Last

LAST is designed for moderately large data (e.g. genomes, DNA reads, proteomes). It's especially good at:

• Finding rearrangements and recombinations: we believe last-split does that more rigorously than anything else.
• Finding DNA-versus-protein related regions, especially protein fossils (but introns are not considered).
• Unusual data, e.g. AT-rich DNA, because we can fit parameters to the data and calculate significance.
• Sensitive DNA-DNA search, due to fitting, sensitive seeding, and calculating significance.

It can also: indicate the confidence/uncertainty of each column in an alignment, and use sequence quality data in a rigorous fashion.