[Biopython] Bio.pairwise2 alignment slow

[Tiberiu Tesileanu]

Hi,

I've noticed that Bio.pairwise2 alignments tend to be very slow; e.g., Bio.pairwise2.align.globalds is about 100 times slower than Matlab's swalign... (this is on a Macbook Air running Mac OS X Lion). Is this expected, or am I doing something wrong? Is there a way to make sure that the C version of the code is used? Is there an alternative that is similarly easy to use, but faster?
Thanks!Tibi