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<tool id="prank" name="PRANK" version="1.0" force_history_refresh='True'>
    <description> Phylogeny Aware Multiple Sequence Alignment </description>
    <requirements>
        <requirement type="package">prank</requirement>
    </requirements>
    <command interpreter="perl">
        prank.pl $input1 $format $missing
    </command>
    <inputs>
        <param format="fasta" name="input1" type="data" label="Sequences in FASTA format" help=""/>
    <param name="format" type="select" label="Output format">
      <option value="fasta">fasta</option>
    </param>
    <param name='missing' type='boolean' checked='false' truevalue='yes' falsevalue='no' label='-F 
option when sequences have terminal missing data'/>
    </inputs>
    <outputs>
	<data from_work_dir="output.1.fas" format="fasta" name="seqs_aligned" label="${tool.name} on ${on_string}: Alignment" />
	<data from_work_dir="output.2.fas" format="fasta" name="seqs_aligned2" label="${tool.name} on ${on_string}: Alignment" />
    </outputs>
    <tests>
    </tests>
    <help>
**What it does**

"PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences. It's based on a novel
algorithm that treats insertions correctly and avoids over-estimation of the number of deletion events. In addition,
PRANK borrows ideas from maximum likelihood methods used in phylogenetics and correctly takes into account the
evolutionary distances between sequences. Lastly, PRANK allows for defining a potential structure for sequences to be
aligned and then, simultaneously with the alignment, predicts the locations of structural units in the sequences."
From the PRANK website: http://code.google.com/p/prank-msa/wiki/PRANK?tm=6

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**Inputs**

FASTA

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**Outputs**

FASTA

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**Additional Information**

Please direct questions or comments to [e-mail] or, if you can, enter them on the osiris_phylogenetics site at bitbucket.org

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**Citations**

This tool is part of the Osiris Phylogenetics Tool Package for Galaxy. If you make extensive use of this tool in a publication, please consider citing the following.

Current Osiris Citation is here

http://osiris-phylogenetics.blogspot.com/2012/10/citation.html

Additional Citations for this tool

PRANK was developed by Ari Löytynoja and Nick Goldman and is maintained at http://code.google.com/p/prank-msa/

The WebCite online citation for PRANK is available here:
http://www.webcitation.org/query.php?url=http://tinyurl.com/prank-msa&refdoi=10.1186/1471-2105-11-579
    </help>
</tool>