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EMMA - Markov Model Algorithms EMMA ("Emma brings you Markov Model Algorithms") is a software package for building, validating and analyzing Markov models based on trajectory data. It is especially suited for Markov models of molecular kinetics based on simulation trajectories from commonly-used simulation packages such as Gromacs, Charmm, NAMD and others. The package is continuously updated.
SciMex - Scientific Computing tools for Molecular Experiments SciMex is a software package for analyzing both single-molecule and ensemble kinetic biophysical experiments of molecules. Experiments for which this is useful include single-molecule FRET or fluorescence measurements, Equilibrium force-probe experiments using optical tweezers or AFM, Temperature-jump experiments, Fluorescence-correlation spectroscopy. Current algorithms:
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