(Unweighted Pair Group Method with Arithmetic mean) is a simple bottom-up data clustering method used in bioinformatics
for the creation of phylogenetic treess
. 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.