UPGMA
Overview
Hierarchical clustering
In statistics, hierarchical clustering is a method of cluster analysis which seeks to build a hierarchy of clusters. Strategies for hierarchical clustering generally fall into two types:...
method used in bioinformatics
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
for the creation of phenetic trees (phenograms). UPGMA assumes a constant rate of evolution (molecular clock hypothesis), and is not a well-regarded method for inferring relationships unless this assumption has been tested and justified for the data set being used. UPGMA was initially designed for use in protein electrophoresis
Protein electrophoresis
Protein electrophoresis is a method for analysing the proteins in a fluid or an extract. The electrophoresis may be performed with a small volume of sample in a number of alternative ways with or without a supporting medium: SDS polyacrylamide gel electrophoresis Protein electrophoresis is a method...
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
Distance matrix
In mathematics, computer science and graph theory, a distance matrix is a matrix containing the distances, taken pairwise, of a set of points...
(or a similarity matrix
Similarity matrix
A similarity matrix is a matrix of scores which express the similarity between two data points. Similarity matrices are strongly related to their counterparts, distance matrices and substitution matrices.-Use in sequence alignment:...
) to then construct a rooted tree (dendrogram
Dendrogram
A dendrogram is a tree diagram frequently used to illustrate the arrangement of the clusters produced by hierarchical clustering...
).
At each step, the nearest two clusters are combined into a higher-level cluster.
