Ensemble Analyzer Documentation
===============================

.. image:: ../../logo.png
   :width: 200px
   :align: right

.. toctree::
   :maxdepth: 2
   :caption: Scientific Background

   theory.md

.. toctree::
   :maxdepth: 2
   :caption: User Guide

   installation.md
   user_guide/workflow.md
   user_guide/cli_tools.md
   user_guide/protocol.md
   user_guide/cli_command.md
   
.. toctree::
   :maxdepth: 2
   :caption: Tutorial and Examples 

   tutorials/quickstart.md
   tutorials/example_1.md
   tutorials/example_2.md
   tutorials/example_3.md
   tutorials/example_4.md


.. toctree::
   :maxdepth: 2
   :caption: API Reference

   api_reference.rst

Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`