R interface for dolpenny

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Description

This function is an R interface for dolpenny in the PHYLIP package (Felsenstein 2013). dolpenny performs Dollo (Le Quesne 1974; Farris 1977) or polymorphism (Inger 1967; Farris 1978; Felsenstein 1979) parsimony using the branch and bound algorithm of Hendy & Penny (1982).

Usage

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

Arguments

X

an object of class "phylip.data" with a binary character; or a matrix. Data should be "0" and "1". The states "P" (or "B"), for polymorphism, and "?" are also permitted.

path

path to the executable containing dolpenny. If path = NULL, the R will search several commonly used directories for the correct executable file.

...

optional arguments to be passed to dolpenny. See details for more information.

Details

Optional arguments include the following: quiet suppress some output to R console (defaults to quiet = FALSE); method indicating whether Dollo (method="dollo", the default) or polymorphism (method="polymorphism") should be used; groups number of groups of 1,000 trees (defaults to groups = 100); report reporting frequency, in numbers of trees (defaults to report = 1000); simple simple branch & bound (defaults to simple = TRUE); threshold threshold value for threshold parsimony (defaults to ordinary parsimony); ancestors 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); outgroup outgroup if outgroup rooting of the estimated tree is desired; and cleanup remove PHYLIP input & output files after the analysis is completed (defaults to cleanup = TRUE).

More information about the dolpenny program in PHYLIP can be found here http://evolution.genetics.washington.edu/phylip/doc/dolpenny.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.

Value

This function returns an object of class "phylo" or "multiPhylo" that is the tree or trees with the best parsimony score. tree$score gives the parsimony score, for "phylo" object tree.

Author(s)

Liam J. Revell, Scott A. Chamberlain

Maintainer: Liam J. Revell <liam.revell@umb.edu>

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.

Hendy, M.D., Penny, D. (1982) Branch and bound algorithms to determine minimal evolutionary trees. Mathematical Biosciences, 60, 133-142.

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

Rdnapars

Examples

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## Not run: 
data(primates.bin)
tree<-Rdolpenny(primates.bin)

## End(Not run)

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