# 使用 Homebrew, apt, Nix 安装 mmseqs2
查看 mmseqs2 的安装路径、可执行文件、元数据以及面向 AI 代理工作流的安全说明。
## 安装
```sh
sudo av install brew:mmseqs2
```
其他安装命令:
### macOS
- Homebrew (100%):
```sh
brew install mmseqs2
```
证据: local Homebrew formula metadata
### Linux
- Debian apt (92%):
```sh
sudo apt install mmseqs2
```
证据: 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
```
证据: nixpkgs package indexes: pkgs/by-name/mm/mmseqs2/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1
## 软件包事实
- **软件包键:** brew:mmseqs2
- **软件包管理器:** Homebrew
- **版本:** 18-8cc5c
- **来源摘要:** Software suite for very fast sequence search and clustering
- **主页:**
- **仓库:**
- **已生成:** 2026-08-03T19:37:03+00:00
## 可执行文件
- mmseqs (别名)
## 安装行为
- Bottle: 不可用
## 版本和新鲜度
- 页面生成时间: 2026-08-03
- 管理器版本: 18-8cc5c
## 项目历史与用法
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.
### 项目历史
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.
### 使用方式
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.
### 来源
-
-
-
-
-
-
## 安全说明
infrastructure mutation or orchestration signal.
- **Geiger 风险:** orange / 中
- infrastructure mutation or orchestration signal
## 其他软件包管理器记录
- 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)
## 来源
- 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