This recently released program is an independent tool used to carry out statistical selection of best-fit models of nucleotide substitution without the aid of PAUP*. It implements five different model selection strategies: hierarchical and dynamical likelihood ratio tests (hLRT and dLRT), Akaike and Bayesian information criteria (AIC and BIC), and a decision theory method (DT). It also provides estimates of model selection uncertainty, parameter importances and model-averaged parameter estimates, including model-averaged phylogenies. Although jModelTest it is optimized for MacOS X Intel, executables are provided to run the program under MacOS X PPC, Windows XP and Linux.
Download this program from the jModelTest home page.