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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.


  • Validated 4/5/2018