Parameter optimizer for Rdnaml
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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