I would like to do simulations using cellular automata to describe the behavior of influenza. What software do you recommend?
Well Mathematica provides a reasonable amount of intrinsic functionality for working with Cellular Automata. It's not an area of the system I have extensive experience of and I don't know how it compares with other software with similar functionality. You might learn more about it's CA capabilities before breaking open your piggy-bank (maybe digging into your trust fund too, Mathematica's not cheap) over at the sister site https://mathematica.stackexchange.com.
Beyond that, I'd have thunk that programming CA's isn't tremendously difficult in many programming languages.