R interface for restml

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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

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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.

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.

Value

This function returns an object of class "dist".

Author(s)

Liam J. Revell, Scott A. Chamberlain

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

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

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

## End(Not run)

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