Create distance matrix object from input alignment in BioPython

Question

[jba462]

In Biopython, is there a way to create a distance matrix (i.e. a distance matrix 'object' that could be read and manipulated), using an alignment as input?

The "distancematrix" method in Bio.Cluster is giving me problems (ValueError: data has incorrect rank (1 expected 2)) when reading in an alignment file using Cluster.read(), and it won't accept a Numpy array either.

I realize there there is likely an easy solution to this problem, but I've spent the better part of today trying to find an easy way to even calculate the distance between two aligned, amino acid sequences using Biopython.

[Peter]

I think we have an open issue on better distance matrix support on the old (RedMine) Biopython issue tracker, but that is currently offline, probably https://redmine.open-bio.org/issues/2034 (link not tested). See also http://lists.open-bio.org/pipermail/biopython/2006-June/003107.html