# mlphylo

##### Estimating Phylogenies by Maximum Likelihood

`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.

- Keywords
- models

##### Usage

```
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)
```

##### Arguments

- 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.

##### Details

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.

##### Value

- 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.

##### Note

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.

##### References

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.

##### See Also

*Documentation reproduced from package ape, version 2.1-1, License: GPL (>= 2)*