Rphylip (version 0.1-21)

Rtreedist: R interface for treedist

Description

This function is an R interface for treedist in the PHYLIP package (Felsenstein 2013). treedist can be used to compute the distance between trees by two different methods.

Usage

Rtreedist(trees, method=c("branch.score","symmetric"), path=NULL, ...)

Value

This function returns a matrix of pairwise distances for distances = "all" and distances = "all.1to2", or a named vector for distances = "adjacent" and distances = "corresponding".

Details

Optional arguments include the following: quiet suppress some output to R console (defaults to quiet = FALSE); trees2 object of class "multiPhylo" or "phylo" - if two sets of trees are to be compared; rooted logical value indicating whether trees should be treated as rooted (defaults to rooted = FALSE); distances argument telling treedist which distances to compute - could be "all" (all pairwise in trees), "all.1to2" (all in trees by all in trees2), "adjacent" (adjacent species in trees only), and "corresponding" (all corresponding trees in trees and trees2); and cleanup remove PHYLIP input & output files after the analysis is completed (defaults to cleanup = TRUE). More information about the treedist program in PHYLIP can be found here http://evolution.genetics.washington.edu/phylip/doc/treedist.html. Obviously, use of any of the functions of this package requires that PHYLIP (Felsenstein 1989, 2013) should first be installed. Instructions for installing PHYLIP can be found on the PHYLIP webpage: http://evolution.genetics.washington.edu/phylip.html.

References

Bourque, M. (1978) Arbres de Steiner et reseaux dont certains sommets sont a localisation variable. Ph.D. Dissertation, Universite de Montreal, Montreal, Quebec. Felsenstein, J. (1989) PHYLIP--Phylogeny Inference Package (Version 3.2). Cladistics, 5, 164-166. Felsenstein, J. (2013) PHYLIP (Phylogeny Inference Package) version 3.695. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle. Kuhner, M.K., Felsenstein, J. (1994) A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Molecular Biology and Evolution, 11, 459-468. Robinson, D.F., Foulds, L.R. (1981) Comparison of phylogenetic trees. Mathematical Biosciences, 53, 131-147.

Examples

trees<-rmtree(n=10,N=10)
D<-Rtreedist(trees,method="symmetric")