PhyloZoo: a unified framework for phylogenetic network analysis in Python.

PhyloZoo provides a unified, open-source Python framework supporting multiple phylogenetic network representations, including semi-directed networks, for reticulate evolution analysis.

• Why it matters: Reticulate evolutionary processes like hybridization and horizontal gene transfer are common but cannot be fully captured by traditional phylogenetic trees, creating a need for versatile modeling tools. Existing software often limits researchers to specific inference methods and lacks support for multiple network types in a programmable environment.
• What they did: The framework offers data structures, algorithms, visualization tools, and robust I/O for major phylogenetic file formats, with a focus on semi-directed networks that explicitly represent root uncertainty, facilitating reproducible workflows and theoretical exploration.
• The result: PhyloZoo enables scalable, interoperable, and reproducible phylogenetic network analyses, supporting applied, methodological, and theoretical studies of reticulate evolution in a flexible Python environment.