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Encyclopedia > UPGMA

UPGMA (Unweighted Pair Group Method with Arithmetic mean) is a simple bottom-up data clustering method used in bioinformatics for the creation of phylogenetic trees. The input data is a collection of objects with their pairwise distances and the output is a rooted tree (dendrogram). It is sometimes used for creating rooted phylogenetic trees under the assumption of a constant evolutionary rate. Initially, each object is in its own cluster. At each step, the nearest two clusters are combined into a higher-level cluster. The distance between any two clusters A and B is taken to be the average of all distances between pairs of objects a in A and b in B. UPGMA is not a well-regarded method for inferring phylogenetic trees unless the constant-rate assumption (molecular clock hypothesis) has been tested and justified for the data set being used. Jump to: navigation, search Bioinformatics or computational biology is the use of techniques from applied mathematics, informatics, statistics, and computer science to solve biological problems. ... In biology, Phylogenetics (Greek: phylon = race and genetic = birth) is the taxonomical classification of organisms based on how closely they are related in terms of evolutionary differences. ... In computer science, a tree is a widely-used computer data structure that emulates a tree structure with a set of linked nodes. ... The molecular clock (based on the molecular clock hypothesis (MCH)) is a technique in genetics, which researchers use to date when two species diverged. ...

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 03-511/711, 15-495/856 Course Notes - Sept 30, 04 (848 words) UPGMA and Neighbor Joining (NJ) are greedy algorithms that will reconstruct the correct tree in polynomial time when D[i,j], the matrix of observed inter-taxon distances, is ultrametric or additive, respectively. UPGMA algorithm is a variant of average linkage. Errors in topology can occur because UPGMA selects pairs of taxa with minimum distance as neighbors, leading to the wrong tree when the closest taxa are not adjacent in the true tree.
 UPGMA (688 words) The UPGMA is the simplest method of tree construction. UPGMA employs a sequential clustering algorithm, in which local topological relationships are identifeid in order of similarity, and the phylogenetic tree is build in a stepwise manner. ABC,DE Although this method leads essentially to an unrooted tree, UPGMA assumes equal rates of mutation along all the branches, as the model of evolution used.
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