Yes.
Use the branching system (AKA forkline, arithmetic method, other names). There is an explanation in Wilmer Miller's web site,
http://www.ringneckdove.com. Go to the contents page, find the "Science & ..." section, and click on "Advances in Classical Genetics". It is in the "Calculation of probabilities" section, though the whole paper is worth reading. You might also google for the combination of words "genetics" and "branching system". I've got at least one file on the subject, and I'll try to e-mail what I can in a few days.
FWIW, I'm pretty sure that at least two people have used the branching system in writing a genetics breeding program, but AFAIK they are all hardcoded for corn snakes. The most versatile genetics program I know of is the Genetics Wizard, and that has some major faults. I think that a program needs external lists of mutant genes so that a user can switch from corn snakes to ball pythons to pigeons to fruit flies to corn just by selecting which list of mutants to use.