Rphylip (version 0.1-21)

Rpars: R interface for pars

Description

This function is an R interface for pars in the PHYLIP package (Felsenstein 2013). pars can be used for MP phylogeny estimation from DNA sequences (Eck & Dayhoff 1966; Kluge & Farris 1969; Fitch 1971).

Usage

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

Value

This function returns an object of class "phylo" that is the optimized tree.

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 parsimony score will be computed on a fixed input topology; thorough logical value indicating whether to conduct a more thorough search (defaults to thorough=TRUE); nsave number of trees to save if multiple equally parsimonious trees are found (defaults to nsave=10000); 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); threshold threshold value for threshold parsimony (defaults to ordinary parsimony); weights vector of weights of length equal to the number of columns in X (defaults to unweighted); 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 pars program in PHYLIP can be found here http://evolution.genetics.washington.edu/phylip/doc/pars.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

Eck. R.V., Dayhoff, M.O. (1966) Atlas of Protein Sequence and Structure 1966. National Biomedical Research Foundation, Silver Spring, Maryland. 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. Fitch, W.M. (1971) Toward defining the course of evolution: Minimu change for a specified tree topology. Systematic Zoology, 20, 406-416. Kluge, A.G., Farris, J.S. (1969) Quantitative phyletics and the evolution of anurans. Systematic Zoology, 18, 1-32.

See Also

Rdnaml, Rdnapenny

Examples

data(primates.bin)
tree<-Rpars(primates.bin)