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However, when the level of sequence divergence is low, this is not the case. Under this principle, the preferred tree is determined by assigning an optimality score to all possible topologies (or all potentially correct topologies) according to a certain procedure and choosing the topology that shows the highest or lowest optimal score.For example, in the case of maximum-parsimony (MP) methods (Eck and Dayhoff 1966 ), the minimum number of evolutionary changes that explains the entire sequence evolution (tree length [TL]) is computed for each topology, and the topology showing the smallest TL value is chosen as the preferred tree (MP tree).
High divergence refers to the case in which the expected number of nucleotide substitutions per site from the root to the tip of the tree is 0.5, and thus the expected number of substitutions between two most distantly related sequences ( is 0.1.
In phylogenetic inference by maximum-parsimony (MP), minimum-evolution (ME), and maximum-likelihood (ML) methods, it is customary to conduct extensive heuristic searches of MP, ME, and ML trees, examining a large number of different topologies.