[Biojava-l] BioJava 2 status

[Mark Schreiber]

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 <matthew.pocock at ncl.ac.uk> 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
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