[Biojava-l] pair-wise alignment

[Matthew Pocock]

Hi

I have spent today optimizing pairwise alignment. I have got my test
case down from 148 secs to 84 secs, which is good but not great. It
spends as long in file IO as in alignment, and I can't see many more
tricks to speed things up. If you are interested in alignments, could
you run dp.PairwiseAlignment, and tell me if the performance is
acceptable?

In a similar vein, we should add the standard substitution matricies
(pam, blosum and background frequencies in swissprot, embl, trembl etc.)
into the distribution package. Any volunteres?

Roll on 1.0!

Matthew