[Biopython] Lots of pairwise alignments

[Alexey Morozov]

Dear colleagues, what's the fastest way to produce a lot of pairwise
alignmnents from (bio)python? Bio::pairwise2 is pretty slow and allows only
for linear gap penalties, not affine ones. So currently I launch a bunch of
subprocesses of NWalign or needle. It works, but is about twice slower then
clustalw pairwise alignments. Which, alas, clustal discards after building
guide tree and doesn't print.

Is this the fastest way it can be or I have missed some other tool?

-- 
Alexey Morozov,
LIN SB RAS, bioinformatics group.
Irkutsk, Russia.
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