The analyze.py script takes the model.xml file as an argument. It constructs the milestoning model, populates it with transition probabilities and simulation times within each milestone, and computes error margins. For a list of arguments that can be used with analyze.py, we can run the script with the -h argument (Summary 3). Figure shows the free energy profile per milestone for the BCD-1-butanol complex, obtained by executing the analyze.py script.