1.8

1.8 (April 1995) is a fairly major revision. Extensive experimental modifications to the priors are in place. The new features in 1.8 relative to 1.7, in reverse chronological order, are:

• Mixture priors and structure-based mixture priors are now supported. The prior file format has changed.
• Constrained simulated annealing is now available in hmmt, if an alignment is known for a subset of the training sequences.
• Staden experiment files are now supported as an input sequence file format.
• Simulated annealing is now the default in hmmt. You can provide a customized annealing schedule with the -S option.
• Full Baum-Welch expectation maximization is now an option in hmmt. This is for experimental purposes only. Simulated annealing appears superior.
• Profile emulation is available; hmm-convert -P converts an HMM to a reasonable approximation of a GCG profile. These profiles can be run on the Compugen Bioccelerator for very fast approximate HMM searches.
• Linear memory (Myers-Miller) alignment was added in 1.7.4. It takes effect automatically, when needed. The only remaining algorithms suffering from memory limitations are simulated annealing and full Baum-Welch EM.
• An "architectural prior" was added to hmmt and hmmb as a semi-principled way of holding model lengths down.
• Numerous minor bugfixes, fixing all reported bugs.