Welcome to the physquirrel docs!

physquirrel is the Python implementation of the Squirrel algorithm for reconstructing level-1 phylogenetic networks from quartet data and/or sequence alignments. It works on networks, MSAs, and distance matrices represented by PhyloZoo, infers 4-leaf subnetworks via the delta heuristic, and then reconstructs semi-directed or rooted networks.

Documentation Overview

New to physquirrel? Start with the Quickstart. For a complete walkthrough of all input types and options, see the Manual. For detailed installation instructions, see the Installation Guide. See the API Reference for detailed documentation of all public symbols, organized by module.

Contents

• Quickstart
  • Install
  • Run Squirrel
  • Visualize (optional)
  • Next steps
• Installation
  • Installing physquirrel
  • Verifying Installation
  • Building Documentation
  • Troubleshooting
• Manual
  • Input data
  • Running Squirrel
  • I/O and plotting
  • Quick Links
• API Reference
  • Datatypes
  • I/O
  • Squirrel pipeline
  • Internal Algorithm Steps
  • Convenience Helpers
  • TSP Solvers
• Changelog
  • Version 2.0.0
  • Version 1.0.7

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, Katharina T. Huber, Leo van Iersel, Mark Jones, Samuel Martin, and Vincent Moulton. Squirrel: Reconstructing semi-directed phylogenetic level-1 networks from four-leaved networks or sequence alignments. Molecular Biology and Evolution, 42(4):msaf067, 2025. doi: 10.1093/molbev/msaf067