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======================================
EMMA -> Emma's Markov Model Algorithms
======================================

This software is a collection of algorithms implemented mostly in
`NumPy <http://www.numpy.org/>`_ and `SciPy <http://www.scipy.org>`_ to analyze
trajectories generated from any kind of simulation (e.g. molecular
trajectories) via Markov state models (MSM). It provides an API for estimation
and analyzing MSM and various utilities to process input data (clustering,
coordinate transformations etc). For documentation of the API, please have a
look at the :ref:`ref_api`. To install this software and additional
dependencies refer to the :ref:`Installation Guide <ref_install>`. For
support/bug reports/sugguestions/complains please visit us at
`GitHub <http://github.com/markovmodel/PyEMMA/>` or post to the PyEMMA mailing
list: pyemma-users@lists.fu-berlin.de

Installation
============

.. toctree::
   :maxdepth: 2

   INSTALL
   Configuration


Documentation
=============

.. toctree::
   :maxdepth: 2

   api/index

Tutorials
=========

.. toctree::
   :maxdepth: 2

   ipython


Development
===========
.. toctree::
   :maxdepth: 2

   CHANGELOG
   DEVELOPMENT


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

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