mmseqs2 ☆
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Description:
Software suite for very fast sequence search and clustering
Type: Formula  |  Latest Version: 18-8cc5c@0  |  Tracked Since: Dec 28, 2025
Links: Homepage  |  @mmseqs2  |  formulae.brew.sh
Category: Other
Tags: bioinformatics sequence-alignment genomics proteomics clustering
Install: brew install mmseqs2
About:
MMseqs2 (Many-to-Many sequence search) is an ultra-fast software suite for protein sequence search and clustering. It leverages accelerated computing to outperform BLAST by orders of magnitude, making it ideal for large-scale biological datasets. The tool utilizes multithreading and SIMD vectorization to deliver sensitive and rapid results.
Key Features:
  • Extreme speed (up to 10,000x faster than BLAST)
  • Sensitive profile-based search (HHsearch/MMseqs2 alignment)
  • Efficient clustering algorithms (Linclust)
  • Low memory footprint options
Use Cases:
  • Large-scale protein database searching (e.g., UniProt)
  • Genome annotation and taxonomic classification
  • Protein sequence clustering and redundancy reduction
  • Metagenomic sequence analysis
Alternatives:
  • BLAST+ – BLAST is the industry standard but significantly slower for large datasets compared to MMseqs2.
  • DIAMOND – DIAMOND is also a fast BLAST alternative, but MMseqs2 offers a more comprehensive suite including clustering and profile search.
Version History
Detected Version Rev Change Commit
Sep 16, 2025 6:11am 18-8cc5c 0 VERSION_BUMP b2256b64
Sep 14, 2024 4:34am 15-6f452 0 VERSION_BUMP a5e91def
Dec 28, 2022 9:05am 14-7e284 0 VERSION_BUMP 62d0fe28
Dec 28, 2022 9:05am 14-7e284 0 VERSION_BUMP 0f2b8a89
Dec 13, 2022 11:11am 14-7e284 0 VERSION_BUMP 1fa8b278
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