phypanda

phypanda is the Python library for PaNDA—an algorithm library for phylogenetic diversity (PD) optimization on directed phylogenetic networks. It builds on phylozoo for network representations and scanwidth for node- and edge-scanwidth–based dynamic programming.

Key Features

• All-paths (MAPPD), Max-tree and Min-tree PD: compute the diversity score of a fixed taxon set for several PD measures, or maximize PD using exact FPT algorithms parameterized by node scanwidth or edge scanwidth.
• Budgeted maximization: assign integer costs to taxa and maximize PD under budget constraints.
• JIT-compilation: speed up algorithms by optional numba JIT compilation.
• High-level API — compute_diversity, marginal_diversities, greedy_max_diversity, and solve_max_diversity work with any measure and dispatch to the appropriate solver.

Installation

pip install phypanda

Runtime dependencies (phylozoo, networkx, scanwidth, numba) are installed automatically. For development or documentation extras:

pip install phypanda[dev]   # testing
pip install phypanda[docs]  # Sphinx documentation

Documentation

For the full manual, API reference, and installation guide, visit the phypanda docs.

Citation

If you use phypanda, please cite:

Niels Holtgrefe, Leo van Iersel, Ruben Meuwese, Yukihiro Murakami, and Jannik Schestag. PaNDA: Efficient Optimization of Phylogenetic Diversity in Networks. Journal of Computational Biology, 2026. doi: 10.1177/15578666261481955

If your work builds specifically on the budgeted node-scanwidth algorithms, please also cite:

Niels Holtgrefe and Jannik Schestag. Tractable Optimization of Budgeted Phylogenetic Diversity on Networks Utilizing Node-Scanwidth. arXiv:2605.23319, 2026.

See also

For the graphical-user interface developed for the first paper, please go to gui/.

For the experimental materials corresponding to the above two papers, please go to experiments/.