Several new parameters exist. See Section 12 . See Section 10.8.4 . Non-default initial models are no longer printed in model files. Mixtures in the earlier format may crash the program.
Mixture priors are particularly useful in database search from a small set of training examples.
See Section 8.1 . 11.5.10 Version 1.1 November, 1995. The default protein regularizer has been changed from having the uniform distribution in the insert states to having the background distribution. This generally helps discrimination experiments, though may hurt sequence alignment. See Section 8.1 .