Hyphy
Description
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.
License
open-source software
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of hyphy and load default version of hyphy as
module avail hyphy/ # list available modules module load hyphy # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail hyphy
and choose explicit version you want to use.
HYPHYMP #using pthreads to do multiprocessing HYPHYMPI #using MPI to do multiprocessing
Documentation
http://www.hyphy.org/w/index.php/User_Guides