Comparison of different nucleotide or amino acid substitution models
Usage
modelTest(object, tree = NULL, model = NULL, G = TRUE, I = TRUE,
FREQ = FALSE, k = 4, control = pml.control(epsilon = 1e-08, maxit = 10,
trace = 1), multicore = FALSE, mc.cores = NULL)Arguments
- object
an object of class phyDat or pml
- tree
a phylogenetic tree.
- model
a vector containing the substitution models to compare with each other or "all" to test all available models
- G
logical, TRUE (default) if (discrete) Gamma model should be tested
- I
logical, TRUE (default) if invariant sites should be tested
- FREQ
logical, FALSE (default) if TRUE amino acid frequencies will be estimated.
- k
number of rate classes
- control
A list of parameters for controlling the fitting process.
- multicore
logical, whether models should estimated in parallel.
- mc.cores
The number of cores to use, i.e. at most how many child processes will be run simultaneously. Must be at least one, and parallelization requires at least two cores.
Value
A data.frame containing the log-likelihood, number of estimated parameters, AIC, AICc and BIC all tested models. The data.frame has an attributes "env" which is an environment which contains all the trees, the data and the calls to allow get the estimated models, e.g. as a starting point for further analysis (see example).
Details
modelTest estimates all the specified models for a given tree and
data. When the mclapply is available, the computations are done in
parallel. modelTest runs each model in one thread. This is may not
work within a GUI interface and will not work under Windows.
References
Burnham, K. P. and Anderson, D. R (2002) Model selection and multimodel inference: a practical information-theoretic approach. 2nd ed. Springer, New York
Posada, D. and Crandall, K.A. (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14(9): 817-818
Posada, D. (2008) jModelTest: Phylogenetic Model Averaging. Molecular Biology and Evolution 25: 1253-1256
Darriba D., Taboada G.L., Doallo R and Posada D. (2011) ProtTest 3: fast selection of best-fit models of protein evolution. . Bioinformatics 27: 1164-1165
Author
Klaus Schliep klaus.schliep@gmail.com
Examples
if (FALSE) { # \dontrun{
example(NJ)
(mT <- modelTest(Laurasiatherian, tree, model = c("JC", "F81", "K80", "HKY",
"SYM", "GTR")))
# extract best model
(best_model <- as.pml(mT))
data(chloroplast)
(mTAA <- modelTest(chloroplast, model=c("JTT", "WAG", "LG")))
# test all available amino acid models
(mTAA_all <- modelTest(chloroplast, model="all", multicore=TRUE, mc.cores=2))
} # }