Rphylip (version 0.1-21)

Rdnaml: R interfaces for dnaml and dnamlk

Description

This function is an R interface for dnaml in the PHYLIP package (Felsenstein 2013). dnaml can be used for ML phylogeny estimation from DNA sequences (Felsenstein 1981; Felsenstein & Churchill 1996).

Usage

Rdnaml(X, path=NULL, ...)
Rdnamlk(X, path=NULL, ...)

Value

This function returns an object of class "phylo" that is the optimized tree.

Details

Optional arguments include the following: quiet suppress some output to R console (defaults to quiet = FALSE); tree object of class "phylo" - if supplied, then the model will be optimized on a fixed input topology; kappa transition:transversion ratio (defaults to kappa = 2.0); bf vector of base frequencies in alphabetical order (i.e., A, C, G, & T) - if not provided, then defaults to empirical frequencies; rates vector of rates (defaults to single rate); rate.categories vector of rate categories corresponding to the order of rates; gamma alpha shape parameter of a gamma model of rate heterogeneity among sites (defaults to no gamma rate heterogeneity); ncat number of rate categories for the gamma model; inv proportion of invariant sites for the invariant sites model (defaults to inv = 0); weights vector of weights of length equal to the number of columns in X (defaults to unweighted); speedier speedier but rougher analysis (defaults to speedier = FALSE); global perform global search (defaults to global = TRUE); random.order add taxa to tree in random order (defaults to random.order = TRUE); random.addition number of random addition replicates for random.order = TRUE (defaults to random.addition = 10); outgroup outgroup if outgroup rooting of the estimated tree is desired; and cleanup remove PHYLIP input & output files after the analysis is completed (defaults to cleanup = TRUE). Finally clock=TRUE enforces a molecular clock. The argument clock is only available for Rdnaml. If clock=TRUE then dnamlk is used internally. For Rdnamlk a molecular clock is assumed, thus Rdnaml(...,clock=TRUE) and Rdnamlk(...) are equivalent. More information about the dnaml and dnamlk programs in PHYLIP can be found here http://evolution.genetics.washington.edu/phylip/doc/dnaml.html, and here http://evolution.genetics.washington.edu/phylip/doc/dnamlk.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

Felsenstein, J. (1981) Evolutionary trees from DNA sequences: A Maximum Likelihood approach. Journal of Molecular Evolution, 17, 368-376. 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. 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.

See Also

opt.Rdnaml, Rcontml, Rproml

Examples

data(primates)
tree<-Rdnaml(primates,kappa=10)
clockTree<-Rdnamlk(primates,kappa=10)