1 #summary Tutorial for multiple sequence alignments and phylogenetic methods in BioRuby -- under development!
5 Tutorial for multiple sequence alignments and phylogenetic methods in BioRuby -- under development!
8 = Multiple Sequence Alignments =
10 == Reading in a Multiple Sequence Alignment from a File ==
14 == Calculating a Multiple Sequence Alignment ==
16 BioRuby can be used to execute a variety of multiple sequence alignment
17 programs (such as [http://mafft.cbrc.jp/alignment/software/ MAFFT], Probcons, ClustalW, Muscle).
18 In the following, examples for using the MAFFT and Muscle are shown.
28 # Calculates the alignment using the MAFFT program on the local
29 # machine with options '--maxiterate 1000 --localpair'
30 # and stores the result in 'report'.
31 options = [ '--maxiterate', '1000', '--localpair' ]
32 mafft = Bio::MAFFT.new('path/to/mafft', options )
33 report = mafft.query_align( seqs)
35 # Accesses the actual alignment
36 align = report.alignment
38 # Prints each sequence to the console.
39 report.align.each { |s| puts s.to_s }
49 # Calculates the alignment using the Muscle program on the local
50 # machine with options '-quiet -maxiters 64'
51 # and stores the result in 'report'.
52 options = [ '-quiet', '-maxiters', '64' ]
53 muscle = Bio::Muscle.new('path/to/muscle', options )
54 report = muscle.query_align( seqs)
56 # Accesses the actual alignment
57 align = report.alignment
59 # Prints each sequence to the console.
60 report.align.each { |s| puts s.to_s }
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