PhyloGNN
========

.. container:: hero

   Practical graph learning tools for phylogenetic trees.

   PhyloGNN converts `ete3.Tree` objects into PyTorch Geometric `Data` graphs,
   adds deterministic node features, and supports local GNN training workflows
   on those graph samples.

   .. container:: hero-actions

      :doc:`Start with the quickstart <quickstart>`
      :doc:`Install the package <installation>`

Fastest path
------------

.. container:: entry-grid

   .. container:: entry-card

      **Install**

      Start with the core package and add optional extras only for docs, `BEAST`
      file input, or experiment tracking.

      :doc:`installation`

   .. container:: entry-card

      **Quickstart**

      Build a small `ete3.Tree`, attach features, convert it to graph data,
      run a tiny training smoke test, and print a prediction.

      :doc:`quickstart`

   .. container:: entry-card

      **User Guide**

      Follow the full workflow from tree input through feature engineering,
      graph conversion, datasets, training, configuration, and tracking.

      :doc:`user_guide/index`

   .. container:: entry-card

      **Examples**

      Launch six runnable scripts that cover feature engineering, graph
      conversion, tree I/O, training, TOML configuration, and prediction.

      :doc:`examples/index`

   .. container:: entry-card

      **Reference**

      Look up curated public APIs for data conversion, models, training, I/O,
      and utilities.

      :doc:`reference/index`

.. container:: workflow-strip

   **Typical workflow:** tree input → feature engineering → graph conversion →
   training → metrics tracking when needed → API lookup for implementation
   details.

.. Maintainers: add new user-facing task pages under user_guide/ and link them
   from user_guide/index.rst. Add lookup pages
   under reference/, and recovery advice in troubleshooting.rst. Keep legacy
   docs/issues, docs/myprompt, and specs out of official toctrees unless the
   content is rewritten for ordinary users.

.. toctree::
   :maxdepth: 2
   :caption: User Documentation

   installation
   quickstart
   user_guide/index
   examples/index
   reference/index
   troubleshooting