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Maximum Parsimony (MP) Algorithm
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MP Algorithm Character-based algorithm – does not use distances, but utilizes the character information in sequences A criticism of distance-based methods is that they do not exploit the structure of the sequences (collapse them to a number – the distance) Main philosophy is “economy of substitutions” – find the tree that requires the fewest mutations (maximum parsimony)
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MP Algorithm The strategy explore a number of possible trees report the tree with smallest score (most parsimonious) Need to be able to solve two problems small parsimony problem -- given a candidate tree compute its parsimony score large parsimony problem -- generate efficiently viable candidate trees (cannot generate all – tree explosion)
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Small Parsimony Problem Given a candidate tree, compute its parsimony score Consider a candidate tree for one-site sequences s1 = A s2 = T s3 = T s4 = G s5 = A A T T G A ATAT AGAG T AGTAGT Final Score = 3
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Solving Small Parsimony Problem explore the tree bottom-up (from leaves to interior) for each internal node one level up if the “labels” at the two child nodes have no symbols in common assign as label at this node the sum of both labels penalize the tree one unit if the “labels” at the two child nodes do have symbols in common, label with common portion no penalty AGCAGC AGAG C AGAG GTGT G
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Solving Small Parsimony Problem For n-site sequences run the algorithm in parallel for each site and add up the parsimony scores for all sites Consider a candidate tree for the following sequences s1 = ATC s2 = ACC s3 = GTA s4 = GCA ATC ACC GTA GCA TCTC AC AGAG T ACAC T CTCT A Final Score = 4
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Solving Large Parsimony Problem Generate efficiently viable candidate trees (cannot try all) Branch-and-bound approach create a possible tree by some method; calculate its score start building a tree from scratch; discarding trees that cost more than current best
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Solving Large Parsimony Problem Branch-and-bound approach http://artedi.ebc.uu.se/course/X3-2004/Phylogeny/Phylogeny-TreeSearch/Phylogeny-Search.html
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MP Summary Character-based algorithm – uses the sequence data Produces unrooted trees Economy of substitution – best tree is one that requires fewest number of substitutions Examines a number of possible trees in search for best one
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