# Research training at Tübingen University with Daniel Huson

*(En français)*
## Topics

### Optimizing the layout of phylogenetic graphs.

To represent the evolution of some species or genes, the classical model is

*the phylogenetic tree*.
But trees are unable to represent horizontal gene transfers,
recombinations and hybridizations. In those
cases,

*phylogenetic networks* are required.

The

SplitsTree software
can represent many of those networks, in particular

*splitsgraphs*.
Those graphs represent

*conflicting signals in a phylogeny*,
with

*boxes* appearing wherever
evolution is uncertain. A splitsgraph can be obtained by a bootstrap on
phylogenetic trees, or by a consensus
of different phylogenetic trees, even if they
have a different number of taxa.

My purpose in this research training is

*to improve the layout of these splitsgraphs* in SplitsTree,
by increasing the area of the boxes which represent
the conflicting signals in the phylogeny.
I worked on this problem with Daniel Huson.

Optimizing the layout of reticulate networks.

When

*reticulations are added to a phylogenetic tree*, the new edges created
may intersect with existing edges. But changing the ordering of the taxa
could lessen the number of such intersections. With Tobias Klöpper, our purpose was to
find a heuristic to

*determine the ordering on the taxa which would minimize
the total number of crossings*. The one we propose is based on the

*dual graph* of the phylogenetic tree,
with a distance which reflects the number of
intersections, and a

*mirroring process*
to improve this distance in a

*simulated annealing* scheme.

Results :

*10 loops of the "box-opening algorithm".*

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