The UPGMA algorithm

Print Friendly, PDF & Email

The UPGMA (Unweighted Pair Group Method with Arithmetic Mean) is a simple agglomerative or hierarchical clustering method. It is one of the most popular methods in ecology for the classification of sampling units (such as vegetation plots) on the basis of their pairwise similarities in relevant descriptor variables (such as species composition). In bioinformatics, UPGMA is used for the creation of phenetic trees (phenograms). In a phylogenetic context, 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 studies, but is currently most often used to produce guide trees for more sophisticated phylogenetic reconstruction algorithms.

Leave a Reply

Your email address will not be published. Required fields are marked *

*

code

This site uses Akismet to reduce spam. Learn how your comment data is processed.