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. 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 was initially designed for use in protein electrophoresis studies and 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.
Topics in phylogenetics v • • e</div> |
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| Relevant fields: phylogenetics | computational phylogenetics | molecular phylogeny | cladistics |
| Basic concepts: synapomorphy | phylogenetic tree | phylogenetic network | long branch attraction |
| Phylogeny inference methods: maximum parsimony | maximum likelihood | neighbour joining | UPGMA | Bayesian inference |
| Current topics: PhyloCode | DNA barcoding |
| List of evolutionary biology topics |
Categories
Bioinformatics | Computational phylogenetics | Phylogenetics