This function is an R interface for clique in the PHYLIP package (Felsenstein 2013). clique can be used for phylogeny inference using the compatibility method (Le Quesne 1969; Estabrook et al. 1976).
an object of class
path to the executable containing clique. If
optional arguments to be passed to clique. See details for more information.
Optional arguments include the following:
quiet suppress some output to R console (defaults to
quiet = FALSE);
ancestral vector of ancestral states;
weights vector of weights of length equal to the number of columns in
X (defaults to unweighted);
minimum.clique, if specified, will cause
Rclique to print out all cliques (and corresponding trees) greater than
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 clique program in PHYLIP can be found here http://evolution.genetics.washington.edu/phylip/doc/clique.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>
Estabrook, G. F., Johnson, C. S. Jr., McMorris, F. R. (1976). A mathematical foundation for the analysis of character compatibility. Mathematical Biosciences, 23, 181-187.
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.
Le Quesne, W.J. (1969) A method of selection of characters in numerical taxonomy. Systematic Zoology, 18, 201-205.
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