Rpenny: R interface for penny

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

View source: R/Rphylip.R


This function is an R interface for penny in the PHYLIP package (Felsenstein 2013). penny performs branch & bound parsimony searching following Hendy & Penny (1982).


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



an object of class "phylip.data" with a binary character; or a matrix. Data should be "0", "1", and "?".


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


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 "W" and "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); method either "Wagner" or "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 "0", "1", and "?"; 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 "phylo" or "multiPhylo" that is the tree or trees with the best parsimony score. tree$score gives the parsimony score, for "phylo" object tree.


Liam J. Revell, Scott A. Chamberlain

Maintainer: Liam J. Revell <[email protected]>


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.

See Also



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Rphylip documentation built on May 30, 2017, 2:43 a.m.