# 使用 Homebrew, apt 安装 hyphy 查看 hyphy 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:hyphy ``` 其他安装命令: ### macOS - Homebrew (100%): ```sh brew install hyphy ``` 证据: local Homebrew formula metadata ### Linux - Debian apt (92%): ```sh sudo apt install hyphy-common ``` 证据: Debian stable package indexes: hyphy-common from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz ## 软件包事实 - **软件包键:** brew:hyphy - **软件包管理器:** Homebrew - **软件包管理器页面:** - **版本:** 2.5.101 - **来源摘要:** Hypothesis testing using Phylogenies - **主页:** - **仓库:** - **上游文档:** - **许可证:** MIT - **源码归档:** - **最后更新:** 2026-06-18T18:40:23Z - **已生成:** 2026-07-08T18:08:21+00:00 ## 可执行文件 - hyphy (cli) - hyphy (别名) ## 依赖 - libomp ## 构建依赖 - cmake ## macOS 提供的库 - curl ## 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: 2.5.101 - 管理器更新时间: 2026-06-18 - 本地数据: OK - 上游仓库: https://github.com/veg/hyphy - 检测到的最新版本: 2.5.101 (当前) ## 项目历史与用法 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. ### 项目历史 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. ### 采用历史 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. ### 使用方式 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. ### 为什么软件包爱好者会关心 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. ### 时间线 - 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. ### 来源 - - - - - - - - - ## 安全说明 没有找到 hyphy 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:** hyphy - **Version Scheme:** 0 - **Revision:** 0 - **Bottle Stable Root URL:** - **Deprecated:** no - **Disabled:** no - **Keg Only:** no - **URL Keys:** stable ## 其他软件包管理器记录 - 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/ ## 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. - [cmake](https://www.automicvault.com/zh-hans/pkg/brew/cmake/) - Build dependency declared by Homebrew. - [fastme](https://www.automicvault.com/zh-hans/pkg/brew/fastme/) - 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. - [paml](https://www.automicvault.com/zh-hans/pkg/brew/paml/) - 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, 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. - [abpoa](https://www.automicvault.com/zh-hans/pkg/brew/abpoa/) - Shares av.db curated category or tags: bioinformatics, cli, science. - [abricate](https://www.automicvault.com/zh-hans/pkg/brew/abricate/) - Shares av.db curated category or tags: bioinformatics, cli, science. - [blast](https://www.automicvault.com/zh-hans/pkg/brew/blast/) - Local package facts share a topical domain. Shared terms: bioinformatics, cli, genomics, libomp, science. - [rna-star](https://www.automicvault.com/zh-hans/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) ## 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