[Biojava-l] Evolutionary distances

[Richard Holland]

You should take a look at the latest 1.5 release, in the
org.biojavax.bio.phylo packages. This code is the beginnings of some
phylogenetics code that will perform tasks as you describe. The future
plan is to extend this code to cover a wider range of use cases. Kimura2P
is already implemented here, in
org.biojavax.bio.phylo.MultipleHitCorrection.

If you can't find code that will do what you want, but have written some
before, then please do feel free to contribute it. Even if it is slow, I'm
sure someone out there will be able to help optimise it!

cheers,
Richard

On Sun, October 21, 2007 5:30 pm, vineith kaul wrote:
> Hi,
>
> Are there functions to calculate evolutionary pairwise distances like
> Kimura2P,Finkelstein etc in Biojava
> I did write smthng on my own but on large sequences it runs terribly
> slow and I am not even sure if thats right.
> --
> Vineith Kaul
> Masters Student Bioinformatics
> The Parker H. Petit Institute for Bioengineering and Bioscience (IBB)
> Georgia Tech, Atlanta
> _______________________________________________
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>


-- 
Richard Holland
BioMart (http://www.biomart.org/)
EMBL-EBI
Hinxton, Cambridgeshire CB10 1SD, UK