The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences
BLAST
Needle
Needleman-Wunsch global alignment of two sequences
Water
Smith-Waterman local alignment of sequences
Dotmatcher
Draw a threshold dotplot of two sequence
Dotpath
Draw a non-overlapping wordmatch dotplot of two sequences
Dottup
Display a wordmatch dotplot of two sequences
Polydot
Draw dotplots for all-against-all comparison of a sequence set