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).
an object of class
path to the executable containing protpars. If
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,
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 <firstname.lastname@example.org>
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.
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