R interface for consense
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.
an object of class
path to the directory containing the executable consense. If
optional arguments to be passed to consense. See details for more information.
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 (
"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.
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.
Liam J. Revell, Scott A. Chamberlain
Maintainer: Liam J. Revell <firstname.lastname@example.org>
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.
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