PyEMMA - Markov Modeling Suite

Python version of EMMA (Emma's Markov Model Algorithms) is a software package for building, validating and analyzing Markov models based on trajectory data. It is especially suited for Markov models of molecular kinetics based on simulation trajectories from commonly-used simulation packages such as Gromacs, Charmm, NAMD and others. The package is continuously updated.

msmtools - Low-level routines for Markov model estimation and analysis

msmtools is a low-level subsidiary Python package for PyEMMA and is installable separately with minimal dependencies (numpy and scipy). msmtools provides robust and efficient functions for Bayesian estimation of Markov chains from discrete-state trajectories and a variety of analysis tools.