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Unformatted text preview: erJcal) height. • UPGMA assumes a constant molecular clock: all species represented by the leaves in the tree are assumed to accumulate mutaJons (and thus evolve) at the same rate. This is a major piaalls of UPGMA. 9 8 6 d(2,3) / 2 2 d(7,8) / 2 7 3 4 5 • The algorithm produces an ultrametric tree : the distance from the root to any leaf is the same 1 65 UPGMA’s Weakness: Example Correct tree UPGMA 3 2 4 1 1 4 2 3 Three Methods of Tree ConstrucJon Distance: a tree that recursively combines two nodes of the smallest distance. Parsimony: A tree with a total minimum number of character changes between nodes. Maximum likelihood : Finding the best Bayesian network of a tree shape. The method of choice nowadays. 68 2 9/24/13 Alignment Matrix vs. Distance Matrix Sequence a gene of length m nucleoJdes in n species to generate an n x m alignment matrix CANNOT be transformed back into alignment matrix because informaJon was lost on the forward transformaJon Transform into n x n distance matrix Character Based Tree ReconstrucJon • Be>er technique: – Character based reconstrucJon algorithms use the n x m alignment matrix...
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 Fall '13
 AsaBenHur

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