R interface for dnapars

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Description

This function is an R interface for dnapars in the PHYLIP package (Felsenstein 2013). dnapars can be used for MP phylogeny estimation from DNA sequences (Eck & Dayhoff 1966; Kluge & Farris 1969; Fitch 1971).

Usage

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

Arguments

X

an object of class "DNAbin".

path

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

...

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

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 parsimony score will be computed on a fixed input topology; thorough logical value indicating whether to conduct a more thorough search (defaults to thorough=TRUE); nsave number of trees to save if multiple equally parsimonious trees are found (defaults to nsave=10000); 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); transversion logical value indicating whether to use transversion parsimony (defaults to transversion=FALSE); 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 dnapars program in PHYLIP can be found here http://evolution.genetics.washington.edu/phylip/doc/dnapars.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" that is the optimized tree.

Author(s)

Liam J. Revell, Scott A. Chamberlain

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

References

Eck. R.V., Dayhoff, M.O. (1966) Atlas of Protein Sequence and Structure 1966. National Biomedical Research Foundation, Silver Spring, Maryland.

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.

Fitch, W.M. (1971) Toward defining the course of evolution: Minimu change for a specified tree topology. Systematic Zoology, 20, 406-416.

Kluge, A.G., Farris, J.S. (1969) Quantitative phyletics and the evolution of anurans. Systematic Zoology, 18, 1-32.

See Also

Rdnaml, Rdnapenny

Examples

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

## End(Not run)

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