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pi_lec7 - 20.181 Lecture 7 Contents 1 quick comment on...

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20.181 Lecture 7 Contents 1 quick comment on upPass o 1.1 definitions 2 Revisit overall strategy o 2.1 Scoring functions 3 ML intro 4 Probability Refresher 5 ML in trees 6 Jukes-Cantor 7 Evolutionary Model Quick comment on upPass not necessary to find the best tree (you won't be tested on it) but here's the correct way to do it (via Dr. Fredrik Ronquist's lecture notes on "Parsimony: Counting Changes," from FSU's Computational Evolutionary Biology course) ( PDF ) Definitions 1. F x : the upPass set we want to get to 2. S x : the downpass set we got to 3. ancestor = a 4. parent = p, node we're looking at 5. children = q,r
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