Allows to compare, align, and assemble large sets of DNA sequences. PHRAP uses a banded version of the Smith-Waterman-Gotoh algorithm to do pairwise comparisons of the sequences. It compares sequences by searching for pairs of perfectly matching “words” or sequence regions that meet criteria, tries to extend the alignment if a match of the designated word size is found and then scores it. The software uses quality values produced by the PHRED basecaller. Cross match/Swat is included in the PHRAP package.