mlphylo {ape} | R Documentation |
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)
x |
an object of class "DNAbin" giving the (aligned) DNA
sequence data. |
phy |
an object of class "phylo" giving the tree. |
model |
an object of class "DNAmodel" giving the model to
be fitted. |
search.tree |
a logical specifying whether to search for the best tree (defaults to FALSE) (not functional for the moment). |
quiet |
a logical specifying whether to display the progress of the analysis. |
value |
a list with elements named 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. |
fixed |
a logical specifying whether to optimize parameters given
in value . |
object |
an object of class "phylo" . |
k |
a numeric value giving the penalty per estimated parameter;
the default is k = 2 which is the classical Akaike
information criterion. |
... |
further arguments passed to or from other methods. |
The model specified by 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.
an object of class "phylo"
. There are possible additional
attributes:
loglik |
the maximum log-likelihood. |
npart |
the number of partitions. |
model |
the substitution model. |
rates |
the estimated substitution rates. |
invar |
the estimated proportion of invariants. |
alpha |
the estimated shape parameter of the inter-sites variation in substitution rates. |
For the moment, it is not possible to estimate neither branch lengths,
nor the topology with mlphylo
. The function may estimate all other
parameters: substitution rates, shape (alpha) of the
inter-sites variation in substitution rates, the proportion of
invariants, and the ``contrast'' parameter (xi) among
partitions.
Alternative topologies can also be compared using likelihood-ratio tests (LRTs) or AICs.
Emmanuel Paradis Emmanuel.Paradis@mpl.ird.fr
Felsenstein, J. (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution, 17, 368–376.
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