Description Usage Arguments Details Value Author(s) References See Also Examples
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).
1 |
X |
an object of class |
path |
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 <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.
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