JAligner – Java implementation of biological sequence alignment algorithms

JAligner is a Java implementation of biological sequence alignment algorithms. Presently, the package implements the pair wise alignment algorithm Smith-Waterman. The basic Dynamic Programming Smith-Waterman algorithm has been modified to support affine (open and extend) gap penalty. Also, Gotoh’s improvement has been added to the algorithm to maintain the quadratic time complexity.
Find JAligner – Java implementation of biological sequence alignment algorithms at: http://jaligner.sourceforge.net