hmmer ☆
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Description:
Build profile HMMs and scan against sequence databases
Type: Formula  |  Tracked Since: Dec 28, 2025
Links: Homepage  |  formulae.brew.sh
Category: Other
Tags: bioinformatics sequence-analysis hmm genomics computational-biology
Install: brew install hmmer
About:
HMMER is a widely used software suite for sequence analysis using profile hidden Markov models (profile HMMs). It enables researchers to build probabilistic models from multiple sequence alignments and scan them against databases to find homologous sequences with high sensitivity.
Key Features:
  • Profile HMM construction and calibration
  • High-sensitivity sequence database scanning
  • Multiple sequence alignment analysis
  • Statistical significance evaluation (E-values)
Use Cases:
  • Identifying remote protein homologs in database searches
  • Building custom domain models for gene family analysis
  • Functional annotation of newly sequenced genomes
Alternatives:
  • BLAST – BLAST is faster but less sensitive for detecting remote homologs compared to HMMER's profile HMMs
  • HHsearch – HHsearch uses HMM-HMM comparison; both are sensitive but HMMER is more widely adopted for standard profile searches
Version History
Detected Version Rev Change Commit
Sep 13, 2024 9:15pm 0 VERSION_BUMP 28c6544e
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