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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'>
2 <description> Multiple Sequence Alignment </description>
3 <requirements>
4 <requirement type="package">mafft</requirement>
5 </requirements>
6 <command interpreter="perl">
7 mafft.pl $Strategy $input1
8 </command>
9 <inputs>
10 <param format="fasta" name="input1" type="data" label="Sequences in fasta format" help=""/>
11 <param name="Strategy" type="select" label="Alignment Strategy">
12 <option value="Auto">Auto</option>
13 <option value="FFT-NS-1">FFT-NS-1</option>
14 <option value="FFT-NS-2">FFT-NS-2</option>
15 <option value="FFT-NS-i">FFT-NS-i</option>
16 <option value="E-INS-i">E-INS-i</option>
17 <option value="L-INS-i">L-INS-i</option>
18 <option value="G-INS-i">G-INS-i</option>
19 <option value="Q-INS-i">Q-INS-i</option>
20 </param>
21 </inputs>
22 <outputs>
23 <data from_work_dir="seqs_aligned.fasta" format="fasta" name="seqs_aligned" label="${tool.name} on ${on_string}: Screen Output" />
24 </outputs>
25 <tests>
26 </tests>
27 <help>
28 **What it does**
29
30 MAFFT is a multiple sequence alignment program. It offers a range of multiple alignment methods.
31 From the MAFFT website: http://mafft.cbrc.jp/alignment/software/
32
33 ------
34
35 **Inputs**
36 Auto (FFT-NS-1, FFT-NS-2, FFT-NS-i or L-INS-i; depends on data size).
37
38 FFT-NS-1 (Very fast; recommended for more than 2,000 sequences; progressive method).
39
40 FFT-NS-2 (Fast; progressive method).
41
42 FFT-NS-i (Slow; iterative refinement method).
43
44 E-INS-i (Very slow; recommended for less than 200 sequences with multiple conserved domains and long gaps).
45
46 L-INS-i (Very slow; recommended for less than 200 sequences with one conserved domain and long gaps).
47
48 G-INS-i (Very slow; recommended for less than 200 sequences with global homology).
49
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).
51
52 ------
53
54 **Output**
55
56 FASTA
57
58 ------
59
60 **Additional Information**
61
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
63
64 -------
65
66 **Citations**
67
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.
69
70 Current Osiris Citation is here
71
72 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
73
74 Additional Citations for this tool
75
76 MAFFT: Katoh, Toh 2008 (Briefings in Bioinformatics 9:286-298)
77 Recent developments in the MAFFT multiple sequence alignment program.
78 </help>
79 </tool>