R: codonTest

codonTest {phangorn} | R Documentation

## 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.

### 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.

### 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.

### Author(s)

Klaus Schliep klaus.schliep@gmail.com

### 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, doi: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:
    # 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")

    ## End(Not run)

[Package phangorn version 2.6.2 Index]