Computing Measures for Tree-Basedness of Phylogenetic Networks

Bachelor thesis (2018)

Authors

A. Mooiman Electrical Engineering, Mathematics and Computer Science

Contributors

J.G. Spandaw (graduation committee member)
K.P. Hart (graduation committee member)
Faculty
Electrical Engineering, Mathematics and Computer Science, Electrical Engineering, Mathematics and Computer Science
Copyright: © 2018 Arthur Mooiman
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Published Date

26-04-2018

Language

English

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Faculty

Electrical Engineering, Mathematics and Computer Science

Abstract

Phylogenetic networks are a type of directed acyclic graph used to represent evolutionary relationships that contain events such as hybridization or horizontal gene transfer. When a network
lacks such events it is a phylogenetic tree. Some phylogenetic networks that are not trees can
however be represented as a tree with additional linking arcs, e.g. representing transfer of genetic
materials. We have implemented an algorithm that can be used to determine whether a given
network is tree-based or not. Moreover if the network is not tree-based, the algorithm shows
how it can be made tree-based by adding a minimum number of additional leaves, representing
possible extinct or un-sampled species. We also describe the theory behind the algorithm and
apply it to several synthetic as well as biological datasets.

Files

VerslagBep.pdf
(.pdf | 0.421 Mb)
Bep_Code.pdf
(.pdf | 0.056 Mb)