We are happy to announce the software package PyEMMA 2 for estimation, validation and analysis of Markov models and other kinetic models from molecular dynamics simulations.
Download instructions, online docs and tutorials are found here:
http://pyemma.org
The paper just appeared in JCTC:
http://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b00743
The source code (LGPL) is hosted here. Contributions are more than welcome:
https://github.com/markovmodel/pyemma
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