Define the likelihood function The likelihood function for phylogenetic trees depends on the dataset, tree topology, and the substitution model (and its parameters). To define a likelihood function, we use a statement like LikelihoodFunction theLikFun = (myFilter,myTree); We name the likelihood function theLikFun, and it uses the data in myFilter along with the tree topology and substitution model stored in in myTree. Recall that the Tree structure myTree inherited the Model F81 by default.
Sergei L. Kosakovsky Pond and Spencer V. Muse, 1997-2002