R interface for dnainvar

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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

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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.

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.

Value

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

Author(s)

Liam J. Revell, Scott A. Chamberlain

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

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

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

## End(Not run)

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