MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. This package provides an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools.
percent identity plot (bot) compared with gene models (top)
percent-identity color coded dotplot of a promer alignment
unordered multiplot of finished vs. draft sequence alignment
ordered and oriented multiplot of finished vs. draft seqs