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HyPhy - Hypothesis testing using Phylogenies
HyPhy is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. It features a complete graphical user interface (GUI) and a rich scripting language for limitless customization of analyses. Additionally, HyPhy features support for parallel computing environments (via message passing interface) and it can be compiled as a shared library and called from other programming environments such as Python or R. HyPhy has over 8000 registered users and has been cited in over 900 peer-reviewed publications (Google Scholar). Continued development of HyPhy is currently supported in part by an NIGMS R01 award 1R01GM093939.
Go to User registrations and download

If you are a developer, come to our github page!

Web Interface

  • 2014-09-06 - Version 2.2.1. Maintenance release while we are still working on v3 (expected release at the end of 2014). New analyses, and over 100 commits, bug fixes, and new (incremental) features.
  • 2013-07-02 - Version 2.2. Over 100 bug fixes, new analyses, speed improvements. The final 2.x release -- we are currently hard at work on a major HyPhy overhaul leading to version 3.
  • 2012-06-21 - Version 2.1.2. Numerous bug fixes, HBL feature adjustments, and stability improvements
  • 2012-04-09 - Version 2.1.1. Numerous bug fixes, speed and stability improvements
  • 2011-11-09 - Revised MediaWiki becomes the new HyPhy frontpage. New installers for Mac OS X and Windows. Source files can once again be used to compile a GTK-based Linux GUI version of HyPhy.
  • 2011-10-31 - Massive overhaul of wiki begins.
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