R interfaces for dnadist
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.
an object of class
method for calculating the distances. Can be
path to the executable containing dnadist. If
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
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
Liam J. Revell, Scott A. Chamberlain
Maintainer: Liam J. Revell <email@example.com>
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.
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