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, path2exec = NULL)
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 binary file. This argument can be left missing under Windows: the
28 default name \code{"phyml_w32"} will then be used.}
29 \item{path2exec}{a character string giving the path to the PHYML
30 binary file. If \code{NULL} the file must be accessible to R (either
31 it is in the computer path, or it is in R's working directory).}
32 \item{x}{an object of class \code{"phymltest"}.}
33 \item{object}{an object of class \code{"phymltest"}.}
34 \item{main}{a title for the plot; if left \code{NULL}, a title is made
35 with the name of the object (use \code{main = ""} to have no
37 \item{col}{a colour used for the segments showing the AIC values (blue
39 \item{...}{further arguments passed to or from other methods.}
42 This function calls the software PHYML and fits successively 28 models
43 of DNA evolution. The results are saved on disk, as PHYML usually
44 does, and returned in R as a vector with the log-likelihood value of
48 The present function has been tested with version 2.4 of PHYML; it
49 should also work with version 2.3, but it won't work with version 2.1.
51 Under unix-like systems, it seems necessary to run R from csh or a
52 similar shell (sh might not work).
54 The user must take care to set correctly the three different paths
55 involved here: the path to PHYML's binary, the path to the sequence
56 file, and the path to R's working directory. The function should work
57 if all three paths are different. Obviously, there should be no problem
58 if they are all the same.
60 If the usual output files of PHYML already exist, they are not
61 deleted and PHYML's results are appended.
63 The following syntax is used for the models:
67 where "X" is the first letter of the author of the model, "Y" and "Z"
68 are possibly other co-authors of the model, "00" is the year of the
69 publication of the model, and "+I" and "+G" indicates whether the
70 presence of invariant sites and/or a gamma distribution of
71 substitution rates have been specified. Thus, Kimura's model is
72 denoted "K80" and not "K2P". The exception to this rule is the general
73 time-reversible model which is simple denoted "GTR" model.
75 The seven substitution models used are: "JC69", "K80", "F81", "F84",
76 "HKY85", "TN93", and "GTR". These models are then altered by adding
77 the "+I" and/or "+G", resulting thus in four variants for each of them
78 (e.g., "JC69", "JC69+I", "JC69+G", "JC69+I+G"). Some of these models
79 are described in the help page of \code{\link{dist.dna}}.
81 When a gamma distribution of substitution rates is specified, four
82 categories are used (which is PHYML's default behaviour), and the
83 ``alpha'' parameter is estimated from the data.
85 For the models with a different substition rate for transitions and
86 transversions, these rates are left free and estimated from the data
87 (and not constrained with a ratio of 4 as in PHYML's default).
90 It is important to note that the models fitted by this function is
91 only a small fraction of the models possible with PHYML. For instance,
92 it is possible to vary the number of categories in the (discretized)
93 gamma distribution of substitution rates, and many parameters can be
94 fixed by the user. The results from the present function should rather
95 be taken as indicative of a best model.
98 \code{phymltest} returns an object of class \code{"phymltest"}: a
99 numeric vector with the models as names.
101 The \code{print} method prints an object of class \code{"phymltest"}
102 as matrix with the name of the models, the number of free parameters,
103 the log-likelihood value, and the value of the Akaike information
104 criterion (AIC = -2 * loglik + 2 * number of free parameters)
106 The \code{summary} method prints all the possible likelihood ratio
107 tests for an object of class \code{"phymltest"}.
109 The \code{plot} method plots the values of AIC of an object of class
110 \code{"phymltest"} on a vertical scale.
113 Posada, D. and Crandall, K. A. (2001) Selecting the best-fit model of
114 nucleotide substitution. \emph{Systematic Biology}, \bold{50},
117 Guindon, S. and Gascuel, O. (2003) A simple, fast, and accurate
118 algorithm to estimate large phylogenies by maximum likelihood.
119 \emph{Systematic Biology}, \bold{52}, 696--704.
120 \url{http://atgc.lirmm.fr/phyml/}
122 \author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
124 \code{\link{read.tree}}, \code{\link{write.tree}},
125 \code{\link{dist.dna}}
128 ### A `fake' example with random likelihood values: it does not
129 ### make sense, but does not need PHYML and gives you a flavour
130 ### of what the output looks like:
131 x <- runif(28, -100, -50)
132 names(x) <- .phymltest.model
133 class(x) <- "phymltest"
137 plot(x, main = "", col = "red")
138 ### This example needs PHYML, copy/paste or type the
139 ### following commands if you want to try them, eventually
140 ### changing setwd() and the options of phymltest()
142 setwd("D:/phyml_v2.4/exe") # under Windows
144 write.dna(woodmouse, "woodmouse.txt")
145 X <- phymltest("woodmouse.txt")