Article · Wikipedia archive · Last revised Jun 2, 2026

JAligner

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.

Last revised
Jun 2, 2026
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JAligner is an open source Java implementation of the Smith-Waterman algorithm1 with Gotoh's improvement2 for biological local pairwise sequence alignment using the affine gap penalty model. It was written by Ahmed Moustafa.

See also

See also

References

References

  1. Smith TF and Waterman MS (1981). Identification of common molecular subsequences. J Mol Biol, 147:195-197.
  2. Gotoh O (1982). An improved algorithm for matching biological sequences. J Mol Biol, 162:705-708.
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