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UPGMA

UPGMA

UPGMA (Unweighted Pair Group Method with Arithmetic mean) is a simple agglomerative or bottom-up data clustering method used in bioinformatics for the creation of phylogenetic trees. UPGMA assumes a constant rate of evolution (molecular clock hypothesis), and is not a well-regarded method for inferring phylogenetic trees unless this assumption has been tested and justified for the data set being used. UPGMA was initially designed for use in protein electrophoresis studies, but is currently most often used to produce guide trees for more sophisticated phylogenetic reconstruction algorithms.

The algorithm examines the structure present in a pairwise distance matrix to then construct a rooted tree (dendrogram).

At each step, the nearest 2 clusters are combined into a higher-level cluster. The distance between any 2 clusters A and B is taken to be the average of all distances between pairs of objects "a" in A and "b" in B.

ee also

*Neighbor-joining

External links

* [http://www.icp.be/~opperd/private/upgma.html Construction of a distance tree using clustering with the Unweighted Pair Group Method with Arithmatic Mean (UPGMA)] — a tutorial
* [http://www.icp.be/~opperd/private/neighbor_doc.html NEIGHBOR: Neighbor-Joining and UPGMA methods]


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