From PyPi

The PPP can also be easily installed via the PyPi repository via pip:

pip install py-popgen

From Conda

The PPP has conda packages available for python versions 3.6 and 3.7. To install in a clean environment, run the following:

conda create -n py-popgen python=3.7.7
conda activate py-popgen
conda install -c jaredgk -c bioconda py-popgen

From Source

The most current version of the PPP can be installed by obtaining the source code from the PPP GitHub repository. This can be done with:

git clone

To install the local repository copy and allow edits to the source code to be included with imports without any additional steps, run the following commands:

cd PPP
pip install -e .

To install the repository without pip, run the following (note that any modifications to the source code will not be used at runtime unless the setup command is run again):

cd PPP
python install


If installing PPP from source, multiple python and non-python depencencies must also be installed.

Python Dependencies

The PPP requries a number of python libraries, including:

We recommend users install and maintain these libraries using either pip or Anaconda 3.

Other Dependencies

The PPP also requries a number of executables to be installed, including:

Please note that VCFtools, BCFtools, Samtools, HTSlib, plink 1.9, plink 2.0, and SHAPEIT may be installed using Anaconda 3.