Difference between revisions of "HyPhy"

From UFRC
Jump to navigation Jump to search
m (Text replace - "==Running the application using modules==" to "==Execution Environment and Modules==")
 
(10 intermediate revisions by 4 users not shown)
Line 1: Line 1:
−
[[Category:Software]][[Category:Bioinformatics]][[Category:Phylogenetics]]
+
[[Category:Software]][[Category:Biology]][[Category:Genomics]]
 
{|<!--CONFIGURATION: REQUIRED-->
 
{|<!--CONFIGURATION: REQUIRED-->
 
|{{#vardefine:app|hyphy}}
 
|{{#vardefine:app|hyphy}}
−
|{{#vardefine:url|http://www.datam0nk3y.org/hyphywiki/index.php/Main_Page}}
+
|{{#vardefine:url|http://www.hyphy.org}}
 
<!--CONFIGURATION: OPTIONAL (1=ON)-->
 
<!--CONFIGURATION: OPTIONAL (1=ON)-->
−
|{{#vardefine:mod|1}} <!--MODULES - NOW REQUIRED-->
 
−
|{{#vardefine:intel|}} <!-- "11.1" - Compiler Module Choice -->
 
−
|{{#vardefine:mpi|}} <!-- "openmpi/1.3.4"- MPI Module Choice -->
 
 
|{{#vardefine:exe|}} <!--RUNNING -->
 
|{{#vardefine:exe|}} <!--RUNNING -->
 
|{{#vardefine:conf|}} <!--CONFIGS-->
 
|{{#vardefine:conf|}} <!--CONFIGS-->
Line 24: Line 21:
  
 
HyPhy has over 7000 registered users and has been cited in over 600 peer-reviewed publications ([http://scholar.google.com/scholar?hl=en&sciodt=0%2C5&q=&cites=17874163875017617061&as_sdt=0%2C5&as_ylo=&as_vis=0 Google Scholar]). Continued development of HyPhy is currently supported in part by an NIGMS R01 award [http://projectreporter.nih.gov/project_info_description.cfm?aid=7937611&icde=7643734 1R01GM093939].
 
HyPhy has over 7000 registered users and has been cited in over 600 peer-reviewed publications ([http://scholar.google.com/scholar?hl=en&sciodt=0%2C5&q=&cites=17874163875017617061&as_sdt=0%2C5&as_ylo=&as_vis=0 Google Scholar]). Continued development of HyPhy is currently supported in part by an NIGMS R01 award [http://projectreporter.nih.gov/project_info_description.cfm?aid=7937611&icde=7643734 1R01GM093939].
−
 
−
<!--Versions-->
 
−
==Available versions==
 
−
* 2.1.2.28
 
 
<!--Modules-->
 
<!--Modules-->
−
{{#if: {{#var: mod}}|==Execution Environment and Modules==
+
==Required Modules==
−
{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
+
[[Modules|modules documentation]]
−
<!--Add additional HPC_FOO_BIN and other ENV VARIABLES below-->
+
===Serial (GNU Compiler)===
 +
*{{#var:app}}
 +
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
 +
*{{#var:app}}
 +
The Intel Compiler build versions provide both a HYPHYSP and a HYPHYMP binaries. The ''hyphy'' alias points to HYPHYMP.
 +
===Parallel (OpenMPI)===
 +
*intel
 +
*openmpi
 +
*{{#var:app}}
 +
This module provides HYPHYS, HYPHYMP, and HYPHYMPI binaries and the ''hyphy'' alias points to the HYPHYMPI binary.
 +
==System Variables==
 +
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
* HPC_HYPHY_BIN - executable directory.
 
* HPC_HYPHY_BIN - executable directory.
−
 
+
<!--Additional-->
−
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:
+
{{#if: {{#var: exe}}|==Additional Information==
−
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.
 
−
<!--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
 
|}}
 
|}}
Line 53: Line 51:
 
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 policy==
+
{{#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)
 
|}}
 
|}}
Line 72: Line 70:
 
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 website  

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

modules documentation

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
Retrieved from "https://help.rc.ufl.edu/mediawiki/index.php?title=HyPhy&oldid=25381"