ape (version 3.1-4)

phymltest: Fits a Bunch of Models with PhyML

Description

This function calls PhyML and fits successively 28 models of DNA evolution. The results are saved on disk, as PhyML usually does, and returned in Ras a vector with the log-likelihood value of each model.

Usage

phymltest(seqfile, format = "interleaved", itree = NULL,
          exclude = NULL, execname = NULL, append = TRUE)
## S3 method for class 'phymltest':
print(x, ...)
## S3 method for class 'phymltest':
summary(object, ...)
## S3 method for class 'phymltest':
plot(x, main = NULL, col = "blue", ...)

Arguments

Value

phymltest returns an object of class "phymltest": a numeric vector with the models as names.

The print method prints an object of class "phymltest" as matrix with the name of the models, the number of free parameters, the log-likelihood value, and the value of the Akaike information criterion (AIC = -2 * loglik + 2 * number of free parameters)

The summary method prints all the possible likelihood ratio tests for an object of class "phymltest".

The plot method plots the values of AIC of an object of class "phymltest" on a vertical scale.

Details

The present function requires version 3.0.1 of PhyML; it won't work with older versions.

The user must take care to set correctly the three different paths involved here: the path to PhyML's binary, the path to the sequence file, and the path to R's working directory. The function should work if all three paths are different. Obviously, there should be no problem if they are all the same.

The following syntax is used for the models:

"X[Y][Z]00[+I][+G]"

where "X" is the first letter of the author of the model, "Y" and "Z" are possibly other co-authors of the model, "00" is the year of the publication of the model, and "+I" and "+G" indicates whether the presence of invariant sites and/or a gamma distribution of substitution rates have been specified. Thus, Kimura's model is denoted "K80" and not "K2P". The exception to this rule is the general time-reversible model which is simple denoted "GTR" model.

The seven substitution models used are: "JC69", "K80", "F81", "F84", "HKY85", "TN93", and "GTR". These models are then altered by adding the "+I" and/or "+G", resulting thus in four variants for each of them (e.g., "JC69", "JC69+I", "JC69+G", "JC69+I+G"). Some of these models are described in the help page of dist.dna.

When a gamma distribution of substitution rates is specified, four categories are used (which is PhyML's default behaviour), and the ``alpha'' parameter is estimated from the data.

For the models with a different substition rate for transitions and transversions, these rates are left free and estimated from the data (and not constrained with a ratio of 4 as in PhyML's default).

The option path2exec has been removed in the present version: the path to PhyML's executable can be specified with the option execname.

References

Posada, D. and Crandall, K. A. (2001) Selecting the best-fit model of nucleotide substitution. Systematic Biology, 50, 580--601.

Guindon, S. and Gascuel, O. (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology, 52, 696--704. http://www.atgc-montpellier.fr/phyml/

See Also

read.tree, write.tree, dist.dna

Examples

Run this code
### A `fake' example with random likelihood values: it does not
### make sense, but does not need PhyML and gives you a flavour
### of what the output looks like:
x <- runif(28, -100, -50)
names(x) <- ape:::.phymltest.model
class(x) <- "phymltest"
x
summary(x)
plot(x)
plot(x, main = "", col = "red")
### This example needs PhyML, copy/paste or type the
### following commands if you want to try them, eventually
### changing setwd() and the options of phymltest()
setwd("D:/phyml_v2.4/exe") # under Windows
data(woodmouse)
write.dna(woodmouse, "woodmouse.txt")
X <- phymltest("woodmouse.txt")
X
summary(X)
plot(X)

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