pi_lec3 - 20.181 Lecture 3 Contents 1 Phylogenetic trees o...

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20.181 Lecture 3 Contents 1 Phylogenetic trees o 1.1 Overview of Approach o 1.2 Possible trees 2 Trees in Python o 2.1 Data Structure o 2.2 Parsing Function Phylogenetic trees Input: (a multiple sequence alignment) 1. AATGC 2. TATGC 3. GGTGG 4. ACTCG Output: tree, an abstract representation of the same data ((1,4),(2,3)) Overview of Approach (in pseudocode) for each possible tree: calculate the score of (tree,data) return tree with BEST score Possible trees how many trees are there? o how does the number of possible trees increase with the number of leaves. .. linearly? . ..exponentially? ± start with the simplest unrooted tree, it has three leaves ± how many ways are there to add another leaf? there are 3 ways- by adding the new leaf attached to each of the 3 existing branches (ignore the center leaf for now because we want to stick to binary trees) ± now there are 5 places to add a leaf to a 4-leaf tree
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± every time you put a new branch down, you gain 2 more places to put a new branch: one from splitting an existing branch into two
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This note was uploaded on 11/11/2011 for the course BIO 20.010j taught by Professor Lindagriffith during the Spring '06 term at MIT.

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pi_lec3 - 20.181 Lecture 3 Contents 1 Phylogenetic trees o...

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