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 24Construction of Phylogenetic Tree: Maximum Parsimony Method
CS Mukhopadhyay and RK Choudhary
School of Animal Biotechnology, GADVASU, Ludhiana
24.1 INTRODUCTION
“Parsimony” means penny‐pinching or thriftiness. Here, the term “maximum parsimony” (MP) indicates extreme caution to opt for simpler hypotheses to select a tree (out of many) with minimum length (sounds like the minimum evolution (ME) method). This approach is applied when the ancestral relationship is required to be reconstructed. The MP method is not the same as the ME method. MP identifies position‐specific differences between all pairs of sequences, while ME indicates the distance (in terms of the number of differences among any two sequences).
24.1.1 Principle
MP is a character‐based method, not distance‐based like ME. The MP method identifies the “most parsimonious tree” through optimality criteria (not by clustering methods like UPGMA or NJ). Thus, the tree that needs a minimum number of evolutionary events (characterized by residue substitutions) to explain the sequence variation is selected.
24.1.2 Assumption
A tree that needs fewer substitutions is better than a tree that requires more (Li, 1997).
24.2 OBJECTIVE
To construct a phylogenetic tree using the MP method from a set of molecular sequences.
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