R interface for treedist
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.
an object of class
method to compute the distance between trees.
path to the directory containing the executable treedist. If
optional arguments to be passed to treedist. See details for more information.
Optional arguments include the following:
quiet suppress some output to R console (defaults to
quiet = FALSE);
trees2 object of class
"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
"all.1to2" (all in
trees by all in
"adjacent" (adjacent species in
trees only), and
"corresponding" (all corresponding trees in
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.
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".
Liam J. Revell, Scott A. Chamberlain
Maintainer: Liam J. Revell <firstname.lastname@example.org>
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.
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