This function is an R interface for dollop in the PHYLIP package (Felsenstein 2013). dollop can be used for Dollo (Le Quesne 1974; Farris 1977) and polymorphism (Inger 1967; Farris 1978; Felsenstein 1979) parsimony tree inference.
an object of class
path to the executable containing dollop. If
optional arguments to be passed to dollop. See details for more information.
Optional arguments include the following:
quiet suppress some output to R console (defaults to
quiet = FALSE);
tree object of class
"phylo" - if supplied, then the Dollo or polymorphism parsimony score will be computed on a fixed input topology;
method indicating whether Dollo (
method="dollo", the default) or polymorphism (
method="polymorphism") should be used;
random.order add taxa to tree in random order (defaults to
random.order = TRUE);
random.addition number of random addition replicates for
random.order = TRUE (defaults to
random.addition = 10);
threshold threshold value for threshold parsimony (defaults to ordinary parsimony);
ancestral vector of ancestral states, which allows for the unordered Dollo parsimony method of Felsenstein (1984);
weights vector of weights of length equal to the number of columns in
X (defaults to unweighted); and
cleanup remove PHYLIP input & output files after the analysis is completed (defaults to
cleanup = TRUE).
More information about the dollop program in PHYLIP can be found here http://evolution.genetics.washington.edu/phylip/doc/dollop.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" that is the optimized tree.
Liam J. Revell, Scott A. Chamberlain
Maintainer: Liam J. Revell <[email protected]>
Farris, J.S. (1977) Phylogenetic analysis under Dollo's Law. Systematic Zoology, 26, 77-88.
Farris, J.S. (1978) Inferring phylogenetic trees from chromosome inversion data. Systematic Zoology, 27, 275-284.
Felsenstein, J. (1979) Alternative methods of phylogenetic inference and their interrelationship. Systematic Zoology, 28, 49-62.
Felsenstein, J. (1984) The statistical approach to inferring evolutionary trees and what it tells us about parsimony and compatibility. pp. 169-191 in: Cladistics: Perspectives in the Reconstruction of Evolutionary History, edited by T. Duncan and T. F. Stuessy. Columbia University Press, New York.
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.
Inger, R.F. (1967) The development of a phylogeny of frogs. Evolution, 21, 369-384.
Le Quesne, W.J. (1974) The uniquely evolved character concept and its cladistic application. Systematic Zoology, 23, 513-517.
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