Assignment7 - BSC5936-Fall 2005-PB,FR Computational...

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Unformatted text preview: BSC5936-Fall 2005-PB,FR Computational Evolutionary Biology Assignment 7 In this assignment, the task is to obtain the maximum likelihood of a tree (topology) and (option- ally) to search for the maximum likelihood tree (topology). We will examine the simplest possible case, the Jukes Cantor model, in which there is no substitution model parameters to optimize. Thus, we need only optimize branch lengths to get the maximum likelihood of a tree (topology). To optimize the branch lengths, we cycle through the branches in the tree and optimize one branch at a time. When we have optimized all branches once, we start over from the first branch, and continue cycling through the tree until the likelihood score does not improve significantly. Optimizing one branch length is easy for the Jukes Cantor model. First, the conditional likelihoods are pulled towards the two end points of the branch from the two subtrees on each side of the branch. Then the maximum likelihood branch length, v conditional on the likelihoods at the two...
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This note was uploaded on 11/27/2011 for the course BSC 5936 taught by Professor Staff during the Spring '08 term at FSU.

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Assignment7 - BSC5936-Fall 2005-PB,FR Computational...

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