[Biojava-l] Is there a Java implementation of SW that also returns N suboptimal alignments

[David Nix]

Hello Folks,
    I'm looking for a local alignment script that uses a variant of the
Smith-Waterman algorithm where, in addition to the highest scoring
alignment, all other alignments above a given score cut off are returned.
Two such programs have already been written in C (LALIGN and SIM), but I
would like to use all native code in my application to preserve the Java
portability.  Any suggestions? -cheers, Dave


-- 
David Austin Nix, PhD
University of California at Berkeley
Lawrence Berkeley National Lab
Mailstop 84-171
One Cyclotron Road
Berkeley, CA  94720-3200

510-486-6791 (lab)
510-786-549-0137 (fax)
Nix at uclink.berkeley.edu