[Biopython] API support for finding polymorphisms?

[Alex Lancaster]

Hi there,

I have a number of already-aligned sequences from the same species and I
can get them into Biopython as a multiple alignment using the following

alignments=AlignIO.parse("foobar.fasta", "fasta")

Before I go off and implement something by hand, I was wondering if
there is any support for finding polymorphisms across the alignments,
and, in particular, whether there is a way to "filter" the polymorphisms
(as there are likely to be too many to look at manually) by type
(e.g. stop codon gains/losses, frameshifts, or large deletions/
insertions).

I know that other packages such as samtools have ways to find
polymorphisms with respect to a specified reference sequence (and I'm
not sure, but I don't think samtools will allow you to filter by type in
any case), but I'd like to find a biopythonish solution.

I did a quick look through the API, Cookbook etc., but didn't find
anything that quite matches what I'm trying to do.

Cheers,
Alex