Searched for: subject%3A%22phylogenetic%255C+network%22
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Broeders, Theo (author)
Reconstructing a minimum reticulation network from phylogenetic trees is used in evolutionary studies. In this thesis, we focus on finding temporal networks using cherry-picking sequences for binary trees with all taxa. Finding such a minimum reticulation temporal network is NP-hard.<br/><br/>We introduce an algorithm to find a minimum...
master thesis 2024
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Reichling, C Z (author)
This thesis is on the subject of phylogenetic networks. These are schematic<br/>visualisations used mainly to investigate the evolutionary history of species,<br/>but which can be used for any set of distinguishable elements which have diverged from a common ancestor through some evolutionary process. The research specifically focuses on a way...
master thesis 2023
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van Gruijthuijsen, Merel (author)
Phylogenetic trees are commonly utilised in evolutionary biology. These trees represent the evolution of a set of species. In case of gene transfer however, a phylogenetic tree is insufficient. In such cases, tree-based phylogenetic networks are more suitable as they can depict reticulate evolution.<br/>Nonetheless, tree-based phylogenetic...
bachelor thesis 2023
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Holtgrefe, Niels (author)
Phylogenetic networks are a specific type of directed acyclic graph (DAG), used to depict evolutionary relationships among, for example, species or other groups of organisms. To solve computationally hard problems, treewidth has been used to parametrize algorithms in phylogenetics. In the hope of simplifying the algorithmic design process, Berry...
master thesis 2023
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Keur, Hans (author)
In biology, phylogenetics is the study of the evolutionary history of and relations between e.g. species. Such data are often represented in trees. Remarkably, trees lack the representation of reticulation events, such as hybridization, while such events are believed to be important. One of the reasons why trees are widely used, is the enormous...
master thesis 2023
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Huijsman, Robbert (author)
TreeContainment is a well-known problem within phylogenetics, which asks whether a binary phylogenetic tree is embedded in a binary phylogenetic network. For this problem, Jones, Weller and van Iersel (2022) have created an algorithm that uses dynamic programming on tree-decompositions to achieve a running time that is exponential in the tree...
master thesis 2023
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van de Klok, Margot (author)
Describing phylogenetic trees or networks with a polynomial is a tool to distinguish between them. In this thesis, a new polynomial for describing rooted binary internally labeled phylogenetic networks and trees is introduced based on the research of P. Liu and J. Pons et al. Two different cases are considered, one where the reticulation nodes...
bachelor thesis 2022
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Nipius, Leonie (author)
Phylogenetic networks generalize evolutionary trees and are commonly used to represent evolutionary relationships between species that undergo reticulate evolutionary processes such as hybridization, recombination and lateral gene transfer. In this thesis all quarnets, networks on four species, of a network are assumed to be known. We prove that...
master thesis 2022
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Susanna, Merel (author)
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. <br/>In the beginning of this thesis, definitions concerning phylogenetic networks and specifically orchard networks are introduced. The characterization of orchard networks involves...
bachelor thesis 2022
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Janisse, Frank (author)
Phylogenetic networks are used to describe evolutionary histories and are a generalisation of evolutionary trees. They can contain so called reticulations, representing reticulate evolution, such as hybridization, lateral gene transfer and recombination. Methods are being developed to construct certain rooted phylogenetic networks from their...
master thesis 2021
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Husanović, Selma (author)
A common tool for exploring the space of phylogenetic networks is applying rearrangement moves, such as <i>tail moves</i>. Recently, it has been shown by Janssen et al that, given a rooted binary phylogenetic network, it is possible to generate any other alternative network, using only tail moves. The aim of this report is to translate this...
bachelor thesis 2020
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Nipius, L. (author)
Phylogenetic networks generalize evolutionary trees and are commonly used to represent evolutionary relationships between species that undergo reticulate processes such as hybridization, recombination and lateral gene transfer. Recently, there has been great interest in knowing which networks are determined or encoded by their trinets, that are...
bachelor thesis 2020
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Kole, Sjors (author)
Phylogenetic networks are a generalization of evolutionary trees that can be used to represent reticulate events. Level-k phylogenetic networks are such networks, but with a at most k reticulations per biconnected component of the network. For level-1 networks there exists an algorithm, called TriLoNet (Trinet Level-one Network algorithm), that...
master thesis 2020
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Borst, Sander (author)
We study the problem of finding a temporal hybridization network for a set of phylogenetic trees that minimizes the number of reticulations. First, we introduce an FPT algorithm for this problem on an arbitrary set of t binary trees with n leaves each with a running time of O(5^k*n*m) where k is the minimum temporal hybridization number. We also...
master thesis 2020
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Huijsman, Robbert (author)
Interest in phylogenetic trees for histories of species and DNA has spawned many problems, one of which is TreeContainment; a problem that asks whether a tree is contained within a network. The TreeContainment problem is proven to be NP-hard for general trees and networks, however it is solvable in polynomial time for networks that meet the tree...
bachelor thesis 2019
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Verzijlbergen, Esmay (author)
This thesis provides you with basic information on graph theory as well as phylogenetic networks, it studies the relationship between undirected (unrooted) and directed (rooted) phylogenetic networks, based on the manuscript 'Rooting for phylogenetic networks' . Undirected phylogenetic networks can be oriented to become a directed network. In...
bachelor thesis 2019
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Mooiman, Arthur (author)
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<br/>lacks such events it is a phylogenetic tree. Some phylogenetic networks that are not trees can<br/>however be represented as a tree with additional...
bachelor thesis 2018
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Janisse, Frank (author)
In computational biology, phylogenetic trees are used to describe evolutionary history. This can be done more generally using phylogenetic networks, which can also describe nontreelike events such as hybridization. Some phylogenetic networks can be obtained from a base tree, a rooted spanning tree with the same leaf set, by adding linking edges....
bachelor thesis 2018
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Jonkman, Niels (author)
Phylogenetic networks represent the evolutionary history of organisms and the relationships among them. In the field of phylogenetics research has been done to reconstruct these networks. Several methods for reconstructing those networks have been developed over the years. One of them is the softwired parsimony score and another, a fairly new...
bachelor thesis 2017
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de Swart, E.A. (author)
To understand the (physical) differences between species, biologist research the common ancestry of these species. This research area is called phylogenetics and the visualisation of the ancestry is displayed with the use of phylogenetic trees or networks. Generally, the phylogenetic networks are not known completely or with certainty. Therefore...
bachelor thesis 2016
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