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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Revisit overall strategy Although up until now we've always started with a tree of known topology, a lot of times you wouldn't know the tree topology beforehand for all possible trees: compute score (tree) return best tree Scoring functions 1. max parsimony (fewest mutations) 2. generalized parsimony (Sankoff: weighted mutation costs)
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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.

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

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