Rphylip (version 0.1-21)

Rprotpars: R interface for protpars

Description

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

Usage

Rprotpars(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; 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); genetic.code, type of genetic code to assume (options are "universal", the default, "mitochondrial", "vertebrate.mitochondrial", "fly.mitochondrial", and "yeast.mitochondrial"); 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 protpars program in PHYLIP can be found here http://evolution.genetics.washington.edu/phylip/doc/protpars.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.

See Also

as.proseq, Rdnapars, read.protein

Examples

data(chloroplast)
tree<-Rprotpars(chloroplast)