Since each nucleojde site evolves independently the

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Unformatted text preview: tree and assign each vertex with opJmal character. Sankoff Algorithm (cont.) And the tree is thus labeled… Sankoff Algorithm (cont.) 9 is derived from 7 + 2 So left child is T, And right child is T 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. 92 6 9/24/13 Maximum Likelihood AssumpJons for Maximum Likelihood •  The method of Maximum Likelihood aYempts to reconstruct a phylogeny using an explicit model of evoluJon. •  The frequencies of DNA transiJons (C<- >T,A<- >G) and transversions (C or T<- >A or G). •  This method works best when it is used to test (or improve) an exisJng tree. •  Even with simple models of evoluJonary change, the computaJonal task is enormous, making this the slowest of all phylogeneJc methods. Computer Sonware for PhylogeneJcs –  PHYLIP is a free package that includes 30 programs that compute various phylogeneJc algorithms on different kinds of data. –  The GCG package (available at most research insJtuJons) contains a full set of programs for phylogeneJc analysis including simple distance- based clustering and to more complex analysis program PAUP (PhylogeneJc Analysis Using Parsimony) –  CLUSTALX is...
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This note was uploaded on 02/10/2014 for the course CS 425 taught by Professor Asaben-hur during the Fall '13 term at Colorado State.

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