'''JAligner''' is an open source Java implementation of the Smith-Waterman algorithm<ref>Smith TF and Waterman MS (1981). Identification of common molecular subsequences. ''J Mol Biol, 147:195-197''.</ref> with Gotoh's improvement<ref>Gotoh O (1982). An improved algorithm for matching biological sequences. ''J Mol Biol, 162:705-708''.</ref> for biological local pairwise sequence alignment using the affine gap penalty model. It was written by Ahmed Moustafa.
== See also == * Sequence alignment software * Clustal
== References == <references/>
== External links == * [https://jaligner.sourceforge.net/ Official website]
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Category:Phylogenetics software