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Application Details

  • Description: HyPhy (Hypothesis Testing using Phylogenies) is an open-source software package for the analysis of genetic sequences (in particular the inference of natural selection) using techniques in phylogenetics, molecular evolution, and machine learning
  • Version: 2.2.7
  • Module: hyphy/2.2.7/gcc-6.3.0/openmpi-2.0.2
  • Licence: Open source

Usage Examples

Currently its available only after through interactive session. its not possible to run it on login nodes of Viper


[username@c001 ~]$ module add hyphy/2.2.7/gcc-6.3.0/openmpi-2.0.2


[username@c001 ~]$ module add hyphy/2.2.7/gcc-6.3.0/openmpi-2.0.2


There are two binaries available.

  • HYPHYMP is openMP implementation that could utilise more than 1 processors.
  • HYPHYMPI is MPI implementation that could run on single or multiple nodes.

you can use the openmp version in side an interactive session to define your input arrguments that you can run later as batch job below

[username@c001 ~]$ interactive
[username@c001 ~]$ HYPHYMP

Batch Script

once you know the input arguments (sections) that you have made to HYPHY using interactive session. you can then create a submission script. below is an example of HYPHY slurm submission script


#SBATCH -J amphibio_meme          # Job Name
#SBATCH -N 1                      # Number of  Nodes to use
#SBATCH  -n 28                    # Number of CPUs
#SBATCH -o %N.%j.%a.out           # Output file name
#SBATCH -e %N.%j.%a.err           # Error file name
#SBATCH -p compute                # Partition to run on
#SBATCH --exclusive               # Request exclusive access to a node (all 28 cores, 128GB of RAM)

module add hyphy/2.2.7/gcc-6.3.0/openmpi-2.0.2

(echo "10"; echo "4"; echo "2"; echo "/pass/to/input1/example.fas"; echo "/pass/to/input2/example.tre"; echo "1"; echo "d") | HYPHYMP