Constructing Phylogenetic Trees using Maximum Likelihood

Maximum likelihood methods are used to estimate the phylogenetic trees for a set of species. The probabilities of DNA base substitutions are mod-eled by continuous-time Markov chains. We use these probabilities to es-timate which DNA bases would produce the data that we observe. The topology of the tree is also determined using base substitution probabili-ties and conditional likelihoods. Felsenstein [2] introduced this method of finding an estimate for the maximum likelihood phylogenetic tree. We will explore this method in detail in this paper. Contents Abstract ii