bookmark HMMER Finds evolutionarily related proteins and/or domains, close and remote homologs. HMMER is based on profile hidden Markov models (HMMs) and gathers four algorithms: phmmer, hmmscan, hmmsearch, and jackhmmer. It assists users in the detection of protein sequence conservation, function, and evolution. This tool can be useful for functional annotations. It offers a solution to make research on protein sequence databases.