pi_lec4

pi_lec4 - 20.181 Lecture 4 Contents 1 Review of Homework#1...

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20.181 Lecture 4 Contents 1 Review of Homework #1 2 Parsimony Continued o 2.1 Down-Pass Algorithm 3 Sankoff Downpass Algorithm Review of Homework #1 1. Fibonacci question o Using recursion is good with Fibonacci if you're returning (and passing) a list. 2. Parsimony: o Review of how to assess the most parsimonious explanation of nodes' states. o Solution/notes on the Parsimony question. Parsimony Continued Why parsimony? o we can suggest infinite alternative explanations involving increasing numbers of mutations but they become less and less plausible o this algorithm is sometimes called "model-free" because the model is implicit o is parsimony better than just an extreme case of maximum likelihood? This is still debated. One not -optimal way to look for the most parsimonious tree: try all four possibilities at every node. But that would require looking at 4^n possibilities! Using recursion in this problem, we can avoid that.

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pi_lec4 - 20.181 Lecture 4 Contents 1 Review of Homework#1...

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