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

   changelog
   installation
   configuration
   usage
   contributing

.. toctree::
   :maxdepth: 4
   :caption: API

   Core package <api/aria.core>
   Conbox package <api/aria.conbox>

.. toctree::
   :maxdepth: 2
   :caption: Tutorial

   tutorial/setup
   tutorial/run
   tutorial/analysis

.. toctree::
   :maxdepth: 2
   :caption: Examples

   examples/bpt1/bpt1
   examples/malecoli/malecoli