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Rprotpars: R interface for protpars

Description Usage Arguments Details Value Author(s) References See Also Examples


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).


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



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


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.


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.


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


Liam J. Revell, Scott A. Chamberlain

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


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


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