Lecture_7_phylogenetics

Dij edit distance between i and j note the dierence

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Unformatted text preview: of nucleo?de/amino acid changes (usually used to illustrate evolu?onary rela?onships only). 28 Three Methods of Tree Construc?on Three Methods of Tree Construc?on 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. 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. 29 30 5 9/16/13 Distances Measurements •  It is oken useful to measure the gene?c distance between two species, between two popula?ons, or even between two individuals. •  The en?re concept of numerical taxonomy is based on compu?ng phylogenies from a table of distances. •  In the case of sequence data, pairwise distances must be calculated between all sequences that will be used to build the tree - thus crea?ng a distance matrix. •  Distance methods give a single measurement of the amount of evolu?onary change between two sequences since divergence from a common ancestor. Distances in Trees •  Edges may have weights reflec?ng: –  Number of muta?ons on evolu?onary path from one species to another –  Time es?mate for evolu?on of one species into another •  In a tree T, we oken comput...
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