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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.
Sean Eddy
Mon Apr 17 09:54:19 CDT 1995