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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="mafft" name="MAFFT" version="1.0" force_history_refresh='True'>
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2 <description> Multiple Sequence Alignment </description>
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3 <requirements>
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4 <requirement type="package">mafft</requirement>
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5 </requirements>
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6 <command interpreter="perl">
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7 mafft.pl $Strategy $input1
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8 </command>
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9 <inputs>
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10 <param format="fasta" name="input1" type="data" label="Sequences in fasta format" help=""/>
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11 <param name="Strategy" type="select" label="Alignment Strategy">
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12 <option value="Auto">Auto</option>
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13 <option value="FFT-NS-1">FFT-NS-1</option>
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14 <option value="FFT-NS-2">FFT-NS-2</option>
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15 <option value="FFT-NS-i">FFT-NS-i</option>
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16 <option value="E-INS-i">E-INS-i</option>
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17 <option value="L-INS-i">L-INS-i</option>
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18 <option value="G-INS-i">G-INS-i</option>
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19 <option value="Q-INS-i">Q-INS-i</option>
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20 </param>
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21 </inputs>
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22 <outputs>
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23 <data from_work_dir="seqs_aligned.fasta" format="fasta" name="seqs_aligned" label="${tool.name} on ${on_string}: Screen Output" />
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24 </outputs>
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25 <tests>
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26 </tests>
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27 <help>
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28 **What it does**
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29
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30 MAFFT is a multiple sequence alignment program. It offers a range of multiple alignment methods.
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31 From the MAFFT website: http://mafft.cbrc.jp/alignment/software/
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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 Auto (FFT-NS-1, FFT-NS-2, FFT-NS-i or L-INS-i; depends on data size).
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37
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38 FFT-NS-1 (Very fast; recommended for more than 2,000 sequences; progressive method).
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39
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40 FFT-NS-2 (Fast; progressive method).
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41
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42 FFT-NS-i (Slow; iterative refinement method).
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43
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44 E-INS-i (Very slow; recommended for less than 200 sequences with multiple conserved domains and long gaps).
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45
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46 L-INS-i (Very slow; recommended for less than 200 sequences with one conserved domain and long gaps).
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47
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48 G-INS-i (Very slow; recommended for less than 200 sequences with global homology).
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49
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50 Q-INS-i (Extremely slow; secondary structure of RNA is considered; recommended for a global alignment of highly diverged ncRNAs with less than 200 sequences × less than 1,000 nucleotides).
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51
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52 ------
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53
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54 **Output**
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55
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56 FASTA
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57
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58 ------
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59
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60 **Additional Information**
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61
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62 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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63
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64 -------
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65
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66 **Citations**
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67
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68 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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69
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70 Current Osiris Citation is here
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71
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72 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
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73
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74 Additional Citations for this tool
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75
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76 MAFFT: Katoh, Toh 2008 (Briefings in Bioinformatics 9:286-298)
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77 Recent developments in the MAFFT multiple sequence alignment program.
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78 </help>
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79 </tool>