[Biopython] Pairwise alignment - is it a generic function?

[João Rodrigues]

Hello all,

A friend of mine was interested in a small simple alignment script for
aminoacids, to which I recommended to have a look at Biopython. We found the
pairwise2 module but we're a bit puzzled. Does it align "any" sequence, aa
or nucleotides? I don't see any scoring matrix referenced there..

Related to this, can you suggest any implementation of an aminoacid pairwise
alignment algorithm, in Python, that does is self contained (ie. doesn't
depend on some other program).

Best,

João [...] Rodrigues
http://nmr.chem.uu.nl/~joao