Program name	Description
oalistat	Statistics for multiple alignment files
ohmmalign	Align sequences with an HMM
ohmmbuild	Build HMM
ohmmcalibrate	Calibrate a hidden Markov model
ohmmconvert	Convert between HMM formats
ohmmemit	Extract HMM sequences
ohmmfetch	Extract HMM from a database
ohmmindex	Index an HMM database
ohmmpfam	Align single sequence with an HMM
ohmmsearch	Search sequence database with an HMM
ehmmalign	Align sequences to an HMM profile
ehmmbuild	Build a profile HMM from an alignment
ehmmcalibrate	Calibrate HMM search statistics
ehmmconvert	Convert between profile HMM file formats
ehmmemit	Generate sequences from a profile HMM
ehmmfetch	Retrieve an HMM from an HMM database
ehmmindex	Create a binary SSI index for an HMM database
ehmmpfam	Search one or more sequences against an HMM database
ehmmsearch	Search a sequence database with a profile HMM