Open Access Senior Thesis
Bachelor of Arts
© 2012 Anna Cho
Maximum likelihood methods are used to estimate the phylogenetic trees for a set of species. The probabilities of DNA base substitutions are modeled by continuous-time Markov chains. We use these probabilities to estimate which DNA bases would produce the data that we observe. The topology of the tree is also determined using base substitution probabilities and conditional likelihoods. Felsenstein  introduced this method of finding an estimate for the maximum likelihood phylogenetic tree. We will explore this method in detail in this paper.
Cho, Anna, "Constructing Phylogenetic Trees Using Maximum Likelihood" (2012). Scripps Senior Theses. 46.