Welcome to the PhyloZoo docs! PhyloZoo is a Python package for working with phylogenetic networks and related evolutionary data. Phylogenetic networks extend evolutionary trees by allowing multiple ancestral paths, capturing complex processes such as hybridization, recombination, or gene exchange.

PhyloZoo provides a unified framework for handling network objects and closely related data types, including split systems, quartets, distance matrices, and sequence alignments. It offers consistent data structures, internal validation, and robust file input/output, and allows users to move seamlessly between representations.

Documentation Overview

This documentation is organized into the following sections. A good starting point is either the Introduction of the manual or the Quickstart tutorial.

Complete user manual for using PhyloZoo

• Manual
  • Introduction
  • Installation
  • Core Module
  • Visualization Module
  • Utilities Module
  • Bibliography

Tutorials for specific workflows with PhyloZoo

• Tutorials
  • Quickstart

Complete function and class API reference

• API Reference
  • Core
  • Visualization
  • Utilities

Development documentation

• Development
  • Contributing
  • Package Principles
  • Code Style Guide
  • Testing Guide
  • Changelog

Citing PhyloZoo

If you use PhyloZoo in your research, please cite the package as follows:

Niels Holtgrefe (2026). PhyloZoo. Version 0.1.0. Available at: https://github.com/nholtgrefe/phylozoo

If applicable, please also make sure to track down any relevant references for the algorithms you are using.

Indices and tables

The documentation provides the following autogenerated indices and tables:

• Index - Index of all functions, classes, and modules.

• Module Index - Index of all modules.

• Search Page - Search the documentation.