Graduation Year

Spring 2012

Document Type

Open Access Senior Thesis

Degree Name

Bachelor of Arts



Reader 1

Christopher Towse

Reader 2

Ami Radunskaya

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© 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 [2] introduced this method of finding an estimate for the maximum likelihood phylogenetic tree. We will explore this method in detail in this paper.