JAligner is an open source Java implementation of biological sequence
alignment algorithms avaliable at <http://jaligner.sourceforge.net>.
Currently, the package provides a clean and efficient implementation
of the pairwise sequence alignment algorithm Smith-Waterman with
Gotoh's improvement <http://jaligner.sourceforge.net/smith-waterman>.
Questions, comments and suggestions are welcome.
Ahmed Moustafa
ahmed [at] users [dot] sourceforge [dot] net
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