Difference between revisions of "HyPhy"

Revision as of 18:54, 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

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_{{#uppercase:hyphy}}_DIR - installation directory
HPC_HYPHY_BIN - executable directory.

@@ Line 4: / Line 4: @@
 |{{#vardefine:url|http://www.datam0nk3y.org/hyphywiki/index.php/Main_Page}}
 <!--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: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].
 <!--Modules-->
 ==Required Modules==
 [[Modules|modules documentation]]
-===Serial===
+===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}}
-<!--Add additional HPC_FOO_BIN and other ENV VARIABLES below-->
-* 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:{{#var:app}}}}_DIR - installation directory
-<!--Run-->
+* HPC_HYPHY_BIN - executable directory.
+<!--Additional-->
-{{#if: {{#var: exe}}|==How To Run==
+{{#if: {{#var: exe}}|==Additional Information==
 DOUBLE_CLICK_TO_WRITE_INSTRUCTIONS_ON_RUNNING_THE_ACTUAL_BINARY
 |}}