## Section: Application Domains

### Phylogeny

Phylogeny is concerned with designing evolutionary trees between species from aligned nucleotide sequences. More
precisely, a nucleotide sequence being an ordered set of sites taking value in a finite
set E (for instance, E = {A, C, G, T} ), the problem is to reconstruct the topology of the evolutionary tree
between the species from aligned sequences for the considered species, and to estimate the tree parameters
(branches length) as well as the parameters of the evolutionary model.
Our research in this domain is twofold. First we are working on a
model selection approach from a semi parametric graphical model whose
parameters to be estimated are the topology, branches lengths and
mutation rate of the evolutionary tree.
Secondly, we are working on the *covarion* model. For this model, a site
can change behavior along the evolutionary tree according to two hidden states, active (ON) or nonactive (OFF).
In this research, we are interested in comparing non nested models.