"Wise2 is package that is focused on comparing DNA sequences at the level of its conceptual translation, regardless of sequencing error and introns. This really is a rewrite of the old wisetools package, which I wrote about 3 years ago. It can compare a single protein or a profile HMM to a genomic DNA sequence, and predict a gene structure. This is algorithm, called genewise, is one of the algorithms available in Wise2. There are other algorithms focused on EST data rather than genomic data, as well as some other algorithm curios." - from the web site (Ewan Birney)