PaNDA

This is the repository corresponding to the paper:

PaNDA: Efficient Optimization of Phylogenetic Diversity in Networks. Niels Holtgrefe, Leo van Iersel, Ruben Meuwese, Yukihiro Murakami, Jannik Schestag. bioRxiv, 2025. doi: 10.1101/2025.11.14.688467

Using PaNDA

The PaNDA software is easy to install and can either be run with a graphical user-interface (GUI) for inexperienced programmers, or as part of our Python package phypanda which allows for more functionality (and is therefore recommended if the user is experienced with Python). For an installation guide and a more detailed overview of the features (including screenshots for the GUI), please click on the links below to visit the README.md files in the respective folders:

• gui, for the graphical user-interface;
• phypanda, for the corresponding Python package.

To test out the GUI or the Python package, we recommend using the Xiphophorus phylogenetic network in the file exp2_xiphophorus_network.txt.

Supplementary data and scripts

The simulation results, data sets and used scripts from the experiments in the paper are all in the folder data. For a more detailed explanation of these files, see the README.md file in the folder.

Citation

If you use any of the code in this repository, please cite the corresponding paper:

PaNDA: Efficient Optimization of Phylogenetic Diversity in Networks. Niels Holtgrefe, Leo van Iersel, Ruben Meuwese, Yukihiro Murakami, Jannik Schestag. bioRxiv, 2025. doi: 10.1101/2025.11.14.688467