JAligner is an open source
Java
Java (; id, Jawa, ; jv, ꦗꦮ; su, ) is one of the Greater Sunda Islands in Indonesia. It is bordered by the Indian Ocean to the south and the Java Sea to the north. With a population of 151.6 million people, Java is the world's mos ...
implementation of the
Smith-Waterman algorithm 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
This list of sequence alignment software is a compilation of software tools and web portals used in pairwise sequence alignment and multiple sequence alignment. See structural alignment software for structural alignment of proteins.
Database searc ...
*
Clustal
Clustal is a series of widely used computer programs used in bioinformatics for multiple sequence alignment. There have been many versions of Clustal over the development of the algorithm that are listed below. The analysis of each tool and its ...
References
External links
Official website
{{bioinformatics-stub
Phylogenetics software