Fastahardmask is a utility which allows to convert lower case characters to *N*s
Parent program: exonerate
Exonerate performs various forms of alignment including Smith-Waterman-Gotoh of DNA or protein against a reference. It uses bounded sparse dynamic programming (BSDP) - a novel heuristic for sequence alignment. Exonerate is written in C, and currently uses the glib library for portablility. It can produce either gapped or ungapped alignments, according to a variety of different alignment models. The C4 library allows sequence alignment using a reduced space full dynamic programming implementation, but also allows automated generation of heuristics from the alignment models, using bounded sparse dynamic programming, so that these alignments may also be rapidly generated. Alignments generated using these heuristics will represent a valid path through the alignment model, yet (unlike the exhaustive alignments), the results are not guaranteed to be optimal.