Mainly developed by "Dr. Wei Wang" at "the Hong Kong University of Science and Technology"
Functions: perform tICA-MSM, MFPT calculation, TPT based on microstate MSM, model selection based on cross valiation..., Chapman-Kolmogorov test.
dependency: python 2.7, numpy, scipy, msmbuilder, sklearn, pyemma, matplotlib
See MSM_for_ala2_v2.ipynb under "songshanhu/" for a complete tutorial for building MSM and extracting thermodynamics & kinetics
hmm_analysis:hidden markov model