Rphylip (version 0.1-21)

Rconsense: R interface for consense

Description

This function is an R interface for consense in the PHYLIP package (Felsenstein 2013). consense can be used to compute the consensus tree from a set of phylogenies.

Usage

Rconsense(trees, path=NULL, ...)

Value

This function returns an object of class "phylo". For methods other than method = "strict", tree$node.label contains the proportion of phylogenies in trees containing that subtree.

Details

Optional arguments include the following: quiet suppress some output to R console (defaults to quiet = FALSE); method which can be "extended" (extended majority rule consensus, the default), "strict" (strict consensus), or regular majority rule consensus ("majority"); "outgroup" single taxon label or vector of taxa that should be used to root all trees before analysis; rooted logical value indicated whether to treat the input trees as rooted (defaults to rooted = FALSE); and cleanup remove PHYLIP input & output files after the analysis is completed (defaults to cleanup = TRUE). More information about the consense program in PHYLIP can be found here http://evolution.genetics.washington.edu/phylip/doc/consense.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

Margush, T., McMorris, F.R. (1981) Consensus n-trees. Bulletin of Mathematical Biology, 43, 239-244. 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.

Examples

trees<-rmtree(n=10,N=10)
tree<-Rconsense(trees)