Description Usage Arguments Details Value Author(s) References See Also Examples
This function is an R interface for protpars in the PHYLIP package (Felsenstein 2013). protpars can be used for MP phylogeny estimation from protein sequences (Eck & Dayhoff 1966; Fitch 1971).
1 |
X |
an object of class |
path |
path to the executable containing protpars. If |
... |
optional arguments to be passed to protpars. 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 parsimony score 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
); threshold
threshold value for threshold parsimony (defaults to ordinary parsimony); genetic.code
, type of genetic code to assume (options are "universal"
, the default, "mitochondrial"
, "vertebrate.mitochondrial"
, "fly.mitochondrial"
, and "yeast.mitochondrial"
); 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 protpars program in PHYLIP can be found here http://evolution.genetics.washington.edu/phylip/doc/protpars.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>
Eck. R.V., Dayhoff, M.O. (1966) Atlas of Protein Sequence and Structure 1966. National Biomedical Research Foundation, Silver Spring, Maryland.
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. (1971) Toward defining the course of evolution: Minimu change for a specified tree topology. Systematic Zoology, 20, 406-416.
as.proseq
, Rdnapars
, read.protein
1 2 3 4 5 | ## Not run:
data(chloroplast)
tree<-Rprotpars(chloroplast)
## End(Not run)
|
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