November 2017
Intermediate to advanced
472 pages
11h 21m
English
book
Basic Applied Bioinformatics
by Chandra Sekhar Mukhopadhyay, Ratan Kumar Choudhary, Mir Asif Iquebal
Content preview from Basic Applied Bioinformatics
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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
- The character states (residues) change independently along the lineages.
- Constant rate of evolution over lapse of time.
- Additivity of the branch length.
- 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.
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