Rdnadist: R interfaces for dnadist

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/Rphylip.R


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.


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



an object of class "DNAbin".


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 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.


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.


This function returns an object of class "dist".


Liam J. Revell, Scott A. Chamberlain

Maintainer: Liam J. Revell <[email protected]>


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



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Rphylip documentation built on May 30, 2017, 2:43 a.m.