Rphylip (version 0.1-23)

Rrestml: R interface for restml

Description

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).

Usage

Rrestml(X, path=NULL, ...)

Arguments

X

an object of class "rest.data" containing data for restriction sites.

path

path to the executable containing restml. If path = NULL, the R will search several paths for restml. See details for more information.

...

optional arguments to be passed to restml. See details for more information.

Value

This function returns an object of class "dist".

Details

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.

References

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.

See Also

Rrestdist

Examples

## Not run: 
# data(restriction.data)
# tree<-Rrestml(restriction.data)
# ## End(Not run)