HMMER is used for searching sequence databases for homologs of protein sequences,
and for making protein sequence alignments. It implements methods using
probabilistic models called “profile hidden Markov models” (profile HMMs).

Compared to BLAST, FASTA, and other sequence alignment and database search tools
based on older scoring methodology, HMMER aims to be significantly more accurate
and more able to detect remote homologs because of the strength of its underlying
mathematical models.