Algorithm for initial tree topology for Parsimony tree
I have been using MEGA software for reconstructing parsimony tree using nucleotide and amino acid sequence files. The software gives different options for 'MP search methods' which are applied on initial tree topology and a tree with minimum number of evolutionary changes is resulted, but on which basis the initial topology is reconstructed? What is the model or formula used for generating a character state matrix which leads to an initial tree reconstruction?
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