Difference between revisions of "HyPhy"
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| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:Genomics]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|hyphy}} | |{{#vardefine:app|hyphy}} | ||
| − | |{{#vardefine:url|http://www. | + | |{{#vardefine:url|http://www.hyphy.org}} |
<!--CONFIGURATION: OPTIONAL (1=ON)--> | <!--CONFIGURATION: OPTIONAL (1=ON)--> | ||
|{{#vardefine:exe|}} <!--RUNNING --> | |{{#vardefine:exe|}} <!--RUNNING --> | ||
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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== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
* HPC_HYPHY_BIN - executable directory. | * HPC_HYPHY_BIN - executable directory. | ||
<!--Additional--> | <!--Additional--> | ||
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See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}} | See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}} | ||
__NOTOC____NOEDITSECTION__ | __NOTOC____NOEDITSECTION__ | ||
| + | =Validation= | ||
| + | * Validated 4/5/2018 | ||
Latest revision as of 18:36, 15 August 2022
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 (GNU Compiler)
- hyphy
The default core module loads a single-threaded version (HYPHYSP) built with GNU compiler and provides a hyphy alias to HYPHYSP.
Serial and Parallel (Intel Compiler)
- intel
- hyphy
The Intel Compiler build versions provide both a HYPHYSP and a HYPHYMP binaries. The hyphy alias points to HYPHYMP.
Parallel (OpenMPI)
- intel
- openmpi
- hyphy
This module provides HYPHYS, HYPHYMP, and HYPHYMPI binaries and the hyphy alias points to the HYPHYMPI binary.
System Variables
- HPC_HYPHY_DIR - installation directory
- HPC_HYPHY_BIN - executable directory.
Validation
- Validated 4/5/2018