Description Usage Arguments Details Value Author(s) References See Also Examples
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).
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X |
an object of class |
path |
path to the executable containing dnaml. If |
... |
optional arguments to be passed to dnaml or dnamlk. See details for more information. |
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.
This function returns an object of class "phylo"
that is the optimized tree.
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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