Hello - Recent versions of biojava contain NW and SW algorithm implementations in org.biojava.bio.alignment. There is aslo a SubstitutionMatrix object that can hold the information found in the BLOSUM etc matrix files that one can download from NCBI.
Hope this helps, - Mark On 9/17/07, Matthew Pocock <[EMAIL PROTECTED]> wrote: > Somebody asked me: > > > I was wondering whether BioJava provides standard scoring matrices > > (e.g. BLOSUM62, etc.) as "constants" anywhere for doing alignments. I > > couldn't seem to find this anywhere in the code but, admittedly, have > > not looked very closely yet. > > And rather embarasingly, I don't know the answer. Does someone here? > > Matthew > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
