Rdnacomp: R interface for dnacomp

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

View source: R/Rphylip.R


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).


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



an object of class "DNAbin".


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


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 <liam.revell@umb.edu>


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.

See Also

Rdnapars, Rdnapenny


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Rphylip documentation built on May 20, 2017, 12:43 a.m.

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