There are very many simulations of evolving populations: indeed, most theoretical research in evolution now involves some kind of simulation.
Some simple examples can be found at the PBS Evolution site.
EvoBeaker provides a sophisticated simulation package for teaching.
EvoTutor is simpler, but free.
MS and SimCoal are two of many packages that simulate the coalescent process (Chapter 15).
Nemo simulates structured populations.
In contrast to simulations of definite evolutionary models, artificial life sets up open-ended simulations that may evolve in unexpected ways. The International Society of Artificial Life keeps a list of programs. A popular system is Avida, from the Digital Life Laboratory.
Felsenstein maintains an index of programs that estimate the relationships between species, currently, 330 of them. Two of the best-known are PHYLIP and PAUP. See Chapter 27.
There are many packages designed to carry out specific statistical analyses: We do not list these.