Lecture_7_part2_phylogenetics

58 an example of upgma an example of upgma 59 60 an

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Unformatted text preview: effecJvely assuming the presence of a molecular clock and daJng every vertex •  Thus, the tree can be imagined as being assembled upwards, each node being added above the others, and the edge lengths being determined by the difference in the heights of the nodes at the top and boYom of an edge. 58 An Example of UPGMA An Example of UPGMA 59 60 An Example of UPGMA An Example of UPGMA 61 62 1 9/24/13 UPGMA Clustering An Example of UPGMA •  Let Ci and Cj be clusters, define distance between them to be d (Ci ,C j ) = 1 ∑ ∑d ( p , q ) | Ci || C j | p∈Ci q ∈C j •  When we combine two cluster, Ci and Cj, to form a new cluster Ck, then | Ci | d (Ci , Cl )+ | C j | d (C j , Cl ) d (Ck , Cl ) = | Ci | + | C j | •  Define a node K and place its children nodes at depth d(Ci, Cj)/2 63 64 UPGMA’s Weakness Another Example UPGMA construcJon on five species. The length of an edge is equal to its (v...
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This note was uploaded on 02/10/2014 for the course CS 425 taught by Professor Asaben-hur during the Fall '13 term at Colorado State.

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