macOS
Homebrewverified · 100%
brew install mmseqs2local Homebrew formula metadata
brew / rank 2667
Install mmseqs2 with Homebrew, apt, Nix
Software suite for very fast sequence search and clustering. Version 18-8cc5c via Homebrew; verified from local package data. Also installable with debian: sudo apt install mmseqs2.
install
Additional install commands
Linux
Debian aptverified · 92%
sudo apt install mmseqs2Debian stable package indexes · mmseqs2 · source: deb.debian.org
Nixverified · 92%
nix profile install nixpkgs#mmseqs2nixpkgs package indexes · pkgs/by-name/mm/mmseqs2/package.nix · source: api.github.com
overview
Package summary
Software suite for very fast sequence search and clustering
Project links
Commands and aliases
- mmseqs
history
Project history and usage
MMseqs2, short for Many-against-Many sequence searching, is a bioinformatics suite from Martin Steinegger, Johannes Soding, and collaborators for searching and clustering very large protein and nucleotide sequence sets. The project README describes it as open-source C++ software for Linux, macOS, and Windows via Cygwin, built for multicore and multi-server scalability. Its 2017 Nature Biotechnology paper introduced MMseqs2 as a sensitive protein sequence search tool for massive datasets, and the project documentation frames it as much faster than BLAST while preserving high sensitivity at practical search settings.
Project history
Its major technical milestones followed the growth of public sequence databases. The 2018 Nature Communications Linclust paper integrated a linear-time clustering workflow into MMseqs2, demonstrating clustering of 1.6 billion metagenomic protein fragments in 10 hours on a single server and showing why quadratic or near-quadratic approaches such as CD-HIT and UCLUST struggled at that scale. A 2019 Bioinformatics paper expanded the ecosystem with an MMseqs2 desktop and local web-server app for interactive searches through custom protein sequence and profile databases, reducing query overhead and exposing MMseqs2 to users outside command-line-only workflows.
How it is used
In practice, users run the `mmseqs` executable as a suite of modules and workflows: creating MMseqs2 databases from FASTA or FASTQ, running `easy-search` for sequence search, `easy-cluster` for cascaded clustering, `easy-linclust` for larger datasets, converting alignment results, and using GPU-backed search modes where available. Its package-manager niche is scientific computing rather than general CLI tooling: Homebrew, Debian, Ubuntu, and Nix packages make a research-grade sequence analysis engine available to workstation and server users without building the full C++ stack by hand.
Sources
security posture
Risk level: orange
infrastructure mutation or orchestration signal.
Risk classifier
orange risk · medium confidence · infrastructure
Why
- infrastructure mutation or orchestration signal
Signals
- text:cluster
Install behavior
- No Homebrew bottle metadata was recorded.
Recommended review
Before unattended agent use, check whether the tool reads plaintext credentials, writes remote state, publishes artifacts, or shells out to plugins.
executables
Installed executables
| Command | Kind | Exposure | Note |
|---|---|---|---|
mmseqs | executable | indexed executable | Discovered from the local executable index. |
freshness
Version and freshness
These signals separate page generation age, package-manager activity, and upstream release comparison. Version lag is warned only when an evidence URL and comparable versions are present.
page generated2026-08-03
manager version18-8cc5c
manager updated
local dataunknown
upstreamnot available
latest detectednot detected
- okNo freshness warnings were generated.
install metadata
Package metadata
| Package key | brew:mmseqs2 |
|---|---|
| Version | 18-8cc5c |
| Package manager | Homebrew |
| Homepage | https://mmseqs.com/ |
| Repository | https://github.com/soedinglab/MMseqs2 |
| Bottle | not recorded |
| Service | none declared |
source database matches
Other package-manager records
Matches are pulled from external package-manager indexes and kept separate from local Automic Vault package links.
Debian apt95%
mmseqs2 15-6f452+ds-2+b3
ultra fast and sensitive protein search and clustering
https://github.com/soedinglab/MMseqs2
sudo apt install mmseqs2- Section: science
- Architecture: amd64
- Source Package: mmseqs2
- 8 dependencies
- normalized package name match
- Matched by: Mmseqs2
Debian apt95%
mmseqs2-examples 15-6f452+ds-2
optional resources for the mmseqs2 package
https://github.com/soedinglab/MMseqs2
sudo apt install mmseqs2-examples- Section: science
- Architecture: all
- Source Package: mmseqs2
- 1 optional deps
- normalized package name match
- Matched by: Mmseqs2
Nix95%
mmseqs2
nix profile install nixpkgs#mmseqs2- normalized package name match
- Matched by: Mmseqs2
Ubuntu apt95%
mmseqs2 15-6f452+ds-2
ultra fast and sensitive protein search and clustering
https://github.com/soedinglab/MMseqs2
sudo apt install mmseqs2- Section: universe/science
- Architecture: amd64
- 8 dependencies
- normalized package name match
- Matched by: Mmseqs2
Ubuntu apt95%
mmseqs2-examples 15-6f452+ds-2
optional resources for the mmseqs2 package
https://github.com/soedinglab/MMseqs2
sudo apt install mmseqs2-examples- Section: universe/science
- Architecture: all
- Source Package: mmseqs2
- 1 optional deps
- normalized package name match
- Matched by: Mmseqs2
source trail
Generated from repository data
This page is generated by av-web from the private package SQLite artifact built by scripts/generate-pkg-sqlite.py.
Combined YAML source
View the package source record on GitHub.
Used sources
- Geiger risk classifier
- cross-ecosystem install command graph
- curated package history
- external package-manager database matches
- pkg.so package database
- pkgdb category and tag curation