# hyphy mit Homebrew, apt installieren Prüfe Installationswege, Executables, Metadaten und Sicherheitshinweise für hyphy in AI-Agent-Workflows. ## Installation ```sh sudo av install brew:hyphy ``` Weitere Installationsbefehle: ### macOS - Homebrew (100%): ```sh brew install hyphy ``` Evidenz: local Homebrew formula metadata ### Linux - Debian apt (92%): ```sh sudo apt install hyphy-common ``` Evidenz: Debian stable package indexes: hyphy-common from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz ## Paketfakten - **Paketschlüssel:** brew:hyphy - **Paketmanager:** Homebrew - **Paketmanager-Seite:** - **Version:** 2.5.101 - **Quellzusammenfassung:** Hypothesis testing using Phylogenies - **Homepage:** - **Repository:** - **Upstream-Dokumentation:** - **Lizenz:** MIT - **Quellarchiv:** - **Zuletzt aktualisiert:** 2026-06-18T18:40:23Z - **Generiert:** 2026-07-08T18:08:21+00:00 ## Executables - hyphy (cli) - hyphy (Alias) ## Abhängigkeiten - libomp ## Build-Abhängigkeiten - cmake ## Von macOS bereitgestellte Bibliotheken - curl ## Installationsverhalten - Post-install-Hook: nicht definiert - Bottle: verfügbar auf arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux ## Version und Aktualität - Seite generiert: 2026-07-08 - Manager-Version: 2.5.101 - Manager aktualisiert: 2026-06-18 - lokale Daten: OK - Upstream-Repository: https://github.com/veg/hyphy - neueste erkannte Version: 2.5.101 (aktuell) ## Projektgeschichte und Nutzung 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. ### Projektgeschichte 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. ### Adoptionsgeschichte 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. ### Wie es verwendet wird 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. ### Warum Paket-Nerds sich dafür interessieren 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. ### Zeitleiste - 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. ### Quellen - - - - - - - - - ## Sicherheitshinweise Für hyphy wurde kein passendes lokales Secret-Handling-Manifest gefunden. Nucleus-Paketmetadaten bleiben hier veröffentlicht, damit künftige Abdeckung eine stabile Paket-URL hat. ## Details aus der Quelldatenbank - **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 ## Andere Paketmanager-Einträge - 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/ ## Verwandte Links - [Terminal utility packages](https://www.automicvault.com/de/pkg/terminal-utilities/) - Matched terminal and command-line workflow metadata. - [Networking and protocol packages](https://www.automicvault.com/de/pkg/networking-protocol-tools/) - Matched network, protocol, or remote-service metadata. - [Scientific computing packages](https://www.automicvault.com/de/pkg/scientific-computing-tools/) - Matched scientific computing metadata. - [Homebrew utility packages](https://www.automicvault.com/de/pkg/brew-utility-packages/) - Matched Homebrew package provider. - [cmake](https://www.automicvault.com/de/pkg/brew/cmake/) - Build dependency declared by Homebrew. - [fastme](https://www.automicvault.com/de/pkg/brew/fastme/) - Shares av.db curated category or tags: bioinformatics, cli, phylogenetics, science. - [mrbayes](https://www.automicvault.com/de/pkg/brew/mrbayes/) - Shares av.db curated category or tags: bioinformatics, cli, phylogenetics, science. - [paml](https://www.automicvault.com/de/pkg/brew/paml/) - Shares av.db curated category or tags: bioinformatics, cli, phylogenetics, science. - [raxml-ng](https://www.automicvault.com/de/pkg/brew/raxml-ng/) - Shares av.db curated category or tags: bioinformatics, cli, phylogenetics, science. - [trimal](https://www.automicvault.com/de/pkg/brew/trimal/) - Shares av.db curated category or tags: bioinformatics, cli, phylogenetics, science. - [veryfasttree](https://www.automicvault.com/de/pkg/brew/veryfasttree/) - Shares av.db curated category or tags: bioinformatics, cli, phylogenetics, science. - [abpoa](https://www.automicvault.com/de/pkg/brew/abpoa/) - Shares av.db curated category or tags: bioinformatics, cli, science. - [abricate](https://www.automicvault.com/de/pkg/brew/abricate/) - Shares av.db curated category or tags: bioinformatics, cli, science. - [blast](https://www.automicvault.com/de/pkg/brew/blast/) - Local package facts share a topical domain. Shared terms: bioinformatics, cli, genomics, libomp, science. - [rna-star](https://www.automicvault.com/de/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) ## Quellen - 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