Wise (GeneWise) is a package focused on comparisons of bio polymers, commonly DNA sequence and protein sequence. There are many other packages which do this, probably the best known being BLAST package (from NCBI) and the FASTA package (from Bill Pearson). There are other packages, such as the HMMER package (Sean Eddy) or SAM package (UC Santa Cruz) focused on hidden Markov models (HMMs) of bio polymers.
Ewan Birney , Richard Copley
:: MORE INFORMATION
Birney, E.; Durbin, R. (2000)
Using GeneWise in the Drosophila annotation experiment
Genome research 10 (4): 547–548.
Birney, E.; Clamp, M.; Durbin, R. (2004)
GeneWise and Genomewise
Genome Research 14 (5): 988–995.