Hypothesis Testing using Phylogenies (HyPhy)#

HyPhy is an open-source software package for comparative sequence analysis using stochastic evolutionary models. It provides a suite of advanced phylogenetic methods to detect and test for natural selection, recombination, co-evolution, and rate variation across genes and lineages.

Key Capabilities & Core Analyses#

HyPhy implements state-of-the-art statistical models to answer fundamental evolutionary questions:

1. Natural Selection Inference#

• Episodic Selection (MEME): Finds individual sites subject to positive selection along a subset of branches. MEME is the preferred approach for identifying site-specific positive selection.
• Pervasive Selection (FUBAR / FEL / SLAC): Detects sites under consistent selective pressure across the entire phylogeny. FUBAR is the fastest, high-power Bayesian method.
• Gene-Wide & Branch-Specific Selection (BUSTED / aBSREL): Tests if a gene has experienced selection on any site/branch (BUSTED) or identifies exactly which branches are subject to episodic selection (aBSREL).
• Selection Relaxation (RELAX): Compares test and reference branches to determine if selective constraints have been relaxed or intensified.

2. Recombination Detection#

• GARD (Genetic Algorithm for Recombination Detection): Identifies recombination breakpoints in alignments and partitions sequence data to avoid phylogenetic artifacts.

Companion Services & Ecosystem#

HyPhy operates within a modern ecosystem designed to simplify analysis and visualize complex datasets:

[ Datamonkey Web Server ] ---> [ HyPhy Engine (CLI/HBL) ] ---> [ HyPhy Vision (Interactive JSONs) ]
      (datamonkey.org)               (Local Execution)                  (vision.hyphy.org)

Datamonkey (https://www.datamonkey.org)#

Datamonkey is the companion web server for HyPhy. It allows researchers to upload sequence data and run computationally intensive HyPhy analyses through a browser interface without local installation. Datamonkey runs on high-performance compute clusters and delivers results directly to your browser.

HyPhy Vision (https://vision.hyphy.org)#

HyPhy analyses generate standard, detailed machine-readable JSON outputs. HyPhy Vision is the interactive visualization platform that parses these JSON files to render responsive phylogenies, site selection plots, fitting parameters, and alignment browsers.

Getting Started with HyPhy#

HyPhy fits your research pipeline, whether you prefer GUI, command line, or writing custom code:

• Interactive CLI: Simply run hyphy -i to launch an interactive command-line helper that guides you step-by-step through choosing an analysis and configuring parameters.
• Scripted CLI: Run standard analyses headlessly in pipelines (e.g., hyphy meme --alignment data.fas --tree tree.nwk).
• HBL (HyPhy Batch Language): Write custom scripts to define novel evolutionary models, perform complex computations, and build bespoke pipelines.

Install HyPhy Now | Follow the CLI Tutorial | Read the HBL Reference