[Biopython] Lots of pairwise alignments

[Peter Cock]

Hi Alexey,

I would look at EMBOSS needleall which would let you do many
comparisons at once (less overhead than calling needle many times):

http://emboss.sourceforge.net/apps/release/6.6/emboss/apps/needleall.html

Peter

On Tue, Mar 31, 2015 at 9:39 AM, Alexey Morozov
<alexeymorozov1991 at gmail.com> wrote:
> 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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