...
HMMER is used for searching sequence databases for homologsof homologs of protein sequences, and for making protein sequence alignments. Itimplements It implements methods using probabilistic models called profile hidden Markovmodels Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequencealignment sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remotehomologs remote homologs because of the strength of its underlying mathematical models. In thepastthe past, this strength came at significant computational expense, but in the newHMMER3 new HMMER3 project, HMMER is now essentially as fast as BLAST.
...