Stochastic or probabilistic methods for phylogeny aim to rank trees according to the probability of observing the data (i.e., the multiple sequence alignment) given the tree’s topology. The probabilistic tree construction methods estimate \(P(x \mid T,t)\) to compute the probability. Here, the data are the set of n sequences (taxa), T is the tree, and t denotes the specific edge lengths of the tree branches. To quantitatively define this probability, an underlying model of evolution is assumed.