Rphylip (version 0.1-23)

Rdnadist: R interfaces for dnadist

Description

This function is an R interface for dnadist in the PHYLIP package (Felsenstein 2013). dnadist can be used to estimate the evolutionary distances between DNA sequences under various models.

Usage

Rdnadist(X, method=c("F84","K80","JC","LogDet"), path=NULL, ...)

Arguments

X

an object of class "DNAbin".

method

method for calculating the distances. Can be "F84" (Kishino & Hasegawa 1989; Felsenstein & Churchill 1996), "K80" (Kimura 1980), "JC" (Jukes & Cantor 1969), or "LogDet" (Barry & Hartigan 1987; Lake 1994; Steel 1994; Lockhart et. al. 1994). Also method="similarity" computes the sequence similarity among the rows of X.

path

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

...

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

Value

This function returns an object of class "dist".

Details

Optional arguments include the following: quiet suppress some output to R console (defaults to quiet = FALSE); gamma alpha shape parameter of a gamma model of rate heterogeneity among sites (defaults to no gamma rate heterogeneity); kappa transition:transversion ratio (defaults to kappa = 2.0); rates vector of rates (defaults to single rate); rate.categories vector of rate categories corresponding to the order of rates; weights vector of weights of length equal to the number of columns in X (defaults to unweighted); bf vector of base frequencies in alphabetical order (i.e., A, C, G, & T) - if not provided, then defaults to empirical frequencies; and cleanup remove PHYLIP input & output files after the analysis is completed (defaults to cleanup = TRUE).

More information about the dnadist program in PHYLIP can be found here http://evolution.genetics.washington.edu/phylip/doc/dnadist.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

Barry, D., Hartigan, J.A. (1987) Statistical analysis of hominoid molecular evolution. Statistical Science, 2, 191-200.

Felsenstein, J. (2013) PHYLIP (Phylogeny Inference Package) version 3.695. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle.

Felsenstein, J., Churchill, G. A. (1996) A Hidden Markov Model approach to variation among sites in rate of evolution. Molecular Biology and Evolution, 13, 93-104.

Jukes, T.H., Cantor, C.R. (1969) Evolution of protein molecules. pp. 21-132 in Mammalian Protein Metabolism Vol. III, ed. M.N. Munro. Academic Press, New York.

Kimura, M. (1980) A simple model for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16, 111-120.

Kishino, H., Hasegawa, M. (1989) Evaluation of the maximum likelihood estimate of teh evolutionary tree topology from DNA sequence data, and the branching order in Hominoidea. Journal of Molecular Evolutioon, 29, 170-179.

Lake, J.A. (1994) Reconstructing evolutionary trees from DNA and protein sequences: Paralinear distances. Proceedings of the National Academy of Sciences, 91, 1455-1459.

Lockhart, P.J., Steel, M.A., Hendy, M.D., Penny, D. (1994) Recovering evolutionary trees under a more realistic model of sequence evolution. Molecular Biology and Evolution, 11, 605-612.

Steel, M.A. (1994) Recovering a tree from the Markov leaf colourations it generates under a Markov model. Applied Mathematics Letters, 7, 19-23.

See Also

Rneighbor

Examples

## Not run: 
# data(primates)
# D<-Rdnadist(primates,kappa=10)
# tree<-Rneighbor(D)
# ## End(Not run)