JAligner (http://jaligner.sourceforge.net) is an open source Java
implementation of the Smith-Waterman algorithm with Gotoh's improvement
for biological pairwise sequence alignment using the affine gap penalty
model.
Version 0.9 includes:
- adding more output alignment formats CLUSTAL and FASTA (beside Pair),
- user-interface enhancements, and
- source code refactoring for design patterns
Ahmed Moustafa
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