Welcome to the phypanda docs!

phypanda is the Python package corresponding to the PaNDA algorithm suite for computing and optimizing phylogenetic diversity (PD) in directed phylogenetic networks. It works on networks represented by PhyloZoo, uses the scanwidth package to compute tree extensions, and provides fixed-parameter tractable algorithms for several budgeted PD problems. For definitions and proofs, see the references below.

You can score a set of taxa under different PD measures—all-paths (MAPPD), max-tree, and min-tree—optimize under an integer budget with taxon costs, and supply precomputed tree extensions to speed up repeated solves on the same network.

Documentation Overview

A good starting point is either the Installation page or the Manual guide.

Contents

• Installation Guide
  • Installing phypanda
  • Verifying Installation
  • Building Documentation
  • Troubleshooting
• Manual
  • Loading a network
  • PD calculations
  • PD Measures
  • Quick Links
• API reference
  • Base helpers
  • Measure protocol
  • Measures

Indices and tables

• Index — index of all functions and classes.

• Module Index — index of all modules.

• Search Page — search the documentation.

Citation

If you use this package in research, please cite:

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

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. 2026.