# 使用 Homebrew, MacPorts 安装 iqtree3

查看 iqtree3 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:iqtree3
```

其他安装命令:

### macOS

- Homebrew (100%):

```sh
brew install iqtree3
```

  证据: local Homebrew formula metadata

- MacPorts (94%):

```sh
sudo port install iqtree3
```

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

## 软件包事实

- **软件包键:** brew:iqtree3
- **软件包管理器:** Homebrew
- **软件包管理器页面:** <https://formulae.brew.sh/formula/iqtree3>
- **版本:** 3.1.2
- **来源摘要:** Phylogenetics by maximum likelihood
- **主页:** <http://www.iqtree.org>
- **仓库:** <https://github.com/iqtree/iqtree3>
- **上游文档:** <https://www.iqtree.org/doc>
- **许可证:** GPL-2.0-or-later
- **源码归档:** <https://github.com/iqtree/iqtree3/archive/refs/tags/v3.1.2.tar.gz>
- **最后更新:** 2026-06-25T13:37:46+02:00
- **已生成:** 2026-07-08T18:08:21+00:00

## 可执行文件

- iqtree3 (cli)
- iqtree3 (别名)

## 构建依赖

- boost
- cmake
- eigen

## 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: 3.1.2
- 管理器更新时间: 2026-06-25
- 本地数据: OK
- 上游仓库: https://github.com/iqtree/iqtree3
- 检测到的最新版本: v3.1.2 (当前)
## 项目历史与用法

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.

### 项目历史

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.

### 采用历史

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.

### 使用方式

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.

### 为什么软件包爱好者会关心

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.

### 时间线

- 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.

### 来源

- <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>


## 安全说明

没有找到 iqtree3 的匹配本地密钥处理 manifest。Nucleus 软件包元数据仍在此发布，以便未来覆盖拥有稳定的软件包 URL。


## 源数据库详情

- **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

## 其他软件包管理器记录

- 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


## 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.
- [Web development packages](https://www.automicvault.com/zh-hans/pkg/web-dev-tools/) - Matched web development metadata.
- [cmake](https://www.automicvault.com/zh-hans/pkg/brew/cmake/) - Build dependency declared by Homebrew.
- [paml](https://www.automicvault.com/zh-hans/pkg/brew/paml/) - Shares av.db curated category or tags: bioinformatics, cli, maximum-likelihood, phylogenetics, science.
- [fastme](https://www.automicvault.com/zh-hans/pkg/brew/fastme/) - Shares av.db curated category or tags: bioinformatics, cli, phylogenetics, science.
- [trimal](https://www.automicvault.com/zh-hans/pkg/brew/trimal/) - 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.
- [raxml-ng](https://www.automicvault.com/zh-hans/pkg/brew/raxml-ng/) - Shares av.db curated category or tags: bioinformatics, cli, maximum-likelihood, phylogenetics, science.
- [hyphy](https://www.automicvault.com/zh-hans/pkg/brew/hyphy/) - Shares av.db curated category or tags: bioinformatics, cli, phylogenetics, science.
- [mrbayes](https://www.automicvault.com/zh-hans/pkg/brew/mrbayes/) - 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.

## Combined YAML source

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