Alignment iterator for the FASTA tool's pairwise alignment output. This is for reading the pairwise alignments output by Bill Pearson's FASTA program when called with the -m 10 command line option for machine readable output. For more details about the FASTA tools, see the website http://fasta.bioch.virginia.edu/ and the paper: W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448 This class is intended to be used via the Bio.AlignIO.parse() function by specifying the format as "fasta-m10" as shown in the following code: from Bio import AlignIO handle = ... for a in AlignIO.parse(handle, "fasta-m10") : assert len(a.get_all_seqs()) == 2, "Should be pairwise!" print "Alignment length %i" % a.get_alignment_length() for record in a : print record.seq, record.name, record.id Note that this is not a full blown parser for all the information in the FASTA output - for example, most of the header and all of the footer is ignored. Also, the alignments are not batched according to the input queries. Also note that there can be up to about 30 letters of flanking region included in the raw FASTA output as contextual information. This is NOT part of the alignment itself, and is not included in the resulting Alignment objects returned.