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")
20 seq3 = "GKKKKGHHHGHRRRGR"
21 seq4 = "KKKGHHHGHRERGR"
22 seqs = [ seq1, seq2, seq3, seq4 ]
26 options = [ '--maxiterate', '1000', '--localpair' ]
27 mafft = Bio::MAFFT.new('/home/zma/SOFTWARE/mafft-6.847-without-extensions/scripts/mafft', options )
28 report = mafft.query_align( seqs)
29 #puts report.alignment.output_fasta
30 report.alignment.each { |x| puts x.to_s }
35 clustalw = Bio::ClustalW.new('/home/zma/SOFTWARE/clustalw-2.1/src/clustalw2' )
36 report = clustalw.query_align( seqs)
37 #puts report.alignment.output_fasta.to_s
38 report.alignment.each { |x| puts x.to_s }
43 options = [ '-quiet', '-maxiters', '64' ]
44 muscle = Bio::Muscle.new('/home/zma/SOFTWARE/muscle3.8.31/src/muscle', options )
45 report = muscle.query_align( seqs)
46 #puts report.alignment.output_fasta.to_s
47 report.alignment.each { |x| puts x.to_s }