Rphylip (version 0.1-23)

Rdnainvar: R interface for dnainvar

Description

This function is an R interface for dnainvar in the PHYLIP package (Felsenstein 2013). dnainvar reads DNA sequences and computest Lake's invariants (Cavender & Felsenstein 1987; Lake 1987).

Usage

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

Arguments

X

an object of class "DNAbin". X cannot contain more than four species.

path

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

...

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

Value

At present, this function merely prints the results of dnainvar to screen.

Details

Optional arguments include the following: quiet suppress some output to R console (defaults to quiet = FALSE); 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 dnainvar program in PHYLIP can be found here http://evolution.genetics.washington.edu/phylip/doc/dnainvar.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

Cavender, J.A., Felsenstein, J. (1987) Invariants of phylogenies in a simple case with discrete states. Journal of Classification, 4, 57-71.

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.

Lake, J.A. (1987) A rate-independent technique for analysis of nucleic acid sequences: evolutionary parsimony. Molecular Biology and Evolution, 4, 167-191.

See Also

Rdnapars

Examples

## Not run: 
# data(primates)
# primates<-primates[sample(nrow(primates),4),]
# tree<-Rdnainvar(primates)
# ## End(Not run)