Models | Find Best DNA/Protein Models (ML)
This option tests a data file (nucleotide or amino acid) for goodness of fit to some popular models of evolution, and returns the values of several criteria which can be used to pick the most appropriate evolutionary model for your analysis. The results also show the estimated values of all parameters for each model (frequencies, transition probabilities, rate variation parameters, etc), plus the count of total parameters. In most cases you would pick a model that has a low number of parameters (to keep variance low) yet is accurate enough (as measured by the goodness-of-fit criteria) for your needs.