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‘TreeDist’ is an R package that implements a suite of metrics that quantify the topological distance between pairs of unweighted phylogenetic trees. It also includes a simple ‘Shiny’ application to allow the visualization of distance-based tree spaces, and functions to calculate the information content of trees and splits.
Distance matrices are used in phylogeny as non-parametric distance methods and were originally applied to phenetic data using a matrix of pairwise distances. These distances are then reconciled to produce a tree (a phylogram, with informative branch lengths).
12 lut 2020 · In this case a distance matrix is created by calculating the distance between every pair of BGC in the data set, basically a pairwise distance calculation was done for all BGCs. I believe that the example that I provided was not a good one.
Paste your distance matrix in the Phylip format into the window (no spaces in the species names; at least one space is required in the end of a species name):
Methods for reconstructing phylogenetic trees from a distance matrix containing missing values, i.e. incomplete matrices.
Calculate the distance between each tree in a list, and each other tree in the same list. Usage CompareAll(x, Func, FUN.VALUE = Func(x[[1]], x[[1]], ...), ...) Arguments x List of trees, in the format expected by Func(). Func distance function returning distance between two trees, e.g. path.dist().
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.
