3 \alias{print.phymltest}
4 \alias{summary.phymltest}
6 \title{Fits a Bunch of Models with PhyML}
8 phymltest(seqfile, format = "interleaved", itree = NULL,
9 exclude = NULL, execname = NULL, append = TRUE)
10 \method{print}{phymltest}(x, ...)
11 \method{summary}{phymltest}(object, ...)
12 \method{plot}{phymltest}(x, main = NULL, col = "blue", ...)
15 \item{seqfile}{a character string giving the name of the file that
16 contains the DNA sequences to be analysed by PhyML.}
17 \item{format}{a character string specifying the format of the DNA
18 sequences: either \code{"interleaved"} (the default), or
20 \item{itree}{a character string giving the name of a file with a tree
21 in Newick format to be used as an initial tree by PhyML. If
22 \code{NULL} (the default), PhyML uses a ``BIONJ'' tree.}
23 \item{exclude}{a vector of mode character giving the models to be
24 excluded from the analysis. These must be among those below, and
25 follow the same syntax.}
26 \item{execname}{a character string specifying the name of the PhyML
27 executable. This argument can be left as \code{NULL} if PhyML's
28 default names are used: \code{"phyml_3.0_linux32"},
29 \code{"phyml_3.0_macintel"}, or \code{"phyml_3.0_win32.exe"}, under
30 Linux, MacOS, or Windows respectively.}
31 \item{append}{a logical indicating whether to erase previous PhyML
32 output files if present; the default is to not erase.}
33 \item{x}{an object of class \code{"phymltest"}.}
34 \item{object}{an object of class \code{"phymltest"}.}
35 \item{main}{a title for the plot; if left \code{NULL}, a title is made
36 with the name of the object (use \code{main = ""} to have no
38 \item{col}{a colour used for the segments showing the AIC values (blue
40 \item{...}{further arguments passed to or from other methods.}
43 This function calls PhyML and fits successively 28 models of DNA
44 evolution. The results are saved on disk, as PhyML usually does, and
45 returned in R as a vector with the log-likelihood value of each model.
48 The present function requires version 3.0 of PhyML; it won't work with
51 The user must take care to set correctly the three different paths
52 involved here: the path to PhyML's binary, the path to the sequence
53 file, and the path to R's working directory. The function should work
54 if all three paths are different. Obviously, there should be no problem
55 if they are all the same.
57 The following syntax is used for the models:
61 where "X" is the first letter of the author of the model, "Y" and "Z"
62 are possibly other co-authors of the model, "00" is the year of the
63 publication of the model, and "+I" and "+G" indicates whether the
64 presence of invariant sites and/or a gamma distribution of
65 substitution rates have been specified. Thus, Kimura's model is
66 denoted "K80" and not "K2P". The exception to this rule is the general
67 time-reversible model which is simple denoted "GTR" model.
69 The seven substitution models used are: "JC69", "K80", "F81", "F84",
70 "HKY85", "TN93", and "GTR". These models are then altered by adding
71 the "+I" and/or "+G", resulting thus in four variants for each of them
72 (e.g., "JC69", "JC69+I", "JC69+G", "JC69+I+G"). Some of these models
73 are described in the help page of \code{\link{dist.dna}}.
75 When a gamma distribution of substitution rates is specified, four
76 categories are used (which is PhyML's default behaviour), and the
77 ``alpha'' parameter is estimated from the data.
79 For the models with a different substition rate for transitions and
80 transversions, these rates are left free and estimated from the data
81 (and not constrained with a ratio of 4 as in PhyML's default).
83 The option \code{path2exec} has been removed in the present version:
84 the path to PhyML's executable can be specified with the option
88 It is important to note that the models fitted by this function is
89 only a small fraction of the models possible with PhyML. For instance,
90 it is possible to vary the number of categories in the (discretized)
91 gamma distribution of substitution rates, and many parameters can be
92 fixed by the user. The results from the present function should rather
93 be taken as indicative of a best model.
96 \code{phymltest} returns an object of class \code{"phymltest"}: a
97 numeric vector with the models as names.
99 The \code{print} method prints an object of class \code{"phymltest"}
100 as matrix with the name of the models, the number of free parameters,
101 the log-likelihood value, and the value of the Akaike information
102 criterion (AIC = -2 * loglik + 2 * number of free parameters)
104 The \code{summary} method prints all the possible likelihood ratio
105 tests for an object of class \code{"phymltest"}.
107 The \code{plot} method plots the values of AIC of an object of class
108 \code{"phymltest"} on a vertical scale.
111 Posada, D. and Crandall, K. A. (2001) Selecting the best-fit model of
112 nucleotide substitution. \emph{Systematic Biology}, \bold{50},
115 Guindon, S. and Gascuel, O. (2003) A simple, fast, and accurate
116 algorithm to estimate large phylogenies by maximum likelihood.
117 \emph{Systematic Biology}, \bold{52}, 696--704.
118 \url{http://atgc.lirmm.fr/phyml/}
120 \author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
122 \code{\link{read.tree}}, \code{\link{write.tree}},
123 \code{\link{dist.dna}}
126 ### A `fake' example with random likelihood values: it does not
127 ### make sense, but does not need PhyML and gives you a flavour
128 ### of what the output looks like:
129 x <- runif(28, -100, -50)
130 names(x) <- .phymltest.model
131 class(x) <- "phymltest"
135 plot(x, main = "", col = "red")
136 ### This example needs PhyML, copy/paste or type the
137 ### following commands if you want to try them, eventually
138 ### changing setwd() and the options of phymltest()
140 setwd("D:/phyml_v2.4/exe") # under Windows
142 write.dna(woodmouse, "woodmouse.txt")
143 X <- phymltest("woodmouse.txt")