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Unformatted text preview: Biological Computation 20.181 Homework 5 In the last homework, you calculated the parsimony score for a particular tree and a set of sequences. In this assignment, you will write Python code to evaluate the Maximum Likelihood (ML) score given a tree and associated sequences. You will be provided with both the tree topology (including branch lengths) and the sequences of leaf nodes. The Evolutionary Model. In general, a model of DNA sequence evolution gives the probability that a nucleotide, x, will change to another nucleotide, y (which may or may not be equal to x), over a certain period of time (actually over a certain distance, since evolutionary rates can vary from branch to branch). In the JukesCantor model of evolution, the probability of mutation to any of the three different nucleotides during a short time interval dt is a. Now consider the probability of a site being a certain base at time t, P(t). What is the probability of the site being the same nucleotide at time t + dt, base at time t, P(t)....
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This note was uploaded on 11/11/2011 for the course BIO 20.010j taught by Professor Lindagriffith during the Spring '06 term at MIT.
 Spring '06
 LindaGriffith

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