# trimal を Homebrew, Nix でインストール

trimal のインストール経路、実行ファイル、メタデータ、AI エージェント向けセキュリティノートを確認します。

## インストール

```sh
sudo av install brew:trimal
```

追加のインストールコマンド:

### macOS

- Homebrew (100%):

```sh
brew install trimal
```

  証拠: local Homebrew formula metadata

### Linux

- Nix (92%):

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

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

## パッケージ情報

- **パッケージキー:** brew:trimal
- **パッケージマネージャ:** Homebrew
- **パッケージマネージャページ:** <https://formulae.brew.sh/formula/trimal>
- **バージョン:** 1.5.1
- **ソース概要:** Automated alignment trimming in large-scale phylogenetic analyses
- **ホームページ:** <https://trimal.readthedocs.io/>
- **リポジトリ:** <https://github.com/inab/trimal>
- **上流ドキュメント:** <https://trimal.readthedocs.io/>
- **ライセンス:** GPL-3.0-only
- **ソースアーカイブ:** <https://github.com/inab/trimal/archive/refs/tags/v1.5.1.tar.gz>
- **最終更新:** 2026-06-14T15:13:52+02:00
- **生成日時:** 2026-07-08T18:08:21+00:00

## 実行可能ファイル

- readal (cli)
- statal (cli)
- trimal (cli)
- readal (エイリアス)
- statal (エイリアス)
- trimal (エイリアス)

## インストール挙動

- post-install フック: 未定義
- Bottle: 利用可能 対象 arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux

## バージョンと鮮度

- ページ生成日: 2026-07-08
- マネージャ版: 1.5.1
- マネージャ更新日: 2026-06-14
- ローカルデータ: OK
- 上流リポジトリ: https://github.com/inab/trimal
- 検出された最新: v1.5.1 (最新)
## プロジェクトの歴史と使われ方

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.

### プロジェクトの歴史

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.

### 採用の歴史

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.

### 使われ方

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.

### パッケージ好きにとっての重要性

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.

### タイムライン

- 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.

### ソース

- <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>


## セキュリティノート

narrow executable package without higher-risk signals.

- **Geiger リスク:** グリーン / 低
- narrow executable package without higher-risk signals

## ソースデータベース詳細

- **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

## 他のパッケージマネージャ記録

- 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


## 関連リンク

- [Terminal utility packages](https://www.automicvault.com/ja/pkg/terminal-utilities/) - Matched terminal and command-line workflow metadata.
- [Networking and protocol packages](https://www.automicvault.com/ja/pkg/networking-protocol-tools/) - Matched network, protocol, or remote-service metadata.
- [Scientific computing packages](https://www.automicvault.com/ja/pkg/scientific-computing-tools/) - Matched scientific computing metadata.
- [Homebrew utility packages](https://www.automicvault.com/ja/pkg/brew-utility-packages/) - Matched Homebrew package provider.
- [fastme](https://www.automicvault.com/ja/pkg/brew/fastme/) - Shares av.db curated category or tags: bioinformatics, cli, phylogenetics, science.
- [paml](https://www.automicvault.com/ja/pkg/brew/paml/) - Shares av.db curated category or tags: bioinformatics, cli, phylogenetics, science.
- [veryfasttree](https://www.automicvault.com/ja/pkg/brew/veryfasttree/) - Shares av.db curated category or tags: bioinformatics, cli, phylogenetics, science.
- [abpoa](https://www.automicvault.com/ja/pkg/brew/abpoa/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequence-alignment.
- [blast](https://www.automicvault.com/ja/pkg/brew/blast/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequence-alignment.
- [bwa](https://www.automicvault.com/ja/pkg/brew/bwa/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequence-alignment.
- [diamond](https://www.automicvault.com/ja/pkg/brew/diamond/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequence-alignment.
- [hmmer](https://www.automicvault.com/ja/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)


## ソース

- 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