R interface for dnapenny

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Description

This function is an R interface for dnapenny in the PHYLIP package (Felsenstein 2013). dnapenny performs branch & bound parsimony searching following Hendy & Penny (1982).

Usage

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

Arguments

X

an object of class "DNAbin".

path

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

...

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

Details

Optional arguments include the following: quiet suppress some output to R console (defaults to quiet = FALSE); groups number of groups of 1,000 trees (defaults to groups = 10000); 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); 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 dnapenny program in PHYLIP can be found here http://evolution.genetics.washington.edu/phylip/doc/dnapenny.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

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.

See Also

Rdnapars

Examples

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## Not run: 
data(primates)
tree<-Rdnapenny(primates)

## End(Not run)

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