R interfaces for dnaml and dnamlk

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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

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

Arguments

X

an object of class "DNAbin".

path

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

...

optional arguments to be passed to dnaml or dnamlk. See details for more information.

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.

Value

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

Author(s)

Liam J. Revell, Scott A. Chamberlain

Maintainer: Liam J. Revell <liam.revell@umb.edu>

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

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## Not run: 
data(primates)
tree<-Rdnaml(primates,kappa=10)
clockTree<-Rdnamlk(primates,kappa=10)

## End(Not run)

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