[BioPython] slow pairwise2 alignment

[Karin Lagesen]

Hi!

I have a task where I need to do a lot of pairwise alignments. I am
using pairwise2.align.localms, since that seemed to fit me nicely.
However, when I try it out with aligning sequences around 350 nts
long, I end up using about 1 1/2 mins per alignment. This is for my
use way too slow. 

When I look in the source code I see something about a c code thingy
that can do this. I am assuming that since it takes so long that I am
not using the c code. Does anybody have any idea of how I can check
this, and how I if I'm not using the c code can get to use it?

TIA,

Karin
-- 
Karin Lagesen, PhD student
karin.lagesen at labmed.uio.no