Rphylip (version 0.1-23)

Rdnacomp: R interface for dnacomp

Description

This function is an R interface for dnacomp in the PHYLIP package (Felsenstein 2013). dnacomp can be used for phylogeny inference from DNA sequences using the compatibility method (Le Quesne 1969; Fitch 1975).

Usage

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

Arguments

X

an object of class "DNAbin".

path

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

...

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

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 number of compatible sites will be computed on a fixed input topology; 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); 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 dnacomp program in PHYLIP can be found here http://evolution.genetics.washington.edu/phylip/doc/dnacomp.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

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. (1975) Toward finding the tree of maximum parsimony. pp. 189-230 in Proceedings of the Eighth International Conference on Numerical Taxonomy, ed. G. F. Estabrook. W. H. Freeman, San Francisco.

Le Quesne, W.J. (1969) A method of selection of characters in numerical taxonomy. Systematic Zoology, 18, 201-205.

See Also

Rdnapars, Rdnapenny

Examples

## Not run: 
# data(primates)
# tree<-Rdnacomp(primates)
# ## End(Not run)