HMMER is a C toolkit for biological sequence analysis using profile hidden Markov models (profile HMMs). It is widely used for protein and DNA homology search and is the engine behind Pfam, InterPro, and many large-scale annotation pipelines. The package is a collection of command-line programs (phmmer, jackhmmer, hmmsearch, hmmscan, nhmmer, nhmmscan, hmmbuild, hmmalign, hmmemit, plus utilities).