mlphylo
estimates a phylogenetic tree by maximum likelihood
given a set of DNA sequences. The model of evolution is specified with
the function DNAmodel
. logLik
, deviance
, and AIC
are generic functions
used to extract the log-likelihood, the deviance (-2*logLik), or the
Akaike information criterion of a tree. If no such values are
available, NULL
is returned.
mlphylo(x, phy, model = DNAmodel(), search.tree = FALSE,
quiet = FALSE, value = NULL, fixed = FALSE)
## S3 method for class 'phylo':
logLik(object, ...)
## S3 method for class 'phylo':
deviance(object, ...)
## S3 method for class 'phylo':
AIC(object, ..., k = 2)
"DNAbin"
giving the (aligned) DNA
sequence data."phylo"
giving the tree."DNAmodel"
giving the model to
be fitted.rates
, alpha
,
and invar
, or at least one of these, giving the initial
values of the parameters of the model. If NULL
, some initial
values are given internally.value
."phylo"
.k = 2
which is the classical Akaike
information criterion."phylo"
. There are possible additional
attributes:DNAmodel
is fitted using the
standard ``pruning'' algorithm of Felsenstein (1981).The implementation of the inter-sites variation in substitution rates follows the methodology developed by Yang (1994).
The difference among partitions is parametrized with a contrast parameter (denoted $\xi$) that specifies the contrast in mean susbtitution rate among the partitions. This methodology is inspired from one introduced by Yang (1996).
The substitution rates are indexed column-wise in the rate matrix: the first rate is set to one.
Yang, Z. (1994) Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. Journal of Molecular Evolution, 39, 306--314.
Yang, Z. (1996) Maximum-likelihood models for combined analyses of multiple sequence data. Journal of Molecular Evolution, 42, 587--596.
DNAmodel
, nj
, read.dna
,
summary.phylo
, bionj
, fastme