Rphylip (version 0.1-21)

Rdollop: R interface for dollop

Description

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.

Usage

Rdollop(X, path=NULL, ...)

Value

This function returns an object of class "phylo" that is the optimized tree.

Details

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.

References

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.

See Also

Rpars, Rdnapars

Examples

data(primates.bin)
tree<-Rdollop(primates.bin)