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: 2.5.48
• Added: March, 2023
• Link: https://stevenweaver.github.io/hyphy-site

See which versions are available:

$ module avail hyphy

Load one version into your environment and run it:

$ module load hyphy/2.5.48
$ hyphy

Note: please make sure to specify the CPU=integer option to control the number of CPU threads used by hyphy (should match your SLURM allocation) or else it will use all CPUs on the system!

Notes from the sysadmin during installation.

$ cd /tmp
$ tar xf hyphy-2.5.48.tar.gz
$ cmake .
$ make MP
$ sudo mkdir -p /export/apps/hyphy/2.5.48/bin
$ sudo cp hyphy /export/apps/hyphy/2.5.48/bin

Note: the cmake -DINSTALL_PREFIX option mentioned in the documentation doesn't seem to work?