Open source Java implementation of Smith-Waterman algorithm

Ahmed Moustafa ahmed at
Mon Apr 26 01:48:22 EST 2004

JAligner <> is an open source Java 
implementation of biological sequence alignment algorithms.

Presently, the package provides a clean and efficient implementation the 
pairwise alignment algorithm Smith-Waterman with Gotoh's improvement 

JAligner is exectuable <> 
through Java Web Start <>.

Questions, comments and suggestions are welcome.

Ahmed Moustafa
ahmed [at] users [dot] sourceforge [dot] net


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