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<tool id="phytab_muscle" name="phytab MUSCLE" version="1.0">
  <description>MUSCLE: Multiple sequence alignment. Input can be FASTA or phytab format.</description>
  <requirements>
    <requirement type="package">muscle</requirement>
  </requirements>
  <command interpreter="python">
    phytab_muscle.py -i $data > $muscle_stdout 2>&amp;1
  </command>
  <inputs>
    <param format="txt" name="data" type="data" label="Sequence data" help="This should be sequence data in fasta or phytab format"/>
  </inputs>
  <outputs>
    <data format="txt" name="muscle_stdout" label="${tool.name} on ${on_string}: stdout" />
    <data format="tabular" name="muscle_results" label="${tool.name} on ${on_string}: results" from_work_dir="data/results.data" />
  </outputs>
  <tests>
  </tests>
    <help>
**What it does**

Uses MUSCLE to perform multiple sequence alignment on multiple gene families in parallel.

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**Inputs**

Can take as input fasta or phytab format. Phytab allows alignment in parallel of multiple separate gene families/paralogs. See: 
http://osiris-phylogenetics.blogspot.com/2012/09/introduction-to-phytab-format.html

------

**Outputs**

Either a fasta file or phytab file of aligned sequences

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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

Runs MUSCLE 3.8 Multiple Sequence Alignment
See MUSCLE help: http://www.drive5.com/muscle/muscle_userguide3.8.html

    </help>
</tool>