To start out you can pick flies with known mutations, or you can ask the program to randomly create mutant flies. A new window appears showing the results of the cross. As a note of historical interest, I believe that this is the original BioQuest program. The program has a nice intuitive interface, making it easy to conduct the crosses and look at the results. Unfortunetly, the program was designed to be run on old macintoshes with small, black and white screens, so everything on the screen is small and there is no color.
All flies look the same, no matter what their mutations.
Despite this small caveat, this program is really well done and engaging. My hunch is that using this program, students will gain a greater understanding of why they make different crosses and what the results mean than they would with a wet lab, because they won't have to worry about taking care of the real flies and everything happens in a few minutes instead of a few weeks. Thus I would guess that this program should be good for either replacing or supplementing a typical introductory fly genetics laboratory.