Applications/HyPhy

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

Module

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

or

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

Description

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.

Batch Script

#!/bin/bash

#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 load 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