Making phylogenetic networks orchard

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

Bachelor thesis (2022)

Authors

M.R. Susanna Electrical Engineering, Mathematics and Computer Science

Contributors

L.J.J. van Iersel Discrete Mathematics and Optimization - EEMCS (mentor)
Yukihiro Murakami Discrete Mathematics and Optimization - EEMCS (mentor)
J.W. van der Woude Mathematical Physics - EEMCS (graduation committee member)
Faculty
Electrical Engineering, Mathematics and Computer Science, Electrical Engineering, Mathematics and Computer Science
Copyright: © 2022 Merel Susanna
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Published Date

05-07-2022

Language

English

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Faculty

Electrical Engineering, Mathematics and Computer Science

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.