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).
License
Free to use and open source. See the HyPhy repository.
Available
- Roihu: 2.5.51hf, via the
bio-appsmodule.
Usage
HyPhy is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the HyPhy module:
HyPhy analyses are run with the hyphy command, giving the method name and the input
alignment and tree. For example, a FEL selection analysis:
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.