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. 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 input data is a collection of objects with their pairwise distances and the output is a rooted tree (dendrogram).

Initially, each object is in its own cluster. 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.

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v t e Phylogenetics
Relevant fields	Computational phylogenetics Molecular phylogenetics Cladistics Taxonomy Evolutionary taxonomy Systematics	Evolutionary biology portal
Basic concepts	Phylogenesis Cladogenesis Phylogenetic tree Cladogram Phylogenetic network Long branch attraction Clade vs Grade Lineage Ghost lineage Ghost population
Inference methods	Maximum parsimony Phylogenetic reconciliation Probabilistic methods Maximum likelihood Bayesian inference Distance-matrix methods Neighbor-joining UPGMA Least squares Three-taxon analysis
Current topics	PhyloCode DNA barcoding Molecular phylogenetics Phylogenetic comparative methods Phylogenetic niche conservatism Phylogenetic signal Phylogenetics software Phylogenomics Phylogeography
Group traits	Primitive Plesiomorphy Symplesiomorphy Derived Apomorphy Synapomorphy Autapomorphy
Group types	Monophyly Paraphyly Polyphyly
Nomenclature	Phylogenetic nomenclature Crown group Sister group Basal Supertree
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