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author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
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1 <tool id="prank" name="PRANK" version="1.0" force_history_refresh='True'>
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2 <description> Phylogeny Aware Multiple Sequence Alignment </description>
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3 <requirements>
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4 <requirement type="package">prank</requirement>
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5 </requirements>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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6 <command interpreter="perl">
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7 prank.pl $input1 $format $missing
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8 </command>
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9 <inputs>
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10 <param format="fasta" name="input1" type="data" label="Sequences in FASTA format" help=""/>
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11 <param name="format" type="select" label="Output format">
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12 <option value="fasta">fasta</option>
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13 </param>
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14 <param name='missing' type='boolean' checked='false' truevalue='yes' falsevalue='no' label='-F
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15 option when sequences have terminal missing data'/>
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16 </inputs>
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17 <outputs>
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18 <data from_work_dir="output.1.fas" format="fasta" name="seqs_aligned" label="${tool.name} on ${on_string}: Alignment" />
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19 <data from_work_dir="output.2.fas" format="fasta" name="seqs_aligned2" label="${tool.name} on ${on_string}: Alignment" />
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20 </outputs>
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21 <tests>
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22 </tests>
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23 <help>
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24 **What it does**
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25
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26 "PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences. It's based on a novel
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27 algorithm that treats insertions correctly and avoids over-estimation of the number of deletion events. In addition,
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28 PRANK borrows ideas from maximum likelihood methods used in phylogenetics and correctly takes into account the
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29 evolutionary distances between sequences. Lastly, PRANK allows for defining a potential structure for sequences to be
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30 aligned and then, simultaneously with the alignment, predicts the locations of structural units in the sequences."
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31 From the PRANK website: http://code.google.com/p/prank-msa/wiki/PRANK?tm=6
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32
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33 ------
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34
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35 **Inputs**
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36
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37 FASTA
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38
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39 ------
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40
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41 **Outputs**
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42
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43 FASTA
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44
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45 -------
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46
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47 **Additional Information**
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48
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49 Please direct questions or comments to ucsb_phylogenetics@lifesci.ucsb.edu or, if you can, enter them on the osiris_phylogenetics site at bitbucket.org
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50
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51 -------
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52
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53 **Citations**
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54
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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55 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.
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56
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57 Current Osiris Citation is here
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58
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59 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
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60
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61 Additional Citations for this tool
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62
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63 PRANK was developed by Ari Löytynoja and Nick Goldman and is maintained at http://code.google.com/p/prank-msa/
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64
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65 The WebCite online citation for PRANK is available here:
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66 http://www.webcitation.org/query.php?url=http://tinyurl.com/prank-msa&refdoi=10.1186/1471-2105-11-579
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67 </help>
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68 </tool>