So, essentially, you're interested in modeling changes in genetics over long periods of time and/or comparing genetic sequences for similarities and differences, right? By diseases, I'm guessing you mean genetic ones, right? (Correct me if I'm wrong.)
If you want to examine different genetic sequences for similarities and differences, I would recommend using a phylogenetic comparative method (PCM). I've seen some good things about one called the Goloboff method, and there's a free program called TNT (you can find information here
and a download link here
) that you can download and use for your analysis.
Hope this helped!