When using software tools to analyze parallelized molecular dynamics (MD) data, it is important to be cautious of default settings and stay informed about the assumptions underlying the analysis. Different tools come with various strengths and limitations, and understanding these will improve the reliability and interpretation of your results. . PyEmma and Deeptime PyEmma and Deeptime are powerful tools for constructing MSMs, performing tICA, and carrying out other essential tasks for analyzing MD simulations . These tools are designed with flexibility in mind and robust dimensionality reduction, them a good choice for users looking to explore features of their dataset using modern ML methods. PyEmma, in particular, is well-suited for building kinetic models, while deeptime offers advanced capabilities for handling non-equilibrium dynamics and applying machine learning techniques .