R interface for protpars

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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

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

Arguments

X

an object of class "proseq" containing aligned amino acid sequences.

path

path to the executable containing protpars. If path = NULL, the R will search several commonly used directories for the correct executable file.

...

optional arguments to be passed to protpars. 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 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.

Value

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

Author(s)

Liam J. Revell, Scott A. Chamberlain

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

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

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## Not run: 
data(chloroplast)
tree<-Rprotpars(chloroplast)

## End(Not run)

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