Lecture_7_part2_phylogenetics

Parsimony a tree with a total minimum number of

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: 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...
View Full Document

Ask a homework question - tutors are online