Ratio of Deleterious Mutations to Beneficial Ones

I don't know the particular software. But I doubt that it is a problem.The thing to remember, is that there is actual evidence of evolution occurring. So software models that are inconsistent with the actual evidence are not very persuasive.Here's the thing to remember with mutations: If a population is well adapted to its environment, then most changes will be changes for the worse. That is, most mutations will be deleterious.This is just the basic principle that, if you are at the top of the mountain, the only way to go is down.For a population that is not as well adapted, there is a greater possibility of beneficial mutations. Or, in mountain climbing terms, if you are only part way up, then a random move is as likely to lead you up as to lead you down.