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Calculating Phase difference from workspace data

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Hi,
As you can see from the diagram below, I have generated two wave functions from the workspace data and now I am interested in calculating/obtaining the phase difference between the two. Is there any efficient way of doing it in MATLAB or some mathematical formulation that I might be able to use?
FYI: My aim is to plot the bode plot eventually from different sets of data, let's say for an unknown system.

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