HyPhy

HyPhy (Hypothesis testing using Phylogenies) is a software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution and machine learning. It is widely used for detecting signatures of natural selection (methods such as FEL, MEME, aBSREL and BUSTED).

• HyPhy
  • License
  • Available
  • Usage
    • Example batch script
  • Support
  • More information

License

Free to use and open source. See the HyPhy repository.

Available

• Roihu: 2.5.51hf, via the bio-apps module.

Usage

HyPhy is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the HyPhy module:

module load bio-apps/v202603
module load hyphy/2.5.51hf

HyPhy analyses are run with the hyphy command, giving the method name and the input alignment and tree. For example, a FEL selection analysis:

hyphy fel --alignment alignment.fasta --tree tree.nwk

Example batch script

#!/bin/bash
#SBATCH --job-name=hyphy
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=08:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=2G

module load bio-apps/v202603
module load hyphy/2.5.51hf

hyphy CPU=$SLURM_CPUS_PER_TASK fel --alignment alignment.fasta --tree tree.nwk

Replace <project> with your CSC project (for example project_2001234).

See creating a batch job script for Roihu for more information about running batch jobs.

Support

CSC Service Desk

More information

• HyPhy home page
• HyPhy GitHub repository

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