Part 7: adding the GTR model

The substitution model implemented in Part 6 was the JC69 model. The only parameters of this model are edge lengths, and thus it does not accommodate even the most basic aspects of molecular evolution, such as transition/transversion bias and unequal base frequencies. Furthermore, our previous model assumed rates were equal across sites and thus did not do anything to accommodate among-site rate heterogeneity. This section introduces the standard GTR+Gamma model, which can handle among-site rate heterogeneity, unequal nucleotide frequencies, and unequal exchangeabilities (including transition/transversion bias).