User:Scray/Sandbox

HYPHY ( HYE-fye) is a free multiplatform (Mac, Windows and UNIX) Computational phylogenetics software package intended to perform maximum likelihood analyses of genetic sequence data and equipped with tools to test various statistical hypotheses. The HYPHY name is an abbreviation for "HYpothesis testing using PHYlogenies".

HYPHY is developed by Sergei Kosakovsky Pond, Simon Frost, and Art Poon of UC San Diego, and Spencer Muse of North Carolina State University.

History
The development of HyPhy started in 1997, with the first public release in 2000 and the most recent version as of Jan 2009 being 0.99+ beta, compiled on May 8, 2008.

Software/code availability and license
HYPHY is distributed as freeware with source code released under the GPL. Compiled binaries for Mac OS (9 and X) and Windows are available for download. There is also a source based distribution (under the GPL license), which can be used to build HyPhy on *nix systems.

A subset of HYPHY methods are also made available by the HYPHY team at UC San Diego in the form of the DataMonkey server