pi_lec2 - 20.181 Lecture 2 Contents 1 Homework 1 Review o...

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20.181 Lecture 2 Contents 1 Homework 1 Review o 1.1 Going over UPGMA 2 What happened to the dentist? 3 What is phylogenetics good for? 4 Newick Notation Homework 1 Review HW1 #2 can be done by hand, you are not required to code for this. Going over UPGMA D(i,j) = 1/(Size(i)*Size(j)) * [SUM(p in i, q in j) d(p,q)] summing over all possible pairs in your subtree. One of the more common ways to go from a set of distances to a full tree. But its not always the right thing to use. o UPGMA assumes distance = time. This is called the ultrametric assumption. o What if the "true" tree has some branches much longer than others? (due to faster evolution in those species) How to traverse a tree (by hand) to find the distance between two nodes on it: o Walk up the tree from node1 to the common ancestor of those two nodes, walk down the tree to node2, adding the branch lengths as you go. o
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pi_lec2 - 20.181 Lecture 2 Contents 1 Homework 1 Review o...

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