After detecting the lines in an image using Hough lines, how can I use it to calculate the change in angle (rotation) of the lines of a reference image?
I am not sure what the MATLAB implementation of the Hough transform is, but the orientation of the line will be simply be at a right angle (90 degrees or pi/2 radians) to the angle you've used to identify the line in the first place.
I hope that helps. There's decent coverage of Hough transforms on the web and Wikipedia is a good place to start.