phangorn (version 2.5.5)

codonTest: codonTest

Description

Models for detecting positive selection

Usage

codonTest(tree, object, model = c("M0", "M1a", "M2a"),
  frequencies = "F3x4", opt_freq = FALSE, codonstart = 1,
  control = pml.control(maxit = 20), ...)

Arguments

tree

a phylogenetic tree.

object

an object of class phyDat.

model

a vector containing the substitution models to compare with each other or "all" to test all available models.

frequencies

a character string or vector defining how to compute the codon frequencies

opt_freq

optimize frequencies (so far ignored)

codonstart

an integer giving where to start the translation. This should be 1, 2, or 3, but larger values are accepted and have for effect to start the translation further within the sequence.

control

a list of parameters for controlling the fitting process.

...

further arguments passed to or from other methods.

Value

A list whith an element called summary containing a data.frame with the log-likelihood, number of estimated parameters, etc. of all tested models. An object called posterior which contains the posterior probability for the rate class for each sites and the estimates of the defined models.

Details

codonTest allows to test for positive selection similar to programs like PAML (Yang ) or HyPhy (Kosakovsky Pond et al. 2005).

There are several options for deriving the codon frequencies. Frequencies can be "equal" (1/61), derived from nucleotide frequencies "F1x4" and "F3x4" or "empirical" codon frequencies. The frequencies taken using the empirical frequencies or estimated via maximum likelihood.

So far the M0 model (Goldman and Yang 2002), M1a and M2a are implemented. The M0 model is always computed the other are optional. The convergence may be very slow and sometimes fails.

References

Ziheng Yang (2014). Molecular Evolution: A Statistical Approach. Oxford University Press, Oxford

Sergei L. Kosakovsky Pond, Simon D. W. Frost, Spencer V. Muse (2005) HyPhy: hypothesis testing using phylogenies, Bioinformatics, 21(5): 676--679, https://doi.org/10.1093/bioinformatics/bti079

Nielsen, R., and Z. Yang. (1998) Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics, 148: 929--936

See Also

pml, pmlMix, modelTest, AIC

Examples

# NOT RUN {
# }
# NOT RUN {
# load woodmouse data from ape
data(woodmouse)
dat_codon <- dna2codon(as.phyDat(woodmouse))
tree <- NJ(dist.ml(dat_codon))
# optimise the model the old way
fit <- pml(tree, dat_codon, bf="F3x4")
M0 <- optim.pml(fit, model="codon1")
# Now using the codonTest function
fit_codon <- codonTest(tree, dat_codon)
fit_codon
plot(fit_codon, "M1a")
# }
# NOT RUN {
# }