phymltest(seqfile, format = "interleaved", itree = NULL,
exclude = NULL, execname = NULL, path2exec = NULL)
## S3 method for class 'phymltest':
print(x, ...)
## S3 method for class 'phymltest':
summary(object, ...)
## S3 method for class 'phymltest':
plot(x, ...)"interleaved" (the default), or
"sequential".NULL (the default), PHYML uses a ``BIONJ'' tree.NULL and the operating system is ``windows'',
the default name "phyml_w32" is used, otherwise the name must
be given.NULL the file must be accessible to R (either
it is in the computer path, or it is in R's working directory)."phymltest"."phymltest".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.
Under unix-like systems, it seems necessary to run R from csh or a similar shell (sh might not work).
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.
If the usual output files of PHYML already exist, they are not deleted and PHYML's results are appended.
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).
Guindon, S. and Gascuel, O. (2003) A simple, fast, and accurate
algorithm to estimate large phylogenies by maximum likelihood.
Systematic Biology, 52, 696--704.
read.tree, write.tree,
dist.dna### A "fake" example with random likelihood values: it does not
### make sense, but does not need PHYML and gives you a flavour
### of how the output looks like:
x <- runif(28, -100, -50)
names(x) <- .phymltest.model
class(x) <- "phymltest"
x
summary(x)
plot(x)
### 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)Run the code above in your browser using DataLab