nhmmer
nhmmer is a command-line program used for sequence similarity searching. It is part of the HMMER software package, which is designed for searching biological sequence databases using profile hidden Markov models (profile HMMs). Profile HMMs are statistical models that represent a family of related protein or nucleotide sequences, capturing conserved patterns and evolutionary relationships.
The primary function of nhmmer is to compare a query sequence against a database of profile HMMs.
The program works by scoring the query sequence against each profile HMM in the database. Sequences that