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