What HMMs can do for you

Multiple sequence alignment

HMMs can be ``trained'' by a learning procedure, given unaligned example sequences. Typically this is somewhat less effective than building an HMM from a trusted, structurally-based alignment. However, HMM alignments can be quite accurate. This package includes a simulated annealing procedure for training HMMs which has produced alignments quite close to several trusted structural alignments.

Database searching

The real power of HMMs is their sensitivity in database searches. This package includes software for several different searching tasks. The most useful search programs have been the local alignment programs hmmsw and hmmfs.