hmmgen generates a hidden Markov model for each alignment in a directory.

Here is a sample session with hmmgen:

% hmmgen

Mandatory qualifiers:

-infpath (string)

Location of sequence alignment files (input).

-infextn (string)

Extension of sequence alignment files.

-outfpath (string)

Location of HMM files (output).

-outfextn (string)

Extension of HMM files.