HyPhy development has received support from the NIH (R01GM151683, U01GM110749, U24AI183870, R01GM093939), and the NSF (2027196, 2419522).

HyPhy distributes a variety of methods for inferring the strength of natural selection in your data using, in the case of codon-based methods, the dN/dS metric.

Overview HyPhy (Hy pothesis Testing using Phy logenies) is an open-source software package for the analysis of genetic sequences (in particular the inference of natural selection) using techniques in …

To download the Desktop/GUI version of HyPhy, follow instructions on this download page. NOTE: The HyPhy GUI is no longer maintained and will be replaced in the near future with a JavaScript front-end.

These tutorials outline how to use the HyPhy Graphical User Interface (GUI) desktop application (HyPhy-GUI) to detect natural selection in protein-coding alignments.

Before we demonstrate how to use HyPhy for simple model fitting, we will introduce the fundamental components required of virtually every HyPhy data analysis.

HyPhy provides a suite of diverse phylogenetic methodologies for testing specific hypotheses about the selection in protein-coding and/or amino-acid multiple sequence alignments.

HyPhy Vision is a platform for visualizing and exploring JSON-formatted results from HyPhy's suite of methods for detecting natural selection.

Most HyPhy analyses take direct advantage of multi-threading, and a large number of common analyses (e.g. FEL, MEME, FUBAR, GARD) can dramatically benefit from an MPI environment.

An implementation of our method is available as part of the HyPhy (hyphy.org) software suite. The HyPhy Batch Language (HBL) code is available here, BUSTED Method