msmtools

Library Markov chain inference Python/C, LGPL license. v1.2.1 (12 releases).

bhmm

Library for Hidden Markov model inference Python/C, LGPL license. v0.5.2 (9 releases).

thermotools 

Library for statistical inference from multi-ensemble data, Python/C, LGPL license. v0.2.6 (22 releases).

molPX

Python module for interactive visualization of projected coordinates of molecular dynamics (MD) trajectories.

deeptime

Deep learning meets molecular dynamics. In development.