phylozoo 0.1.1

A phylogenetic networks analysis package

PhyloZoo is a Python package for working with phylogenetic networks and related evolutionary data types. PhyloZoo aims to provide the foundational infrastructure for phylogenetic network analysis in Python — a common framework that other packages can build on.

Key Features

• Directed & semi-directed networks — represent phylogenetic networks as fully directed rooted DAGs or as semi-directed/mixed graphs that allow root uncertainty. Both representations are validated on construction to guarantee well-formed phylogenetic objects. Includes a rich library of operations: network classifications, generators, conversions between representations, and much more.
• Quartets, splits & distance matrices — support for quartet systems, split systems, and pairwise distance matrices: the core building blocks for phylogenetic inference and comparison.
• Multiple sequence alignments — store and manipulate sequence data with efficient NumPy-backed arrays, including bootstrapping and site-pattern extraction.
• Flexible visualization — plot networks with different layouts and fine-grained control over styling, labels, and coloring via Matplotlib.
• Standard file formats — read and write common phylogenetic formats including eNewick, DOT, FASTA, and NEXUS, making it easy to integrate with existing workflows.
• Performance — leverages NumPy and optional Numba JIT compilation for computationally intensive algorithms.

Installation

To install the recommended version that includes vizualization, do:

pip install phylozoo[viz]

Documentation

For detailed documentation, installation instructions, tutorials, and API reference, visit the PhyloZoo docs.

Citation

If you use PhyloZoo in your research, please cite:

Niels Holtgrefe (2026). PhyloZoo. Available at: https://github.com/nholtgrefe/phylozoo