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brew

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.

Install commandSecurity notes

install

Additional install commands

macOS

Homebrewverified · 100%
brew install mmseqs2

local Homebrew formula metadata

Linux

Debian aptverified · 92%
sudo apt install mmseqs2

Debian stable package indexes · mmseqs2 · source: deb.debian.org

Nixverified · 92%
nix profile install nixpkgs#mmseqs2

nixpkgs 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

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.

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 post-install hook is recorded in formula metadata.
  • Homebrew bottle metadata is available for 6 platform targets.
  • Installs with 2 runtime dependencies.
  • Build metadata lists 1 build dependencies.

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

CommandKindExposureNote
mmseqscliglobal executable

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 generated2026-07-08
manager version18-8cc5c
manager updated
local dataok
upstreamnot checked
latest detectednot detected

https://github.com/soedinglab/MMseqs2

install metadata

Package metadata

Package keybrew:mmseqs2
Version18-8cc5c
Package managerHomebrew
Package manager pagehttps://formulae.brew.sh/formula/mmseqs2
Homepagehttps://mmseqs.com/
Repositoryhttps://github.com/soedinglab/MMseqs2
Upstream docshttps://github.com/soedinglab/MMseqs2/blob/master/README.md
LicenseMIT
Source archivehttps://github.com/soedinglab/MMseqs2/archive/refs/tags/18-8cc5c.tar.gz
Dependencieslibomp, wget
Build dependenciescmake
Uses from macOSbzip2
Bottleavailable (on arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux)
Homebrew post-installnot defined
Servicenone declared

registry facts

Source database details

Source DatabaseHomebrew formula API
Taphomebrew/core
Full Namemmseqs2
Version Scheme0
Revision0
Head VersionHEAD
Bottle Stable Root URLhttps://ghcr.io/v2/homebrew/core
Deprecatedno
Disabledno
Keg Onlyno
URL Keys
  • head
  • stable

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 stable package indexes · deb.debian.org · Debian stable package indexes: mmseqs2 from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz
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
Debian stable package indexes · deb.debian.org · Debian stable package indexes: mmseqs2-examples from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz
Nix95%

mmseqs2

nix profile install nixpkgs#mmseqs2
  • normalized package name match
  • Matched by: Mmseqs2
nixpkgs package indexes · api.github.com · nixpkgs package indexes: pkgs/by-name/mm/mmseqs2/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1
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 24.04 LTS package indexes · archive.ubuntu.com · Ubuntu 24.04 LTS package indexes: mmseqs2 from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz
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
Ubuntu 24.04 LTS package indexes · archive.ubuntu.com · Ubuntu 24.04 LTS package indexes: mmseqs2-examples from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz

package graph

Links come from deterministic package relationships, av.db category and tag curation, ecosystem matches, and package hub membership.

Related tools

  • wgetRuntime dependency declared by Homebrew.
  • cmakeBuild dependency declared by Homebrew.

Same workflow

  • hmmerShares av.db curated category or tags: bioinformatics, cli, science, sequence-analysis, sequence-search.
  • seqkitShares av.db curated category or tags: bioinformatics, cli, science, sequence-analysis.
  • seqtkShares av.db curated category or tags: bioinformatics, cli, science, sequence-analysis.
  • kraken2Shares av.db curated category or tags: bioinformatics, cli, metagenomics, science.
  • pamlShares av.db curated category or tags: bioinformatics, cli, protein-sequences, science.
  • ropebwt3Shares av.db curated category or tags: bioinformatics, cli, science, sequence-search.

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.

Used sources

  • Geiger risk classifier
  • Nucleus package database
  • av.db category and tag curation
  • cross-ecosystem install command graph
  • curated package history
  • external package-manager database matches
  • package relationship graph
  • package version freshness
  • package-page enrichment