<prompt lang="en">Circular RNA molecules (-circ)?</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -circ" : ""</code>
<code proglang="python">( "" , " -circ" )[ value ]</code>
</format>
<comment>
<text lang="en">Assume circular (instead of linear) RNA molecules.</text>
</comment>
</parameter>
<parameter>
<name>noLP</name>
<prompt lang="en">Avoid structures without lonely pairs (helices of length 1) (-noLP)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -noLP" : ""</code>
<code proglang="python">( "" , " -noLP" )[ value ]</code>
</format>
<comment>
<text lang="en">Produce structures without lonely pairs (helices of length 1). For partition function folding this only disallows pairs that can only occur isolated. Other pairs may still occasionally occur as helices of length 1.</text>
</comment>
</parameter>
<parameter>
<name>noGU</name>
<prompt lang="en">Do not allow GU pairs (-noGU)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -noGU" : ""</code>
<code proglang="python">( "" , " -noGU" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>noCloseGU</name>
<prompt lang="en">Do not allow GU pairs at the end of helices (-noCloseGU)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -noCloseGU" : ""</code>
<code proglang="python">( "" , " -noCloseGU" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>nsp</name>
<prompt lang="en">Non standard pairs (comma seperated list) (-nsp)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value)? " -nsp $value" : "" </code>
<code proglang="python">( "" , " -nsp " + str(value) )[ value is not None ]</code>
</format>
<comment>
<text lang="en">Allow other pairs in addition to the usual AU,GC,and GU pairs. pairs is a comma seperated list of additionally allowed pairs. If a the first character is a '-' then AB will imply that AB and BA are allowed pairs. e.g. RNAfold -nsp -GA will allow GA and AG pairs. Nonstandard pairs are given 0 stacking energy.</text>
</comment>
</parameter>
<parameter>
<name>parameter</name>
<prompt lang="en">Energy parameter file (-P)</prompt>
<type>
<datatype>
<class>EnergyParameterFile</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value)? " -P $value" : ""</code>
<code proglang="python">( "" , " -P " + str(value) )[ value is not None ]</code>
</format>
<comment>
<text lang="en">Read energy parameters from paramfile, instead of using the default parameter set. A sample parameterfile should accompany your distribution. See the RNAlib documentation for details on the file format.</text>
</comment>
</parameter>
<parameter>
<name>ribosum_matrix</name>
<prompt lang="en"> use specified Ribosum Matrix instead of normal energy model.</prompt>
<type>
<datatype>
<class>ribosum_matrix</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value)? " -P $value" : ""</code>
<code proglang="python">( "" , " -P " + str(value) )[ value is not None ]</code>
</format>
<comment>
<text lang="en">use specified Ribosum Matrix instead of normal energy model. Matrices to use
should be 6x6 matrices, the order of the terms is AU, CG, GC, GU, UA, UG.</text>
</comment>
</parameter>
<parameter>
<name>use_ribosum_matrix</name>
<prompt lang="en"> use Ribosum scoring matrix.</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value)? " -r $value" : ""</code>
<code proglang="python">( "" , " -r ")[ value ]</code>
</format>
<comment>
<text lang="en"> use Ribosum scoring matrix. The matrix is chosen according to the minimal
and maximal pairwise identities of the sequences in the file. When using
Ribosum scores, best benchmark results were achieved with options -cv 0.6
-nc 0.5 (see above).</text>
</comment>
</parameter>
<parameter>
<name>constraints</name>
<prompt lang="en">Calculate structures subject to constraints (-C)</prompt>
<type>
<datatype>
<class>Constraint</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value)? " -C < $value" : ""</code>
<code proglang="python">( "" , " -C <" + str( value) )[ value is not None ]</code>
</format>
<comment>
<text lang="en">The programm reads first the sequence then the a string containg constraints on the structure encoded with the symbols: </text>
<text lang="en">| (the corresponding base has to be paired x (the base is unpaired)</text>
<text lang="en">< (base i is paired with a base j>i)</text>
<text lang="en">> (base i is paired with a base j<i)</text>
<text lang="en">matching brackets ( ) (base i pairs base j)</text>
<text lang="en">Pf folding ignores constraints of type '|' '<' and '>', but disallow all pairs conflicting with a constraint of type 'x' or '( )'. This is usually sufficient to enforce the constraint.</text>
</comment>
</parameter>
<!-- core dumped on raclette
<parameter>
<name>energy</name>
<prompt lang="en">Energy parameters for the artificial ABCD... alphabet (-e)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>Null</value>
</vdef>
<vlist>
<velem undef="1">
<value>Null</value>
<label>No energy for the artificial ABCD</label>
</velem>
<velem>
<value>1</value>
<label>Use energy parameters for GC pairs (1)</label>
</velem>
<velem>
<value>2</value>
<label>Use energy parameters for AU pairs (2)</label>
</velem>
</vlist>
<format>
<code proglang="perl">($value)? " -e $value" : ""</code>
<code proglang="python">( "" , " -e " + str(value) )[ value is not None and value!=vdef]</code>
</format>
</parameter>
-->
</parameters>
</paragraph>
<paragraph>
<name>output_options</name>
<prompt lang="en">Output options</prompt>
<parameters>
<parameter>
<name>informative</name>
<prompt lang="en">Print most informative sequence instead of simple consensus (-mis)?</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -mis" : ""</code>
<code proglang="python">( "" , " -mis" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>color</name>
<prompt lang="en">Produce a colored version of the consensus strcture plot (-color)?</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -color" : ""</code>
<code proglang="python">( "" , " -color" )[ value ]</code>
</format>
<comment>
<text lang="en">Produce a colored version of the consensus strcture plot "alirna.ps" (default black and white).</text>
</comment>
</parameter>
<parameter>
<name>aln</name>
<prompt lang="en">Produce a colored and structure annotated alignment in PostScript format (-aln) ?</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -aln" : ""</code>
<code proglang="python">( "" , " -aln" )[ value ]</code>
</format>
<comment>
<text lang="en">Produce a colored and structure annotated alignment in PostScript format in the file "aln.ps".</text>
</comment>
</parameter>
</parameters>
</paragraph>
<parameter isout="1">
<name>psfiles</name>
<prompt>Postscript file</prompt>
<type>
<datatype>
<class>PostScript</class>
<superclass>Binary</superclass>
</datatype>
</type>
<filenames>
<code proglang="perl">"*.ps"</code>
<code proglang="python">"*.ps"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>alifold_out</name>
<prompt>list of likely pairs</prompt>
<type>
<datatype>
<class>vienna_likely_pairs</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$partition</code>
<code proglang="python">partition</code>
</precond>
<filenames>
<code proglang="perl">"alifold.out"</code>
<code proglang="python">"alifold.out"</code>
</filenames>
<comment>
<text lang="en">The file "alifold.out" will contain a list of likely pairs sorted by
credibility, suitable for viewing with "AliDot.pl"</text>
</comment>
</parameter>
</parameters>
</program>
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