The Alignment class: comparison of sequences and structures

This section describes the commands for reading, writing, making, analyzing and using the alignments of sequences and structures (pairwise and multiple). For the underlying dynamic programming methods see Section A.1.

An Alignment object acts like a regular Python list, where each element in the list represents a sequence in the alignment, as a Sequence object (see Section 6.17). The list can be indexed in standard Python fashion or by alignment code. Thus, given an Alignment object aln, len(aln) gives the number of sequences in the alignment, aln[0] the first sequence, aln[-1] the last sequence, and aln['1abcA'] the sequence with alignment code '1abcA'.