R interfaces for proml and promlk

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Description

This function is an R interface for proml in the PHYLIP package (Felsenstein 1989, 2013). proml can be used for ML phylogeny estimation from amino acid sequences.

Usage

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Rproml(X, path=NULL, ...)
Rpromlk(X, path=NULL, ...)

Arguments

X

an object of class "proseq".

path

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

...

optional arguments to be passed to proml or promlk. 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; model amino acid model - could be "JTT" (Jones et al. 1992), "PMB" (Veerassamy et al. 2003), or "PAM" (Dayhoff & Eck 1968; Dayhoff et al. 1979; Koisol & Goldman 2005); rates vector of rates (defaults to single rate); rate.categories vector of rate categories corresponding to the order of rates; gamma alpha shape parameter of a gamma model of rate heterogeneity among sites (defaults to no gamma rate heterogeneity); ncat number of rate categories for the gamma model; inv proportion of invariant sites for the invariant sites model (defaults to inv = 0); weights vector of weights of length equal to the number of columns in X (defaults to unweighted); speedier speedier but rougher analysis (defaults to speedier = FALSE); 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).

Finally clock=TRUE enforces a molecular clock. The argument clock is only available for Rproml. If clock=TRUE then promlk is used internally. For Rpromlk a molecular clock is assumed, thus Rproml(...,clock=TRUE) and Rpromlk(...) are equivalent. Note that in PHYLIP 3.695 my tests of promlk yielded peculiar results (all branch lengths zero length, random topology), so I'm not sure what to make of that.

More information about the proml and promlk programs in PHYLIP can be found here http://evolution.genetics.washington.edu/phylip/doc/proml.html, and here http://evolution.genetics.washington.edu/phylip/doc/promlk.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

Dayhoff, M.O., Eck, R.V. (1968) Atlas of Protein Sequence and Structure 1967-1968. National Biomedical Research Foundation, Silver Spring, Maryland.

Dayhoff, M.O., Schwartz, R.M., Orcutt, B.C. (1979) A model of evolutionary change in proteins. pp. 345-352 in Atlas of Protein Sequence and Structure, Volume 5, Supplement 3, 1978, ed. M.O. Dayhoff. National Biomedical Research Foundataion, 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.

Jones, D.T., Taylor, W.R., Thornton, J.M. (1992) The rapid generation of mutation data matrices from protein sequences. Computer Applications in the Biosciences (CABIOS), 8, 275-282.

Koisol, C., Goldman, N. (2005) Different versions of the Dayhoff rate matrix. Molecular Biology and Evolution, 22, 193-199.

Veerassamy, S., Smith, A., Tillier, E.R. (2003) A transition probability model for amino acid substitutions from blocks. Journal of Computational Biology, 10, 997-1010.

See Also

as.proseq, Rdnaml, read.protein

Examples

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## Not run: 
data(chloroplast)
tree<-Rproml(chloroplast)

## End(Not run)

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