calcDist: Calculate the distance between trees using different methods

In DomBennett/MoreTreeTools: Tools for manipulating phylogenetic trees

Description

Calculate the normalised tree distance (topological and branch length) between trees

Usage

calcDist(tree1, tree2, method = c("all", "PH85", "score", "dmat", "trip"),
  normalised = TRUE)

Arguments

tree1	first tree of comparison
tree2	second tree of comparison
method	'all', 'PH85', 'score', 'trip' or 'dmat'. Default 'all'
normalised	boolean, return distances of 0-1

Details

This functions uses four different methods for calculating the distance between trees: the 'PH85' and 'score' methods of ape's topo.dist, 1 - Pearson's r calculated from the cophenetic matrix of the tip distances ('dmat') or the triplet distance of Critchlow et al. (1996). The function returns the normalised distances by default. Trees of different numbers of tips are pruned to the same size. Function will also rescale branch distances to sum to 1 before calculating distances. Note, triplet metric will only work for bifurcating and rooted trees otherwise it will return NA.

References

Critchlow DE, Pearl DK, Qian C. (1996) The Triples Distance for rooted bifurcating phylogenetic trees. Systematic Biologly, 45, 323–34.

Billera, L. J., Holmes, S. P. and Vogtmann, K. (2001) Geometry of the space of phylogenetic trees. Advances in Applied Mathematics, 27, 733–767.

Kuhner, M. K. and Felsenstein, J. (1994) Simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Molecular Biology and Evolution, 11, 459–468.

Nei, M. and Kumar, S. (2000) Molecular Evolution and Phylogenetics. Oxford: Oxford University Press.

Penny, D. and Hendy, M. D. (1985) The use of tree comparison metrics. Systemetic Zoology, 34, 75–82.

Rzhetsky, A. and Nei, M. (1992) A simple method for estimating and testing minimum-evolution trees. Molecular Biology and Evolution, 9, 945–967.

DomBennett/MoreTreeTools documentation built on May 6, 2019, 2:51 p.m.