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JAligner is an open source Java implementation of the Smith-Waterman algorithm with Gotoh's improvement for biological local pairwise sequence alignment using the affine gap penalty model. It was written by Ahmed Moustafa.
- Smith TF and Waterman MS (1981). Identification of common molecular subsequences. J Mol Biol, 147:195-197.
- Gotoh O (1982). An improved algorithm for matching biological sequences. J Mol Biol, 162:705-708.
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