Basic Applied Bioinformatics

CHAPTER 21Construction of Phylogenetic Tree: Unweighted‐Pair Group Method with Arithmetic Mean (UPGMA)

CS Mukhopadhyay and RK Choudhary

School of Animal Biotechnology, GADVASU, Ludhiana

21.1 INTRODUCTION

UPGMA is a clustering algorithm that works by joining the branches of a tree on the basis of maximum similarity criteria among pairs of sequences, and by calculating the means of joined pairs. UPGMA is “ultrametric”, so all the terminal nodes are equally distanced from the root. Hence, at the end, when a root is added, the rooted tree is produced.

• Unweighted: It indicates equal contribution of all the pair‐wise distances. There is no weighting of any specific taxa‐pairs to indicate a different evolutionary rate compared with another pair(s). This is the opposite of the Weighted‐Pair Group Method with Arithmetic mean (WPGMA).
• Pair‐groups: Any two taxa or any two clusters (clade) or one taxon and a cluster are always combined in pairs (that is, interpreted as dichotomies).
• Arithmetic mean: Pair‐wise distance of each group is the mean distance to all members of that group.

21.2 ASSUMPTIONS

1. Constant rate of evolution (i.e., mutation‐rate) amongst all the sequences.
2. Distance data are ultrametric: This enables clustering by satisfying the “three point condition” to generate the tree.

TERMINOLOGIES AND POINTS

1. Neighbors: the external nodes with the smallest number of mismatches.
2. Ultrametric: in distance methods, an ultrametric tree is characterized by a “Three point condition”, ...