JAligner

JAligner is an open source Java implementation of the Smith-Waterman algorithmSmith TF and Waterman MS (1981). Identification of common molecular subsequences. J Mol Biol, 147:195-197. with Gotoh's improvementGotoh 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.