====== hyphy ======
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.

===== Information =====

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

===== Usage =====

See which versions are available:
<code>$ module avail hyphy</code>

Load one version into your environment and run it:
<code>$ module load hyphy/2.5.48
$ hyphy</code>

**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!

===== Installation ======
Notes from the sysadmin during installation.

<code>$ 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</code>

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