Rcontml: R interface for contml
Description
This function is an R interface for contml in the PHYLIP package (Felsenstein 2013). contml can be used for ML phylogeny estimation from gene frequency data or continuous characters. The continuous characters should be rotated so as to be uncorrelated before analysis.Usage
Rcontml(X, path=NULL, ...)
Value
This function returns an object of class "phylo" that is the optimized tree.Details
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 model will be optimized on a fixed input topology; global perform global search (defaults to global = TRUE); 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); 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 contml program in PHYLIP can be found here http://evolution.genetics.washington.edu/phylip/doc/contml.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.References
Felsenstein, J. (1981) Maximum likelihood estimation of evolutionary trees from continuous characters. American Journal of Human Genetics, 25, 471-492.
Felsenstein, J. (1981) Maximum likelihood estimation of evolutionary trees from continuous characters. American Journal of Human Genetics, 25, 471-492.
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.