The premier computer tool for simulating evolutionary processes has the name Avida. Researchers have reported studies on the evolution of complexity, altruism, changes to genetic architecture, and even the evolution of sex. Avida can be used to illustrate numerous concepts and mechanisms of Darwinian evolution and it has achieved a reputation as a platform for carrying out evolution experiments with digital organisms. As someone who has used simulation as a research tool, the question I have always asked (but to which I have struggled to find a satisfactory answer) concerns validation. It appears that Avida authors have made little or no attempt to cross-validate digital evolution with biological evolution. They have not attempted to move out of their virtual reality world by drawing attention to empirical experiments that give credibility to their conclusions. So how does Avida relate to the real world? At last, a paper has appeared which appears to ask similar questions:
More.