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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, treebased phylogenetic networks are more suitable as they can depict reticulate evolution.<br/>Nonetheless, treebased 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 wellknown 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 treedecompositions to achieve a running time that is exponential in the tree...master thesis 2023
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van der Made, Frank (author)The problem considered in this thesis is the box set optimization problem. In<br/>this problem the goal is to find the optimal dimensions of a number of shipping<br/>boxes which have to provide an optimal fit on a set of items. The application<br/>considered is ecommerce, and hence the number of items is relatively large<br/>compared to other...master thesis 2022
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Nardi Dei Da Filicaia Dotti, Andrea (author)In this paper we give a historical and theoretical background to minimal triangulation and its relation to minimal separators.<br/>We introduce a new type of minimal separators, the minimal meta separator, which its size is a lower bound for the treewidth problem, its fillin is a lower bound for the minimum fillin problem and can be used for...master thesis 2022
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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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Druijf, Teun (author)In the current economy, there is an increasing focus on sustainability. Green transport solutions, like rail freight, are becoming more and more popular. We will look into the shunting operations at Kijfhoek shunting yard. This yard functions as the central hub for DB Cargo Nederland and connects the Port of Rotterdam with the hinterland. About...master thesis 2022
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van Belkom, Myrte (author)When processing a trace DNA sample at the Netherlands Forensic Institute, an STR electropherogram can be created. An analyst uses this electropherogram and analysis software to read out peaks signifying DNA. After analysis, the DNA profile is used in the interpretation process, which can include the comparison to a reference DNA profile of a...master thesis 2021
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Simon, Alexandre (author)Interval graphs play an important role in graph theory and have intensively been studied for over sixty years due to their wide range of applications and because most NPhard problems on general graphs become solvable in linear time on interval graphs. However, the class of interval graphs is restricted and does not even contain a cycle of...master thesis 2021
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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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Dijksman, Calvin (author)For NPhard optimisation problems no polynomialtime algorithms exist for finding a solution. Therefore, heuristic methods are often used, especially when approximate solutions can be satisfactory. One such method is quantum annealing, a method where some initial Hamiltonian is slowly perturbed to anneal towards a problem Hamiltonian. The...bachelor thesis 2021
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Deen, Elise (author)In this report, the bounded Maximum Parsimony distance will be considered when<br/>applying three different reduction rules. The distance is a measure on how dissimilar two trees are and is calculated based on the number of mutations that occur when looking at heritable traits. The first rule considered, is the chain reduction. For this rule, it...bachelor thesis 2021
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van Oosterom, Simon (author)In this thesis, we consider investment optimization for airport infrastructure which is required charge and refuel electric and hydrogen powered aircraft using battery and hydrogen canister swaps respectively. The task at hand is to determine the most costeffective infrastructure, consisting of spare batteries, and battery chargers for electric...master thesis 2021
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Versendaal, Bryan (author)In this thesis we look at three different algorithms within the field of phylogenetics and create a proof of concept for using machine learning to improve the algorithms. The problems are the maximum agreement forest problem, the hybridization number problem and finally the tail move problem. A study of the problems show that they can all...master thesis 2020
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Mol, Riche (author)Van Iersel, Moulton, and Murakami (2020) proved that a level2 binary phylogenetic network can be uniquely reconstructed based on the matrix of mulitsets of the distances of the leaves. Using a handful of lemma’s each<br/>describing the steps of identifying cherries, uncontained leaves and blobs in the network, I created an algorithm for...bachelor thesis 2020
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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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