Lecture_7_part2_phylogenetics

begin at leaves calculate and keep track of a score

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Unformatted text preview: a single character, because the characters in the string are independent. 3 9/24/13 Scoring Matrices Weighted Small Parsimony Problem •  A more general version of Small Parsimony Problem •  Input includes a k x k scoring matrix describing the cost of transformaJon of each of k states into another one •  For Small Parsimony problem, the scoring matrix is based on Hamming distance dH(v, w) = 0 if v=w dH(v, w) = 1 otherwise Small Parsimony Problem A A0 T1 G1 C1 T 1 0 1 1 Weighted Parsimony Problem GC 11 11 01 10 A T G C A 0 3 4 9 T 3 0 2 4 GC 49 24 04 40 Unweighted vs. Weighted Small Parsimony Scoring Matrix: A A0 T1 G1 C1 T 1 0 1 1 Unweighted vs. Weighted Weighted Parsimony Scoring Matrix: GC 11 11 01 10 Small Parsimony Score: 5 Weighted Small Parsimony Problem: FormulaJon •  Input: Tree T...
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