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).
an object of class
path to the executable containing pars. If
optional arguments to be passed to pars. 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;
thorough logical value indicating whether to conduct a more thorough search (defaults to
nsave number of trees to save if multiple equally parsimonious trees are found (defaults to
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.
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.
Kluge, A.G., Farris, J.S. (1969) Quantitative phyletics and the evolution of anurans. Systematic Zoology, 18, 1-32.
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