physquirrel 1.0.8

Package for reconstructing semi-directed phylogenetic level-1 networks from four-leaved networks and sequence alignments

physquirrel

physquirrel is the Python library for Squirrel—an algorithm for reconstructing semi-directed phylogenetic level-1 networks from quarnets and/or sequence alignments. It uses networkx for network representations and numpy, scipy, and matplotlib for computation and visualization.

Key Features

• δ-heuristic: construct quarnets (4-leaf subnetworks) from multiple sequence alignments in .fasta or .nexus format
• Squirrel algorithm: reconstruct semi-directed phylogenetic level-1 networks from quarnets
• Visualization: basic plotting of phylogenetic networks
• eNewick export: serialize phylogenetic trees and networks in eNewick format

Installation

pip install physquirrel

Runtime dependencies (numpy, networkx, matplotlib, scipy) are installed automatically.

Documentation

For more detailed usage instructions visit the physquirrel docs and/or check the docstrings in the source code.

Citation

If you use physquirrel, 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

See also

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

For the experimental materials corresponding to the paper, please go to experiments/.