Wikipedia
BFAST
BFAST is a universal DNA sequence aligner tool developed at UCLA by Nils Homer.
The BFAST Web Server is a user-friendly way to quickly align short reads to reference sequences in both nucleotide space as well as ABI SOLiD color space.
Utilities include BFAST alignment, conversion between nucleotide and color space, calculating the a priori power of the alignments, as well as a utility to perform smith-waterman local alignment.