# 使用 Homebrew, Nix 安装 trimal

查看 trimal 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:trimal
```

其他安装命令:

### macOS

- Homebrew (100%):

```sh
brew install trimal
```

  证据: local Homebrew formula metadata

### Linux

- Nix (92%):

```sh
nix profile install nixpkgs#trimal
```

  证据: nixpkgs package indexes: pkgs/by-name/tr/trimal/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:trimal
- **软件包管理器:** Homebrew
- **软件包管理器页面:** <https://formulae.brew.sh/formula/trimal>
- **版本:** 1.5.1
- **来源摘要:** Automated alignment trimming in large-scale phylogenetic analyses
- **主页:** <https://trimal.readthedocs.io/>
- **仓库:** <https://github.com/inab/trimal>
- **上游文档:** <https://trimal.readthedocs.io/>
- **许可证:** GPL-3.0-only
- **源码归档:** <https://github.com/inab/trimal/archive/refs/tags/v1.5.1.tar.gz>
- **最后更新:** 2026-06-14T15:13:52+02:00
- **已生成:** 2026-07-08T18:08:21+00:00

## 可执行文件

- readal (cli)
- statal (cli)
- trimal (cli)
- readal (别名)
- statal (别名)
- trimal (别名)

## 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: 1.5.1
- 管理器更新时间: 2026-06-14
- 本地数据: OK
- 上游仓库: https://github.com/inab/trimal
- 检测到的最新版本: v1.5.1 (当前)
## 项目历史与用法

trimAl is a bioinformatics command-line tool for automated trimming of multiple sequence alignments before phylogenetic analysis. Its package history is rooted in reproducible scientific pipelines: remove unreliable columns or sequences, then feed cleaner alignments into downstream tree-building tools.

### 项目历史

The trimAl documentation describes the tool as software for automatically removing spurious sequences or poorly aligned regions from a multiple sequence alignment. It can select reliable positions using gap proportion, residue similarity, consistency across multiple alignments, or manual column and sequence selections.

The official documentation cites the 2009 Bioinformatics paper 'trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses' by Capella-Gutiérrez, Silla-Martínez, and Gabaldón, establishing the tool's origin in large-scale phylogenetics rather than general text processing.

### 采用历史

trimAl's adoption came from computational biology workflows that needed a command-line way to standardize alignment trimming across many datasets. The documentation's examples and installation flow assume shell use, compiled binaries, and repeatable invocations over input/output alignment files.

Homebrew and Nix packaging matter because biology users often need the same tools on lab Macs, Linux workstations, and cluster login nodes. Packaging `trimal`, `readal`, and `statal` makes the workflow easier to reproduce without manual source builds.

### 使用方式

The basic pattern is `trimal -in <inputfile> -out <outputfile> -<trimming_method>`. The official usage page documents supported input formats such as clustal, fasta, nexus, phylip, and pir, plus output conversion, HTML reports, statistics, backtranslation, and automated methods including `-gappyout`, `-strict`, `-strictplus`, and `-automated1`.

The algorithm documentation separates manual column selection, threshold-based trimming, overlap trimming for incomplete sequences, and automated methods. This makes trimAl useful both for quick pipeline defaults and for explicit, paper-method-style parameter reporting.

### 为什么软件包爱好者会关心

For package nerds, trimAl is the kind of small scientific binary that keeps old-school Unix bioinformatics alive: it has named executables, stable flags, plain files in and out, and no service layer.

It is also historically relevant because its value is not novelty UI but repeatability. A package-manager install lets researchers pin a formula or derivation and rerun phylogenetic trimming methods consistently across datasets.

### 时间线

- 2009: trimAl paper published in Bioinformatics for automated alignment trimming in large-scale phylogenetic analyses.
- Current docs: Version 1.5.1 binaries and source builds are documented for Linux, macOS, and Windows.
- Current docs: trimAl/readAl installation check uses example alignments from the dataset directory.
- Current docs: Usage documents manual, threshold, overlap, and automated trimming methods.

### Related projects

- Related tools and concepts include readAl, statAl, multiple sequence alignment formats, phylogenetic tree reconstruction, gap/similarity/consistency scoring, and downstream maximum-likelihood or neighbor-joining workflows.

### 来源

- <https://trimal.readthedocs.io/>
- <https://trimal.readthedocs.io/en/latest/algorithms.html>
- <https://trimal.readthedocs.io/en/latest/installation.html>
- <https://trimal.readthedocs.io/en/latest/usage.html>


## 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:** trimal
- **Version Scheme:** 0
- **Revision:** 0
- **Head Version:** HEAD
- **Bottle Stable Root URL:** <https://ghcr.io/v2/homebrew/core>
- **Deprecated:** no
- **Disabled:** no
- **Keg Only:** no
- **URL Keys:** head, stable

## 其他软件包管理器记录

- Nix - trimal: normalized package name match | nixpkgs package indexes: pkgs/by-name/tr/trimal/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1


## 相关链接

- [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.
- [Homebrew utility packages](https://www.automicvault.com/zh-hans/pkg/brew-utility-packages/) - Matched Homebrew package provider.
- [fastme](https://www.automicvault.com/zh-hans/pkg/brew/fastme/) - Shares av.db curated category or tags: bioinformatics, cli, phylogenetics, science.
- [paml](https://www.automicvault.com/zh-hans/pkg/brew/paml/) - Shares av.db curated category or tags: bioinformatics, cli, phylogenetics, science.
- [veryfasttree](https://www.automicvault.com/zh-hans/pkg/brew/veryfasttree/) - Shares av.db curated category or tags: bioinformatics, cli, phylogenetics, science.
- [abpoa](https://www.automicvault.com/zh-hans/pkg/brew/abpoa/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequence-alignment.
- [blast](https://www.automicvault.com/zh-hans/pkg/brew/blast/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequence-alignment.
- [bwa](https://www.automicvault.com/zh-hans/pkg/brew/bwa/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequence-alignment.
- [diamond](https://www.automicvault.com/zh-hans/pkg/brew/diamond/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequence-alignment.
- [hmmer](https://www.automicvault.com/zh-hans/pkg/brew/hmmer/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequence-alignment.

## Combined YAML source

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