HMMER is a collection of programs that create a hidden Markov model (HMM) of a sequence family which can be utilized as a query against a sequence database to identify (and/or align) additional homologs of the sequence family. HMMER was developed by Sean Eddy at Washington University. For details, see Section 10.1 at the end of this chapter.
Each program and their respective options are listed below. We're using Version 2.2 of HMMER.