# 使用 Homebrew, apt, Nix 安装 kalign

查看 kalign 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:kalign
```

其他安装命令:

### macOS

- Homebrew (100%):

```sh
brew install kalign
```

  证据: local Homebrew formula metadata

### Linux

- Debian apt (92%):

```sh
sudo apt install kalign
```

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

- Nix (92%):

```sh
nix profile install nixpkgs#kalign
```

  证据: nixpkgs package indexes: pkgs/by-name/ka/kalign/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:kalign
- **软件包管理器:** Homebrew
- **软件包管理器页面:** <https://formulae.brew.sh/formula/kalign>
- **版本:** 3.5.1
- **来源摘要:** Fast multiple sequence alignment program for biological sequences
- **主页:** <https://github.com/TimoLassmann/kalign>
- **仓库:** <https://github.com/TimoLassmann/kalign>
- **上游文档:** <https://github.com/TimoLassmann/kalign#readme>
- **许可证:** Apache-2.0
- **源码归档:** <https://github.com/TimoLassmann/kalign/archive/refs/tags/v3.5.1.tar.gz>
- **已生成:** 2026-07-08T18:08:21+00:00

## 可执行文件

- kalign (cli)
- kalign (别名)

## 依赖

- libomp

## 构建依赖

- cmake

## 安装行为

- post-install 钩子: 未定义
- Bottle: 可用 于 arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux

## 版本和新鲜度

- 页面生成时间: 2026-07-08
- 管理器版本: 3.5.1
- 本地数据: OK
- 上游仓库: https://github.com/TimoLassmann/kalign
- 检测到的最新版本: v3.5.1 (当前)
- 信息: No package-manager update timestamp was available.
## 项目历史与用法

Kalign is a fast multiple-sequence-alignment program for protein, DNA, and RNA sequences, distributed as a command-line bioinformatics tool.

### 项目历史

Timo Lassmann and Erik Sonnhammer published the original Kalign method in BMC Bioinformatics on 2005-12-12. The paper described a Wu-Manber-based progressive alignment method intended to improve both speed and accuracy for large comparative-genomics workloads.

### 采用历史

Kalign remained in the bioinformatics toolchain because multiple sequence alignment is a routine upstream step for homology, conserved-motif, phylogeny, and structure-oriented analyses. Kalign 3, published in Bioinformatics in 2019, was presented as a complete rewrite to handle larger protein and nucleotide sequence sets, using SIMD-accelerated distance estimation and fast guide-tree construction.

### 使用方式

Users run kalign on FASTA-like biological sequence inputs to produce multiple alignments. The modern README describes progressive alignment with multi-threading support, source builds with CMake, and alternatives such as Zig builds and Python packaging.

### 为什么软件包爱好者会关心

Kalign is a classic science CLI package: a published algorithm wrapped in a small executable, useful in scripts and pipelines, with package-manager availability making a cited method reproducible without hand-building a lab-specific binary.

### 时间线

- 2005-12-12: Original Kalign paper published in BMC Bioinformatics.
- 2019-10-26: Kalign 3 paper published in Bioinformatics.
- 2019-10-28: GitHub release 3.1 published.
- 2020-11-06: v3.3 release added multi-threading.
- 2026-02-27: Kalign 3.5.1 published.

### Related projects

- Related multiple-sequence-alignment tools include ClustalW, MAFFT, MUSCLE, T-Coffee, and other progressive or consistency-based MSA programs.

### 来源

- <https://academic.oup.com/bioinformatics/article/36/6/1928/5607735>
- <https://api.github.com/repos/TimoLassmann/kalign/releases?per_page=100>
- <https://github.com/TimoLassmann/kalign>
- <https://link.springer.com/article/10.1186/1471-2105-6-298>


## 安全说明

narrow executable package without higher-risk signals.

- **Geiger 风险:** 绿色 / 低
- narrow executable package without higher-risk signals

## 源数据库详情

- **Source Database:** Homebrew formula API
- **Tap:** homebrew/core
- **Full Name:** kalign
- **Version Scheme:** 0
- **Revision:** 0
- **Bottle Stable Root URL:** <https://ghcr.io/v2/homebrew/core>
- **Deprecated:** no
- **Disabled:** no
- **Keg Only:** no
- **URL Keys:** stable

## 其他软件包管理器记录

- Debian apt - kalign - 1:3.4.0-1+b3: normalized package name match | Debian stable package indexes: kalign from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | Global and progressive multiple sequence alignment | https://msa.sbc.su.se/
- Nix - kalign: normalized package name match | nixpkgs package indexes: pkgs/by-name/ka/kalign/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1
- Ubuntu apt - kalign - 1:3.3.5-1: normalized package name match | Ubuntu 24.04 LTS package indexes: kalign from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | Global and progressive multiple sequence alignment | https://msa.sbc.su.se/


## 相关链接

- [Source-control packages](https://www.automicvault.com/zh-hans/pkg/source-control-tools/) - Belongs to a source-control command family.
- [Terminal utility packages](https://www.automicvault.com/zh-hans/pkg/terminal-utilities/) - Matched terminal and command-line workflow metadata.
- [Networking and protocol packages](https://www.automicvault.com/zh-hans/pkg/networking-protocol-tools/) - Matched network, protocol, or remote-service metadata.
- [Scientific computing packages](https://www.automicvault.com/zh-hans/pkg/scientific-computing-tools/) - Matched scientific computing metadata.
- [cmake](https://www.automicvault.com/zh-hans/pkg/brew/cmake/) - Build dependency declared by Homebrew.
- [bbtools](https://www.automicvault.com/zh-hans/pkg/brew/bbtools/) - Shares av.db curated category or tags: bioinformatics, cli, dna, rna, science.
- [mummer](https://www.automicvault.com/zh-hans/pkg/brew/mummer/) - Shares av.db curated category or tags: bioinformatics, cli, dna, protein, science.
- [breseq](https://www.automicvault.com/zh-hans/pkg/brew/breseq/) - Shares av.db curated category or tags: bioinformatics, cli, dna, science.
- [bwa](https://www.automicvault.com/zh-hans/pkg/brew/bwa/) - Shares av.db curated category or tags: bioinformatics, cli, dna, science.
- [jellyfish](https://www.automicvault.com/zh-hans/pkg/brew/jellyfish/) - Shares av.db curated category or tags: bioinformatics, cli, dna, science.
- [lastz](https://www.automicvault.com/zh-hans/pkg/brew/lastz/) - Shares av.db curated category or tags: bioinformatics, cli, dna, science.
- [minimap2](https://www.automicvault.com/zh-hans/pkg/brew/minimap2/) - Shares av.db curated category or tags: bioinformatics, cli, dna, science.
- [paml](https://www.automicvault.com/zh-hans/pkg/brew/paml/) - Shares av.db curated category or tags: bioinformatics, cli, dna, science.
- [seqtk](https://www.automicvault.com/zh-hans/pkg/brew/seqtk/) - Local package facts share a topical domain. Shared terms: analysis, bioinformatics, cli, science, sequence.

## Combined YAML source

View the package source record on GitHub. [combined/kalign.yml](https://github.com/automic-vault/db/blob/main/combined/kalign.yml)


## 来源

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