Difference between revisions of "HyPhy"
Moskalenko (talk | contribs) m (Text replace - "<!--Versions--> ==Available versions== .* <!--Modules-->" to "<!--Modules-->") |
Moskalenko (talk | contribs) m (Text replace - "Usage policy" to "Usage Policy") |
||
| Line 50: | Line 50: | ||
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | ||
<!--Policy--> | <!--Policy--> | ||
| − | {{#if: {{#var: policy}}|==Usage | + | {{#if: {{#var: policy}}|==Usage Policy== |
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used) | WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used) | ||
|}} | |}} | ||
Revision as of 16:32, 10 August 2012
Description
HyPhy is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.
HyPhy has over 7000 registered users and has been cited in over 600 peer-reviewed publications (Google Scholar). Continued development of HyPhy is currently supported in part by an NIGMS R01 award 1R01GM093939.
Execution Environment and Modules
To use hyphy with the environment modules system at HPC the following commands are available:
Get module information for hyphy:
$module spider hyphy
Load the default application module:
$module load hyphy
The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
- HPC_HYPHY_DIR - directory where hyphy is located.
- HPC_HYPHY_BIN - executable directory.
The default core module loads a single-threaded version (HYPHYSP) built with GNU compiler and provides a hyphy alias to HYPHYSP. To load the single- and multi-threaded versions built with the Intel Compiler load the intel/2012 module:
module load intel/2012 hyphy
This module provides both a HYPHYSP and a HYPHYMP versions and the hyphy alias points to HYPHYMP.
To load the MPI-enabled version of HYPHY add the openmpi/1.6 module:
module load intel/2012 openmpi/1.6 hyphy
This module provides HYPHYS, HYPHYMP, and HYPHYMPI binaries and the hyphy alias points to the HYPHYMPI binary.