parsimony-phylogeny

parsimony-phylogeny - Parsimony-Based Approaches to...

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Parsimony-Based Approaches to Inferring Phylogenetic Trees BMI/CS 576 www.biostat.wisc.edu/bmi576.html Mark Craven craven@biostat.wisc.edu Fall 2011 Phylogenetic tree approaches three general types distance : find tree that accounts for estimated evolutionary distances parsimony : find the tree that requires minimum number of changes to explain the data maximum likelihood : find the tree that maximizes the likelihood of the data
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Parsimony based approaches given : character-based data do : find tree that explains the data with a minimal number of changes focus is on finding the right tree topology, not on estimating branch lengths Parsimony example AA G AAA G GA AGA AAA AAA A G A AA G A G AAA GG AAA AAA AAA there are various trees that could explain the phylogeny of the sequences AAG , AAA , GGA , AGA including these two: parsimony prefers the first tree because it requires fewer substitution events
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Parsimony based approaches usually these approaches involve two separate components 1. a procedure to find the minimum number of changes needed to explain the data (for a given tree topology) 2. a search through the space of trees Finding minimum number of changes for a given tree basic assumptions – any state (e.g. nucleotide, amino acid) can convert to any other state – the “costs” of these changes are uniform – positions are independent; we can compute the min number of changes for each position separately
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Finding minimum number of changes for a given tree brute force approach – for each possible assignment of states to the internal nodes, calculate the number of changes – report tne min number of changes found runtime is O ( Nk N ) k = number of possible character states (4 for DNA) N = number of leaves Fitch’s Algorithm [1971] 1. traverse tree from leaves to root determining set of possible states (e.g. nucleotides) for each internal node 2. traverse tree from root to leaves picking ancestral states for internal nodes
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Fitch’s algorithm: Step 1 possible states for internal nodes do a post-order (from leaves to root) traversal of tree determine possible states of internal node i with children j and k i R this step calculates the number of changes required # of changes = # union operations , if , otherwise j k j k i j k R R R R R R R ! " = # $ % & & = ( " & & ) * Fitch’s algorithm: step 1 example G T A T C T {GT} {AGT} {T} {T} {C T} ! {A G T} = {CT} {C} # {T} =
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This note was uploaded on 12/15/2011 for the course BMI 576 taught by Professor Staff during the Fall '11 term at Wisc Green Bay.

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parsimony-phylogeny - Parsimony-Based Approaches to...

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