Once you have calculated the eigenvalues for one or more potential function, the transition matrix is easily calculated. From the ‘Graph’ menu, choose ‘New Transition Matrix’. A window will appear that instructs you to click on the graph window of two graphs to specify for which graphs the matrix should be calculated.
Clicking on the same graph twice will calculate the transition matrix for transitions within a single potential function. Once two graphs have been selected, a new window will appear showing the transition matrix.