6 \title{Estimating Phylogenies by Maximum Likelihood}
8 mlphylo(x, phy, model = DNAmodel(), search.tree = FALSE,
9 quiet = FALSE, value = NULL, fixed = FALSE)
10 \method{logLik}{phylo}(object, ...)
11 \method{deviance}{phylo}(object, ...)
12 \method{AIC}{phylo}(object, ..., k = 2)
15 \item{x}{an object of class \code{"DNAbin"} giving the (aligned) DNA
17 \item{phy}{an object of class \code{"phylo"} giving the tree.}
18 \item{model}{an object of class \code{"DNAmodel"} giving the model to
20 \item{search.tree}{a logical specifying whether to search for the best
21 tree (defaults to FALSE) (not functional for the moment).}
22 \item{quiet}{a logical specifying whether to display the progress of
24 \item{value}{a list with elements named \code{rates}, \code{alpha},
25 and \code{invar}, or at least one of these, giving the initial
26 values of the parameters of the model. If \code{NULL}, some initial
27 values are given internally.}
28 \item{fixed}{a logical specifying whether to optimize parameters given
30 \item{object}{an object of class \code{"phylo"}.}
31 \item{k}{a numeric value giving the penalty per estimated parameter;
32 the default is \code{k = 2} which is the classical Akaike
33 information criterion.}
34 \item{...}{further arguments passed to or from other methods.}
37 \code{mlphylo} estimates a phylogenetic tree by maximum likelihood
38 given a set of DNA sequences. The model of evolution is specified with
39 the function \code{\link{DNAmodel}}.
41 \code{logLik}, \code{deviance}, and \code{AIC} are generic functions
42 used to extract the log-likelihood, the deviance (-2*logLik), or the
43 Akaike information criterion of a tree. If no such values are
44 available, \code{NULL} is returned.
47 The model specified by \code{\link{DNAmodel}} is fitted using the
48 standard ``pruning'' algorithm of Felsenstein (1981).
50 The implementation of the inter-sites variation in substitution rates
51 follows the methodology developed by Yang (1994).
53 The difference among partitions is parametrized with a contrast
54 parameter (denoted \eqn{\xi}{xi}) that specifies the contrast in mean
55 susbtitution rate among the partitions. This methodology is inspired
56 from one introduced by Yang (1996).
58 The substitution rates are indexed column-wise in the rate matrix: the
59 first rate is set to one.
62 For the moment, it is not possible to estimate neither branch lengths,
63 nor the topology with \code{mlphylo}. The function may estimate all other
64 parameters: substitution rates, shape (\eqn{\alpha}{alpha}) of the
65 inter-sites variation in substitution rates, the proportion of
66 invariants, and the ``contrast'' parameter (\eqn{\xi}{xi}) among
69 Alternative topologies can also be compared using likelihood-ratio
73 an object of class \code{"phylo"}. There are possible additional
76 \item{loglik}{the maximum log-likelihood.}
77 \item{npart}{the number of partitions.}
78 \item{model}{the substitution model.}
79 \item{rates}{the estimated substitution rates.}
80 \item{invar}{the estimated proportion of invariants.}
81 \item{alpha}{the estimated shape parameter of the inter-sites
82 variation in substitution rates.}
85 Felsenstein, J. (1981) Evolutionary trees from DNA sequences: a
86 maximum likelihood approach. \emph{Journal of Molecular Evolution},
89 Yang, Z. (1994) Maximum likelihood phylogenetic estimation from DNA
90 sequences with variable rates over sites: approximate methods.
91 \emph{Journal of Molecular Evolution}, \bold{39}, 306--314.
93 Yang, Z. (1996) Maximum-likelihood models for combined analyses of
94 multiple sequence data. \emph{Journal of Molecular Evolution},
97 \author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
99 \code{\link{DNAmodel}}, \code{\link{nj}}, \code{\link{read.dna}},
100 \code{\link{summary.phylo}}, \code{\link{bionj}}, \code{\link{fastme}}