HMMER3 is a biosequence analysis software package based on Hidden Markov Models (HMMs). Its core tools include: hmmsearch (searching sequence databases using HMM models), hmmscan (searching HMM databases using sequences), hmmbuild (constructing HMM models from multiple sequence alignments), etc. HMMER3 is more sensitive than BLAST in protein family identification and domain annotation, especially suitable for the detection of distantly related homologous sequences. It is the core engine for the construction and search of protein family databases such as Pfam.