To estimate the tree structure for a set of taxa, we typically use a statistical model for evolution and compute the maximum likelihood estimate. Molecular Biologists recognize that the model is a rough approximation to reality and there is considerable literature on the effects of model deviations. In this talk, I will develop the standard Markov models used for phylogeny and then examine some of the likely deviations from the model. Will illustrate in a couple of settings that the deviations do have an effect on the results.
Group for Research in Decision Analysis