Basic Applied Bioinformatics

CHAPTER 25Construction of Phylogenetic Tree: Minimum Evolution Method

CS Mukhopadhyay and RK Choudhary

School of Animal Biotechnology, GADVASU, Ludhiana

25.1 INTRODUCTION

The minimum evolution (ME) method is a distance‐based method, and simple enough to avoid the least‐squares approach to determine the optimal tree with minimum branch length. The ME method described here is different from the maximum parsimony (MP) method in its approach. ME identifies the number of sites differing among the input sequences to produce the distance matrix, and ME yields an unrooted tree from the given set of sequences.

25.1.1 Principle

The tree length is obtained by summing up the character differences, and finally the tree with minimum branch length is reconstructed.

25.1.2 Assumptions

1. The character states (residues) change independently along the lineages.
2. Constant rate of evolution over lapse of time.
3. Additivity of the branch length.
4. The tree with the smallest summed branch length is the true one (Rzhetsky and Nei, 1993).

25.2 OBJECTIVE

To construct a phylogenetic tree using the ME method from a given set of nucleotide sequences.

1. ME is quick and is not a resource‐intensive method.
2. It is applicable for a set of sequences derived from closely related organisms.
3. Results are not reliable for the sequences derived from distantly related species, due to generation of many differences in the sequences, which inflates distances.
4. The algorithm does not differentiate between transversion and ...