R interface for penny
This function is an R interface for penny in the PHYLIP package (Felsenstein 2013). penny performs branch & bound parsimony searching following Hendy & Penny (1982).
an object of class
path to the executable containing penny. If
optional arguments to be passed to penny. See details for more information.
Optional arguments include the following:
quiet suppress some output to R console (defaults to
quiet = FALSE);
mixture, a vector containing
"C" in upper or lower case indicating which characters should be evaluated using Wagner (Eck & Dayhoff 1966; Kluge & Farris 1969) or Camin-Sokal (Camin & Sokal 1965) parsimony methods, respectively - this argument takes precedence over
method (see below);
"Camin-Sokal", in upper or lower case, indicating whether Wagner (Eck & Dayhoff 1966; Kluge & Farris 1969) or Camin-Sokal (Camin & Sokal 1965) parsimony should be used;
groups number of groups of 1,000 trees (defaults to
groups = 100);
report reporting frequency, in numbers of trees (defaults to
report = 1000);
simple simple branch & bound (defaults to
simple = TRUE);
threshold threshold value for threshold parsimony (defaults to ordinary parsimony);
ancestral a vector of length equal to the number of columns in
X containing the the ancestral state at the root of the tree for each character, these should be
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 penny program in PHYLIP can be found here http://evolution.genetics.washington.edu/phylip/doc/penny.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
"multiPhylo" that is the tree or trees with the best parsimony score.
tree$score gives the parsimony score, for
Liam J. Revell, Scott A. Chamberlain
Maintainer: Liam J. Revell <email@example.com>
Camin, J.H., Sokal, R.R. (1965) A method for deducing branching sequences in phylogeny. Evolution, 19, 311-326.
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.
Kluge, A.G., Farris, J.S. (1969) Quantitative phyletics and the evolution of anurans. Systematic Zoology, 18, 1-32.
Hendy, M.D., Penny, D. (1982) Branch and bound algorithms to determine minimal evolutionary trees. Mathematical Biosciences, 60, 133-142.
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