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 MAFFT, Probcons, ClustalW, Muscle).
18 In the following, examples for using the MAFFT and
28 # Calculates the alignment using the MAFFT program
29 # on the local machine with options
30 # '--maxiterate', '1000', '--localpair'
31 # and stores the result in 'report'.
32 options = [ '--maxiterate', '1000', '--localpair' ]
33 mafft = Bio::MAFFT.new('path/to/mafft', options )
34 report = mafft.query_align( seqs)
36 # Accesses the actual alignment
37 align = report.alignment
39 # Prints each sequence to the console.
40 report.align.each { |s| puts s.to_s }
50 # Calculates the alignment using the MAFFT program
51 # on the local machine, 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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