1.5

1.5 (April 1994) introduces the new search program hmmsw, and two new styles of model constructed by hmmb. Changes from 1.4:

• hmmsw (Smith/Waterman database searching with HMMs) is now a fully supported program. It now includes all the options that hmmls and hmms do.
• hmmb is expanded to include the new HMM construction rules. hmmb -q constructs ``shepherd'' hidden Markov models from an alignment, compensating for biased sequence representation in the training dataset. hmmb -w uses the Sonnhammer sequence weighting algorithm to compensate for biased representation.
• The sorry excuse for a user guide, userguide.ps, is updated to reflect the hmmsw and hmmb additions.
• Several minor bugs and portability problems have been fixed.