Tree Models [JF:33]

The non-clock model is the standard model used in phylogenetic inference. As mentioned in one of the previous lectures, it can be considered as a branch-breaking model which allows the evolutionary rate to be different for each branch in the tree. Because of this, the non-clock tree model has a large number of free parameters, one for each branch in the tree. If there are n tips in the tree, there are 2n− 3 branches and hence branch length parameters in the tree model. This means that, for a typical phylogenetic problem, the largest number of free parameters comes from the branch lengths. For instance, consider a GTR model applied to a non-clock tree with 100 tips. There are 8 free parameters in the GTR model (3 free parameters from the stationary state frequencies and 5 from the substitution rates) but an astonishing 197 branch length parameters.