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17 mar 2021 · If we have a weighted phylogenetic tree, we can find the total weight (length) of the shortest path between a pair of leaves by summing up the individual branch lengths in the path. Considering all such pairs of leaves, we have a distance matrix representing the data.
protdist calculates a distance matrix from amino acid sequences, under five different models of amino acid substitutions: the Dayhoff PAM matrix, the JTT (Jones-Taylor-Thornton) model, the PMB (Probability Matrix from Blocks) model, Kimura’s distance, and Categories distances).
Distance-based methods. Evolutionary Models and Distance Correction. Pairwise Distances. Calculating the distance between two sequences is important for at least two reasons: it’s the first step in distance-based phylogeny reconstruction.
Distance-based phylogeny problem. Input: distance matrix of pairwise distances for N species. Goal: find a tree consistent with the distance matrix. This means that the sum of edge lengths connecting each pair of leaves ij corresponds to a distance Mij.
Distance matrix methods. A major family of phylogenetic methods has been the distance matrix methods, intro duced by Cavalli-Sforza and Edwards (1967) and by Fitch and Margoliash (1967; see also Horne, 1967). They were influenced by the clustering algorithms of Sokal and Sneath (1963).
Our focuses in this paper shall be the step 4 in the process, to determine and access tree building methods, in particular, the distance based methods. The paper starts with some preliminary knowledge and definitions in the area, including finite directed graphs, directed trees and matrices.
