This page describes Bio.AlignIO, a new multiple sequence Alignment Input/Output interface for BioPython which is currently only in our source code repository. It should be included in the next release of Biopython.
You may already be familiar with the Bio.SeqIO module which deals with files containing one or more sequences represented as SeqRecord objects. Similarly, Bio.AlignIO deals with files containing one or more sequence alignments represented as Alignment objects. The same set of functions is provided for input and output.