Description Usage Arguments Details Value Author(s) References See Also Examples
This function is an R interface for restml in the PHYLIP package (Felsenstein 2013). restml can be used to conduct ML phylogeny inference from restriction site or fragment data (Nei & Li 1979; Smouse & Li 1987; Felsenstein 1992).
1 |
X |
an object of class |
path |
path to the executable containing restml. If |
... |
optional arguments to be passed to restml. 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; 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
); site.length
the restriction site length (defaults to site.length=6
); 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
).
More information about the restml program in PHYLIP can be found here http://evolution.genetics.washington.edu/phylip/doc/restml.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 "dist"
.
Liam J. Revell, Scott A. Chamberlain
Maintainer: Liam J. Revell <liam.revell@umb.edu>
Felsenstein, J. (1989) PHYLIP–Phylogeny Inference Package (Version 3.2). Cladistics, 5, 164-166.
Felsenstein, J. (1992) Phylogenies from restriction sites, a maximum likelihood approach. Evolution, 46, 159-173.
Felsenstein, J. (2013) PHYLIP (Phylogeny Inference Package) version 3.695. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle.
Nei, M., Li, W.-H. (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Sciences, 76, 5269-5273.
Smouse, P. E., Li, W.-H. (1987) Likelihood analysis of mitochondrial restriction-cleavage patterns for the human-chimpanzee-gorilla trichotomy. Evolution, 41, 1162-1176.
1 2 3 4 5 | ## Not run:
data(restriction.data)
tree<-Rrestml(restriction.data)
## End(Not run)
|
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