Install hyphy with Homebrew, apt

Project links

• Homepage
• Repository
• Upstream docs
• Package manager page

Commands and aliases

• hyphy

Project history

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.

Adoption history

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.

How it is used

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.

Why package nerds care

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.

Timeline

• 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.

Sources

• 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/