This project is no longer supported. Please switch to pyEMMA: http://pyemma.org

Markov models, often called Markov state models (MSMs) or kinetic transition networks, are concise and easy-to-analyze discrete models of continuous stochastic processes. They have been extensively used in the analysis of molecular dynamics (MD).
The EMMA software provides a number of command line tools that provide the basics of construction, validation and analysis of Markov models. EMMA is Java-based.