Description Usage Arguments Details Value Author(s) References See Also Examples
This function is an R interface for restdist in the PHYLIP package (Felsenstein 2013). restdist can be used to estimate the evolutionary distances between populations based on restriction site or fragment data.
1 |
X |
an object of class |
path |
path to the executable containing restdist. If |
... |
optional arguments to be passed to restdist. See details for more information. |
Optional arguments include the following: quiet
suppress some output to R console (defaults to quiet = FALSE
); method
, the method for calculating the genetic distance - options are "Modified"
(the default), and "Nei/Li"
(Nei & Li 1979); data
, the type of data - either "sites"
or "fragments"
; gamma
alpha shape parameter of a gamma model of rate heterogeneity among sites (defaults to no gamma rate heterogeneity); kappa
transition:transversion ratio (defaults to kappa = 2.0
); site.length
the restriction site length (defaults to site.length=6
); and cleanup
remove PHYLIP input & output files after the analysis is completed (defaults to cleanup = TRUE
).
More information about the restdist program in PHYLIP can be found here http://evolution.genetics.washington.edu/phylip/doc/restdist.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. (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.
1 2 3 4 5 | ## Not run:
data(restriction.data)
D<-Rrestdist(restriction.data)
## End(Not run)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.