R interface for contml

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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

1
Rcontml(X, path=NULL, ...)

Arguments

X

either (a) a matrix of continuous valued traits (in columns) with rownames containing species names; or (b) a list of matrices in which each row contains the relative frequency of alleles at a locus for a species. In the latter case the rownames of each matrix in the list should contain the species names.

path

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

...

optional arguments to be passed to contml. See details for more information.

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.

Value

This function returns an object of class "phylo" that is the optimized tree.

Author(s)

Liam J. Revell, Scott A. Chamberlain

Maintainer: Liam J. Revell <liam.revell@umb.edu>

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.

See Also

Rdnaml, Rproml

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