msmtools is an open source collection of algorithms for the estimation and analysis of discrete state space Markov chains via Markov state models (MSM).

The algorithms are implemented using NumPy and SciPy.

With pip:

pip install msmtools

with conda:

conda install -c https://conda.binstar.org/omnia msmtools

or install latest devel branch with pip:

pip install git+https://github.com/markovmodel/msmtools.git@devel

For bug reports/sugguestions/complains please file an issue on GitHub.

Or start a discussion on our mailing list: pyemma-users@lists.fu-berlin.de