pyemma (conda): PyEMMA (EMMA = Emma's Markov Model Algorithms) is an open source Python/C package for analysis of extensive molecular dynamics simulations. In particular, it includes algorithms for estimation, validation and analysis of:   * Clustering and Featurization   * Markov state models (MSMs)   * Hidden Markov models (HMMs)   * Multi-ensemble Markov models (MEMMs)   * Time-lagged independent component analysis (TICA)   * Transition Path Theory (TPT)
Keywords: analysis|bayesian-methods|hidden-markov-model|hmm|kinetic-modeling|markov-model|markov-state-model|mbar|molecular-dynamics|molecular-modeling|python|tica|time-series|umbrella-sampling