This function is an R interface for dnacomp in the PHYLIP package (Felsenstein 2013). dnacomp can be used for phylogeny inference from DNA sequences using the compatibility method (Le Quesne 1969; Fitch 1975).
an object of class
path to the executable containing dnacomp. If
optional arguments to be passed to dnacomp. 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 number of compatible sites 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);
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 dnacomp program in PHYLIP can be found here http://evolution.genetics.washington.edu/phylip/doc/dnacomp.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>
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. (1975) Toward finding the tree of maximum parsimony. pp. 189-230 in Proceedings of the Eighth International Conference on Numerical Taxonomy, ed. G. F. Estabrook. W. H. Freeman, San Francisco.
Le Quesne, W.J. (1969) A method of selection of characters in numerical taxonomy. Systematic Zoology, 18, 201-205.
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