Making phylogenetic networks orchard

Making phylogenetic networks orchard: Algorithms to determine if a phylogenetic network is orchard and to transform non-orchard to orchard networks

Susanna, Merel (TU Delft Electrical Engineering, Mathematics and Computer Science)

van Iersel, L.J.J. (mentor)
Murakami, Yukihiro (mentor)
van der Woude, J.W. (graduation committee)

Delft University of Technology

Applied Mathematics

2022-07-05

Phylogenetic networks are used to represent evolutionary histories of a set of taxa. In this thesis, we look at a certain network class, called orchard networks.
In the beginning of this thesis, definitions concerning phylogenetic networks and specifically orchard networks are introduced. The characterization of orchard networks involves time-labelling of the vertices.
Then, an algorithm is given to see if a given network is orchard. The next section, explores a non-recursive labelling of a given network. There is not an explicit algorithm for the labelling. An algorithm for the labelling is given.
The last chapter is about non-orchard networks. It contains multiple actions that can be performed on the non-orchard networks in order to transform the non-orchard networks into orchard networks.

phylogenetic networks
orchard networks
non-orchard networks

http://resolver.tudelft.nl/uuid:724ac2af-e569-4586-b367-288fef890252

Student theses

bachelor thesis

© 2022 Merel Susanna