Description Usage Arguments Details Value Author(s) References See Also Examples

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).

1 | ```
opt.Rdnaml(X, path=NULL, ...)
``` |

`X` |
an object of class |

`path` |
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 `kappa`

and `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: `kappa`

, `gamma`

, `bf`

(see Details), and `logLik`

(the log-likelihood of the fitted model).

Liam J. Revell, Scott A. Chamberlain

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

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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