# iqtree3 を Homebrew, MacPorts でインストール

iqtree3 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:iqtree3
```

追加のインストールコマンド:

### macOS

- Homebrew (100%):

```sh
brew install iqtree3
```

  証拠: local Homebrew formula metadata

- MacPorts (94%):

```sh
sudo port install iqtree3
```

  証拠: MacPorts ports tree: science/iqtree3/Portfile from https://api.github.com/repos/macports/macports-ports/git/trees/master?recursive=1

## パッケージ情報

- **パッケージキー:** brew:iqtree3
- **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/iqtree3>
- **バージョン:** 3.1.2
- **ソース概要:** Phylogenetics by maximum likelihood
- **ホームページ:** <http://www.iqtree.org>
- **リポジトリ:** <https://github.com/iqtree/iqtree3>
- **上流ドキュメント:** <https://www.iqtree.org/doc>
- **ライセンス:** GPL-2.0-or-later
- **ソースアーカイブ:** <https://github.com/iqtree/iqtree3/archive/refs/tags/v3.1.2.tar.gz>
- **最終更新:** 2026-06-25T13:37:46+02:00
- **生成日時:** 2026-07-08T18:08:21+00:00

## 実行可能ファイル

- iqtree3 (cli)
- iqtree3 (エイリアス)

## ビルド依存関係

- boost
- cmake
- eigen

## 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: 3.1.2
- マネージャ更新日: 2026-06-25
- ローカルデータ: OK
- 上流リポジトリ: https://github.com/iqtree/iqtree3
- 検出された最新: v3.1.2 (最新)
## プロジェクトの歴史と使われ方

IQ-TREE 3 is the third major generation of the IQ-TREE maximum-likelihood phylogenetic inference software. It packages a command-line engine for tree search, model selection, bootstrap support, topology tests, simulation, and complex evolutionary models used in phylogenomics.

### プロジェクトの歴史

The IQ-TREE README says the software was created as the successor of IQPNNI and TREE-PUZZLE, which explains the name. It was motivated by the growth of phylogenomic data and the need for efficient software that could handle larger alignments and more complex models of sequence evolution.

The first widely cited IQ-TREE paper appeared in 2015, presenting a fast stochastic algorithm for estimating maximum-likelihood phylogenies. The README also points to the 2020 IQ-TREE 2 paper for new models and efficient methods in the genomic era, and the 2026 IQ-TREE 3 citation for complex evolutionary models.

IQ-TREE 3 continues the line in a separate GitHub repository while preserving lineage to IQ-TREE 1 and IQ-TREE 2 releases. Its README highlights features such as ModelFinder, ultrafast bootstrap, partition and mixture models, AliSim, topology tests, checkpointing, multicore execution, and distributed parallel computing.

### 採用の歴史

IQ-TREE was adopted in computational biology because it combined speed, model breadth, and practical command-line ergonomics. Its feature papers for UFBoot, ModelFinder, W-IQ-TREE, IQ-TREE 2, and IQ-TREE 3 document a path from standalone tree search to a broad phylogenomic platform.

The README advertises GitHub release downloads, BioConda installs, web-server access, and package-manager distribution. Homebrew's iqtree3 formula gives macOS command-line users a versioned package for the third major generation.

### 使われ方

Users run iqtree3 on sequence alignments in formats such as PHYLIP, FASTA, Nexus, Clustal, and MSF. Outputs include an .iqtree report and a Newick .treefile that can be viewed in tree visualization tools.

Common workflows include maximum-likelihood tree inference, automatic substitution-model selection, ultrafast bootstrap support analysis, partitioned analyses, mixture models, topology tests, polymorphism-aware models, and alignment simulation.

### パッケージ好きにとっての重要性

IQ-TREE 3 is package-nerd significant because scientific command-line packaging has to preserve exact executable names, citations, bundled model support, OpenMP/MPI-style performance expectations, and reproducible outputs. A package upgrade is not just a binary refresh; it can affect published methods and citation guidance.

It also illustrates the biology-tool pattern where the README is part manual, part citation map, and part dependency history, linking features to papers and predecessor projects.

### タイムライン

- 2013: UFBoot is published as an ultrafast bootstrap approximation associated with IQ-TREE workflows.
- 2015: IQ-TREE version 1 paper presents fast maximum-likelihood phylogeny estimation.
- 2016: W-IQ-TREE web server paper documents online IQ-TREE access.
- 2017: ModelFinder paper documents fast model selection used by IQ-TREE.
- 2020: IQ-TREE 2 paper presents new models and efficient genomic-era methods.
- 2023: AliSim-HPC paper documents parallel sequence simulation support.
- 2026: IQ-TREE 3 citation describes phylogenomic inference software using complex evolutionary models.

### Related projects

- IQ-TREE 3 relates to IQPNNI, TREE-PUZZLE, IQ-TREE 1, IQ-TREE 2, RAxML, PhyML, ModelFinder, UFBoot, AliSim, W-IQ-TREE, BioConda, CIPRES, FigTree, Dendroscope, and iTOL.

### ソース

- <https://formulae.brew.sh/formula/iqtree3>
- <https://github.com/iqtree/iqtree3>
- <https://raw.githubusercontent.com/iqtree/iqtree3/master/README.md>
- <https://www.iqtree.org/doc>
- <https://www.iqtree.org/doc/iqtree-doc.pdf>


## セキュリティノート

iqtree3 に一致するローカルシークレット処理マニフェストは見つかりませんでした。将来の対応で安定したパッケージ URL を使えるよう、Nucleus パッケージメタデータはここに公開されています。


## ソースデータベース詳細

- **Source Database:** Homebrew formula API
- **Tap:** homebrew/core
- **Full Name:** iqtree3
- **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

## 他のパッケージマネージャ記録

- MacPorts - iqtree3: normalized package name match | MacPorts ports tree: science/iqtree3/Portfile from https://api.github.com/repos/macports/macports-ports/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.
- [Web development packages](https://www.automicvault.com/ja/pkg/web-dev-tools/) - Matched web development metadata.
- [cmake](https://www.automicvault.com/ja/pkg/brew/cmake/) - Build dependency declared by Homebrew.
- [paml](https://www.automicvault.com/ja/pkg/brew/paml/) - Shares av.db curated category or tags: bioinformatics, cli, maximum-likelihood, phylogenetics, science.
- [fastme](https://www.automicvault.com/ja/pkg/brew/fastme/) - Shares av.db curated category or tags: bioinformatics, cli, phylogenetics, science.
- [trimal](https://www.automicvault.com/ja/pkg/brew/trimal/) - 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.
- [raxml-ng](https://www.automicvault.com/ja/pkg/brew/raxml-ng/) - Shares av.db curated category or tags: bioinformatics, cli, maximum-likelihood, phylogenetics, science.
- [hyphy](https://www.automicvault.com/ja/pkg/brew/hyphy/) - Shares av.db curated category or tags: bioinformatics, cli, phylogenetics, science.
- [mrbayes](https://www.automicvault.com/ja/pkg/brew/mrbayes/) - 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.

## Combined YAML source

View the package source record on GitHub. [combined/iqtree3.yml](https://github.com/automic-vault/db/blob/main/combined/iqtree3.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