You cannot display an animated GIF with standard MATLAB methods.
Usually a progressbar is displayed for such jobs. Beside MATLAB's WAITBAR, there are a surprising large number of submissions in the Fex: progressbar? .
If your code contains a loop, you can update an image after a certain time step. Or you can create a timer object, which updates an image object. A DRAWNOW might be needed to allow the timer's callback to be executed.
If you call a single command, which takes a lot of time (e.g. invert a giantic matrix), I do not know a sufficient method, because MATLAB is a single threaded application (even if it calls multi-threaded subfunctions) and the main thread cannot be interrupted. It should be possible to start an independent external function, which updates an animation, but this will niot appear inside the MATLAB figure.
