JAligner

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. Is was written by Ahmed Moustafa.

See also

* Sequence alignment software
* Clustal

References

External links

* [http://jaligner.sourceforge.net/ Official website]


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