A year ago, I asked a couple questions about a world I was building where the all the ecosystems in a planet were designed from scratch by a galactic consortium of species (1, 2, 3). I'm revisiting that world, and trying to dig deeper to look at some of the issues the scientific group would have to deal with.
In particular, I'm interested in how the group could model evolution (though I'm not asking about that). To try to better figure out what methods they could use, I'd like to do some simulations of my own. I know that computational evolution is an active field, and I've seen a Stack Overflow question about simulations that have been done, and some packages available to people wanting to do things themselves. However, I'm more interested in planet-wide (or at least continent-size) simulations - because, after all, the alien experiment involves an entire planet.
What programs or resources are out there that can be used to simulate evolutionary processes across an Earth-like planet? I'm looking for things along the lines of SimEarth, although I don't know how good that particular one is - and it seems more like a game than a worldbuilding tool.