|   | HMM | 
Hidden markov model analysis
| 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 |