Description Usage Arguments Details Value Author(s) References Examples
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.
1 |
trees |
an object of class |
path |
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 ("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.
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 <liam.revell@umb.edu>
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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