LAGAN

LAGAN is our highly parametrizable pairwise global alignment program. It takes local alignments generated by CHAOS as anchors, and limits the search area of the Needleman-Wunsch algorithm around these anchors;... CHAOS is a pairwise local aligner optimized for non-coding, and other poorly conserved regions of the genome. It uses both exact matching and degenerate seeds, and is able to find homology in the presence of gaps.