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)