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 > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > -- Richard Holland BioMart (http://www.biomart.org/) EMBL-EBI Hinxton, Cambridgeshire CB10 1SD, UK _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
