Difference between revisions of "HyPhy"
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module load intel/2012 openmpi/1.6 hyphy | 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. | This module provides HYPHYS, HYPHYMP, and HYPHYMPI binaries and the ''hyphy'' alias points to the HYPHYMPI binary. | ||
| + | ==System Variables== | ||
| + | * HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory | ||
<!--Run--> | <!--Run--> | ||
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{{#if: {{#var: exe}}|==How To Run== | {{#if: {{#var: exe}}|==How To Run== | ||
DOUBLE_CLICK_TO_WRITE_INSTRUCTIONS_ON_RUNNING_THE_ACTUAL_BINARY | DOUBLE_CLICK_TO_WRITE_INSTRUCTIONS_ON_RUNNING_THE_ACTUAL_BINARY | ||
Revision as of 17:22, 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.
Required Modules
Serial
- hyphy
- 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.
System Variables
- HPC_{{#uppercase:hyphy}}_DIR - installation directory