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**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 :doc:`Introduction <manual/introduction>` of the manual or the :doc:`Quickstart <tutorials/quickstart>` tutorial.

.. toctree::
   :maxdepth: 2
   :caption: Complete user manual for using PhyloZoo
   
   manual/index

.. toctree::
   :maxdepth: 2
   :caption: Tutorials for specific workflows with PhyloZoo
   
   tutorials/index

.. toctree::
   :maxdepth: 2
   :caption: Complete function and class API reference
   
   api/index

.. toctree::
   :maxdepth: 2
   :caption: Development documentation
   
   develop/index

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:

* :ref:`genindex` - Index of all functions, classes, and modules.
* :ref:`modindex` - Index of all modules.
* :ref:`search` - Search the documentation.