Description Usage Arguments Details Value Author(s) References See Also Examples
This function is an R interface for dnainvar in the PHYLIP package (Felsenstein 2013). dnainvar reads DNA sequences and computest Lake's invariants (Cavender & Felsenstein 1987; Lake 1987).
1 |
X |
an object of class |
path |
path to the executable containing dnainvar. If |
... |
optional arguments to be passed to dnainvar. See details for more information. |
Optional arguments include the following: quiet
suppress some output to R console (defaults to quiet = FALSE
); weights
vector of weights of length equal to the number of columns in X
(defaults to unweighted); and cleanup
remove PHYLIP input & output files after the analysis is completed (defaults to cleanup = TRUE
).
More information about the dnainvar program in PHYLIP can be found here http://evolution.genetics.washington.edu/phylip/doc/dnainvar.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.
At present, this function merely prints the results of dnainvar to screen.
Liam J. Revell, Scott A. Chamberlain
Maintainer: Liam J. Revell <liam.revell@umb.edu>
Cavender, J.A., Felsenstein, J. (1987) Invariants of phylogenies in a simple case with discrete states. Journal of Classification, 4, 57-71.
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.
Lake, J.A. (1987) A rate-independent technique for analysis of nucleic acid sequences: evolutionary parsimony. Molecular Biology and Evolution, 4, 167-191.
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