4 # creating a Bio::Sequence::NA object containing ambiguous alphabets
5 #as = Bio::Sequence::NA.new("atgcyrwskmbdhvn")
12 #seq1 = Bio::Sequence::AA.new("gggggg")
13 #seq2 = Bio::Sequence::AA.new("ggggt")
14 #seq3 = Bio::Sequence::AA.new("ggt")
18 seqs = [ "KMLFGVVFFFGG",
25 options = [ '--maxiterate', '1000', '--localpair' ]
26 mafft = Bio::MAFFT.new('/home/zma/SOFTWARE/mafft-6.847-without-extensions/scripts/mafft', options )
27 report = mafft.query_align( seqs)
29 # Accesses the actual alignment
30 align = report.alignment
32 # Prints each sequence to the console.
33 align.each { |s| puts s.to_s }
40 clustalw = Bio::ClustalW.new('/home/zma/SOFTWARE/clustalw-2.1/src/clustalw2' )
41 report = clustalw.query_align( seqs)
42 #puts report.alignment.output_fasta.to_s
43 report.alignment.each { |x| puts x.to_s }
48 options = [ '-quiet', '-maxiters', '64' ]
49 muscle = Bio::Muscle.new('/home/zma/SOFTWARE/muscle3.8.31/src/muscle', options )
50 report = muscle.query_align( seqs)
51 #puts report.alignment.output_fasta.to_s
52 report.alignment.each { |x| puts x.to_s }