Güngör Budak's Blog

Bioinformatics, web programming, coding in general

UPGMA Algorithm Described - Unweighted Pair-Group Method with Arithmetic Mean

UPGMA is an agglomerative clustering algorithm that is ultrametric (assumes a molecular clock - all lineages are evolving at a constant rate) by Sokal and Michener in 1958.

The idea is to continue iteration until only one cluster is obtained and at each iteration, join two nearest clusters (which become a higher cluster). The distance between any two clusters are calculated by averaging distances between elements of each cluster.

To understand better, see UPGMA worked example by Dr Richard Edwards.