Open source Java implementation of Smith-Waterman algorithm

[Ahmed Moustafa]

JAligner <http://jaligner.sourceforge.net> 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 
<http://jaligner.sourceforge.net/smith-waterman>.

JAligner is exectuable <http://jaligner.sourceforge.net/jaligner.jnlp> 
through Java Web Start <http://java.sun.com/products/javawebstart>.

Questions, comments and suggestions are welcome.

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

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