# 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

```sh
sudo av install brew:mmseqs2
```

Additional install commands:

### macOS

- Homebrew (100%):

```sh
brew install mmseqs2
```

  Evidence: local Homebrew formula metadata

### Linux

- Debian apt (92%):

```sh
sudo apt install mmseqs2
```

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

- Nix (92%):

```sh
nix profile install nixpkgs#mmseqs2
```

  Evidence: nixpkgs package indexes: pkgs/by-name/mm/mmseqs2/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1

## Package facts

- **Package key:** brew:mmseqs2
- **Package manager:** Homebrew
- **Version:** 18-8cc5c
- **Source summary:** Software suite for very fast sequence search and clustering
- **Homepage:** <https://mmseqs.com/>
- **Repository:** <https://github.com/soedinglab/MMseqs2>
- **Generated:** 2026-08-03T19:37:03+00:00

## Executables

- mmseqs (alias)

## Install behavior

- Bottle: not available

## Freshness

- Page generated: 2026-08-03
- Package-manager version: 18-8cc5c
## 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

- <https://academic.oup.com/bioinformatics/article/35/16/2856/5280135>
- <https://formulae.brew.sh/formula/mmseqs2>
- <https://github.com/soedinglab/MMseqs2>
- <https://github.com/soedinglab/MMseqs2/wiki>
- <https://www.nature.com/articles/nbt.3988>
- <https://www.nature.com/articles/s41467-018-04964-5>


## Security Notes

infrastructure mutation or orchestration signal.

- **Geiger risk:** orange / medium
- infrastructure mutation or orchestration signal

## Other Package-Manager Records

- Debian apt - mmseqs2 - 15-6f452+ds-2+b3: normalized package name match | Debian stable package indexes: mmseqs2 from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | ultra fast and sensitive protein search and clustering | https://github.com/soedinglab/MMseqs2
- Debian apt - mmseqs2-examples - 15-6f452+ds-2: normalized package name match | Debian stable package indexes: mmseqs2-examples from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | optional resources for the mmseqs2 package | https://github.com/soedinglab/MMseqs2
- Nix - mmseqs2: normalized package name match | nixpkgs package indexes: pkgs/by-name/mm/mmseqs2/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1
- Ubuntu apt - mmseqs2 - 15-6f452+ds-2: normalized package name match | Ubuntu 24.04 LTS package indexes: mmseqs2 from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | ultra fast and sensitive protein search and clustering | https://github.com/soedinglab/MMseqs2
- Ubuntu apt - mmseqs2-examples - 15-6f452+ds-2: normalized package name match | Ubuntu 24.04 LTS package indexes: mmseqs2-examples from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | optional resources for the mmseqs2 package | https://github.com/soedinglab/MMseqs2


## Combined YAML source

View the package source record on GitHub. [combined/mmseqs2.yml](https://github.com/mxcl/pkgdb/blob/main/combined/mmseqs2.yml)


## Sources

- pkg.so package database
- Geiger risk classifier
- curated package history
- pkgdb category and tag curation
- external package-manager database matches
- cross-ecosystem install command graph