Rphylip (version 0.1-21)

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, ...)

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

data(primates)
D<-Rdnadist(primates,kappa=10)
tree<-Rneighbor(D)