This function is an wrapper for
Rdnaml that attempts to optimize
gamma (the alpha shape parameter of the gamma model of rate heterogeneity among sites),
kappa (the transition:transversion ratio), and
bf (the base frequencies).
an object of class
path to the executable containing dnaml. If
optional arguments. See details for more information.
Optional arguments include the following:
tree fixed tree to use in optimization - if not provided, it will be estimated using
Rdnaml under the default conditions;
bounds a list with bounds for optimization - for
gamma this should be a two-element vector, whereas for
bf this should be a 4 x 2 matrix with lower bounds in column 1 and upper bounds in column 2.
More information about the dnaml program in PHYLIP can be found here http://evolution.genetics.washington.edu/phylip/doc/dnaml.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 a list with the following components:
bf (see Details), and
logLik (the log-likelihood of the fitted model).
Liam J. Revell, Scott A. Chamberlain
Maintainer: Liam J. Revell <firstname.lastname@example.org>
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.
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