Making phylogenetic networks orchard
Algorithms to determine if a phylogenetic network is orchard and to transform non-orchard to orchard networks
M.R. Susanna (TU Delft - Electrical Engineering, Mathematics and Computer Science)
L.J.J. van Iersel – Mentor (TU Delft - Electrical Engineering, Mathematics and Computer Science)
Y. Murakami – Mentor (TU Delft - Electrical Engineering, Mathematics and Computer Science)
J.W. van der Woude – Graduation committee member (TU Delft - Electrical Engineering, Mathematics and Computer Science)
More Info
expand_more
Other than for strictly personal use, it is not permitted to download, forward or distribute the text or part of it, without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license such as Creative Commons.
Abstract
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.