ProDy comes with two sets of applications that automate structural dynamics and sequence coevolution analysis:

On Linux, when installing ProDy from source, application scripts are placed into a default folder that is included in PATH environment variable, e.g. /usr/local/bin/.

On Windows, installer places the scripts into the Scripts folder under Python distribution folder, e.g. C:\Python27\Scripts. You may need to add this path to PATH environment variable yourself.