This model contains a set of edges, each of which implements a General Time Reversible model. 4 This is used to specify a list of allowed states (state_names), and a parallel array of their (observed?) frequencies. The Binary State Speciation and Extinction model of Maddison et al. 2007 This is the class of edges upon which DNA sites change according to a JukesCantorMatrix. A transition matrix. This is some sort of array or multidimensional matrix of ParameterValues. This is a function whose output could be a constraint value or an estimated parameter (this is almost like a closure or something) This is a branch in a tree (i.e. topology), to which we can attach the bits that go into a single model, but we can mix and match in order to specify a mixture model (with ratios as weight). This is a tree shape, we would use this to organize edges, to which we can link models. This is a class of models that generate or estimate tree shapes. This is a Hidden Markov Model. The DataMap captures the interactions between two or more characters expressed in terms of a covariance matrix and estimated model parameters. This is the superclass of data types that phylogenetic models might estimate. This contains a set of edges that each implement a JukesCantor model. A parameter value constrained to a (specified) constant value 0.25