Lecture_7_part2_phylogenetics

Since each nucleojde site evolves independently the

Info iconThis preview shows page 1. Sign up to view the full content.

View Full Document Right Arrow Icon
This is the end of the preview. Sign up to access the rest of the document.

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...
View Full Document

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.

Ask a homework question - tutors are online