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. The purpose of the SeqIO module is to provide a simple uniform interface to assorted file formats.
Similarly, Bio.AlignIO deals with files containing one or more sequence alignments represented as Alignment objects. Bio.AlignIO uses the same set of functions for input and output as in Bio.SeqIO, and the same names for the file formats supported.
Note that the inclusion of Bio.AlignIO does lead to some duplication or choice in how to deal with some file formats. For example, Bio.SeqIO and Bio.Clustalw will both read sequences from Clustal files - but Bio.Clustalw also includes a command line wrapper to call the program.
My vision is that for manipulating sequence alignments you should try Bio.AlignIO as your first choice. In some cases you may only care about the sequences themselves, in which case try using Bio.SeqIO on the alignment file directly. Unless you have some very specific requirements, I hope this should suffice.
|fasta||Yes||Yes||This refers to the input file format introduced for Bill Pearson's FASTA tool, where each record starts with a ">" line. Note that storing more than one alignment in this format is ambiguous.|
|clustal||Yes||Yes||See also Bio.Clustalw for calling the command line tool.|
|nexus||Yes||No||Also known as PAUP format. Uses Bio.Nexus|
|phylip||Yes||Yes||Truncates names at 10 characters.|
|stockholm||Yes||Yes||Also known as PFAM format.|
In addition, you can store the (gapped) sequences from an alignment in any of the file formats supported by Bio.SeqIO. The most common example of this is storing multiple alignments in the simple fasta format. However, storing more than one alignment in a single such file is ambiguous - see the section below on alignment input.