# hyphy を Homebrew, apt でインストール

hyphy 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:hyphy
```

追加のインストールコマンド:

### macOS

- Homebrew (100%):

```sh
brew install hyphy
```

  証拠: local Homebrew formula metadata

### Linux

- Debian apt (92%):

```sh
sudo apt install hyphy-common
```

  証拠: Debian stable package indexes: hyphy-common from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz

## パッケージ情報

- **パッケージキー:** brew:hyphy
- **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/hyphy>
- **バージョン:** 2.5.101
- **ソース概要:** Hypothesis testing using Phylogenies
- **ホームページ:** <https://www.hyphy.org>
- **リポジトリ:** <https://github.com/veg/hyphy>
- **上流ドキュメント:** <https://www.hyphy.org/batchlan>
- **ライセンス:** MIT
- **ソースアーカイブ:** <https://github.com/veg/hyphy/archive/refs/tags/2.5.101.tar.gz>
- **最終更新:** 2026-06-18T18:40:23Z
- **生成日時:** 2026-07-08T18:08:21+00:00

## 実行可能ファイル

- hyphy (cli)
- hyphy (エイリアス)

## 依存関係

- libomp

## ビルド依存関係

- cmake

## macOS 提供ライブラリ

- curl

## 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: 2.5.101
- マネージャ更新日: 2026-06-18
- ローカルデータ: OK
- 上流リポジトリ: https://github.com/veg/hyphy
- 検出された最新: 2.5.101 (最新)
## プロジェクトの歴史と使われ方

HyPhy, short for Hypothesis Testing using Phylogenies, is an open-source computational phylogenetics package for likelihood-based analysis of molecular sequence evolution, natural selection, recombination, co-evolution, and rate variation.

### プロジェクトの歴史

HyPhy was originally released in 2000, and its 2005 Bioinformatics paper described it as a flexible unified platform for likelihood-based analyses of multiple sequence alignments. The project combined a graphical application, a scriptable batch language, and a library of analyses aimed at molecular evolution researchers.

The HyPhy 2.5 paper describes a major modernization of the computational core and analysis library, with new evolutionary models, statistical tests, performance and stability improvements, and a focus on reproducible end-to-end workflows. GitHub release metadata records an active 2.5.x maintenance line after the 2019 2.5.0 release.

### 採用の歴史

HyPhy spread through academic citation, the Datamonkey web application, Bioconda, Homebrew, Debian, Ubuntu, Docker, and source builds. Its README states that HyPhy is the computational backbone powering datamonkey.org, which made several HyPhy methods accessible without local installation.

### 使われ方

Command-line use centers on commands such as `hyphy absrel`, `hyphy busted`, `hyphy fel`, `hyphy fubar`, `hyphy gard`, `hyphy meme`, `hyphy relax`, and `hyphy slac` with alignment and tree inputs. Advanced users can write or modify analyses in HBL, the HyPhy Batch Language.

### パッケージ好きにとっての重要性

HyPhy is significant because it is both a long-lived scientific codebase and a package-manager citizen. It crosses GUI, CLI, library, MPI, Conda, Homebrew, Debian, Docker, and WebAssembly packaging boundaries while preserving a domain-specific scripting language for evolutionary hypothesis testing.

### タイムライン

- 2000: HyPhy was originally released.
- 2005: The Bioinformatics paper described HyPhy as a likelihood-based platform for molecular sequence analysis.
- 2019: HyPhy 2.5.0 was released with a re-engineered computational core and analysis library.
- 2020: The HyPhy 2.5 paper appeared in Molecular Biology and Evolution.
- 2026: The 2.5.x release line continued in GitHub release metadata.

### Related projects

- HyPhy is closely related to Datamonkey and to comparative phylogenetics tools such as PAML, MrBayes, BEAST, RevBayes, and Galaxy workflows that wrap HyPhy methods.

### ソース

- <https://api.github.com/repos/veg/hyphy/releases?per_page=100>
- <https://formulae.brew.sh/formula/hyphy>
- <https://github.com/veg/hyphy>
- <https://pmc.ncbi.nlm.nih.gov/articles/PMC8204705/>
- <https://pubmed.ncbi.nlm.nih.gov/15509596/>
- <https://pubmed.ncbi.nlm.nih.gov/31504749/>
- <https://raw.githubusercontent.com/veg/hyphy/master/README.md>
- <https://www.datamonkey.org/citations>
- <https://www.hyphy.org/about/>


## セキュリティノート

hyphy 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:** hyphy
- **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

- Debian apt - hyphy-common - 2.5.69+dfsg-1: normalized package name match | Debian stable package indexes: hyphy-common from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | Hypothesis testing using Phylogenies (common files) | https://hyphy.org/
- Debian apt - hyphy-mpi - 2.5.69+dfsg-1: normalized package name match | Debian stable package indexes: hyphy-mpi from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | Hypothesis testing using Phylogenies (MPI version) | https://hyphy.org/
- Debian apt - hyphy-pt - 2.5.69+dfsg-1: normalized package name match | Debian stable package indexes: hyphy-pt from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | Hypothesis testing using Phylogenies (pthreads version) | https://hyphy.org/
- Ubuntu apt - hyphy-common - 2.5.59+dfsg-1build3: normalized package name match | Ubuntu 24.04 LTS package indexes: hyphy-common from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | Hypothesis testing using Phylogenies (common files) | https://hyphy.org/
- Ubuntu apt - hyphy-mpi - 2.5.59+dfsg-1build3: normalized package name match | Ubuntu 24.04 LTS package indexes: hyphy-mpi from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | Hypothesis testing using Phylogenies (MPI version) | https://hyphy.org/
- Ubuntu apt - hyphy-pt - 2.5.59+dfsg-1build3: normalized package name match | Ubuntu 24.04 LTS package indexes: hyphy-pt from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | Hypothesis testing using Phylogenies (pthreads version) | https://hyphy.org/


## 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.
- [cmake](https://www.automicvault.com/ja/pkg/brew/cmake/) - Build dependency declared by Homebrew.
- [fastme](https://www.automicvault.com/ja/pkg/brew/fastme/) - 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.
- [paml](https://www.automicvault.com/ja/pkg/brew/paml/) - 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, 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.
- [abpoa](https://www.automicvault.com/ja/pkg/brew/abpoa/) - Shares av.db curated category or tags: bioinformatics, cli, science.
- [abricate](https://www.automicvault.com/ja/pkg/brew/abricate/) - Shares av.db curated category or tags: bioinformatics, cli, science.
- [blast](https://www.automicvault.com/ja/pkg/brew/blast/) - Local package facts share a topical domain. Shared terms: bioinformatics, cli, genomics, libomp, science.
- [rna-star](https://www.automicvault.com/ja/pkg/brew/rna-star/) - Local package facts share a topical domain. Shared terms: bioinformatics, cli, genomics, libomp, science.

## Combined YAML source

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