ivy.align module

ivy.align.find(aln, substr)

generator that yields (seqnum, pos) tuples for every position of subseq in aln

ivy.align.find_id(aln, regexp)

ivy.align.gapcols(aln, c=u'-')

ivy.align.muscle(seqs, cmd=None)

ivy.align.musclep(seqs1, seqs2, cmd=u'/usr/bin/muscle')

ivy.align.read(data, format=None, name=None)

ivy.align.write(data, f, format=u'fasta')