physquirrel 2.0.0

a package for reconstructing level-1 phylogenetic networks from sequence alignments or 4-leaf subnetworks

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 builds on phylozoo for network representations and numba for JIT-accelerated computation.

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
• eNewick export: serialize phylogenetic trees and networks in eNewick format
• Visualization: plot phylogenetic networks via the optional viz dependency

Installation

pip install physquirrel

Runtime dependencies (phylozoo, numpy, networkx, numba) are installed automatically. For visualization extras:

pip install physquirrel[viz]

Documentation

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

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/.