Forest-Based Binary Phylogenetic Networks: Finding Optimal Base Forests with Integer Linear Programming

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...

A new polynomial for describing Phylogenetic Networks

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...

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

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...

Tail move rearrangement algorithm for rooted binary phylogenetic networks

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...

Rooted binary level-3 phylogenetic networks are encoded by quarnets

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...

Tree-child Network Containment

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...

Orienting phylogenetic networks

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...

Computing Measures for Tree-Basedness of Phylogenetic Networks

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...

Measuring how far a nonbinary phylogenetic network is from being tree-based

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....

Parental Parsimony on Phylogenetic Networks: Computing the Maximum Parsimony Scores of Phylogenetic Networks

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...

Resolving contradicting binets and finding similarities in networks

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...

Constructing Evolutionary Supernetworks from Binets

Constructing the evolutionary history of species is a task with a lot of mathematics involved. Given a collection of small pieces of history we try to construct the bigger picture. The evolutionary history of species can be represented in a phylogenetic tree. For a given set of smaller phylogenetic trees a bigger supertree can be constructed....

Characterising tree-based phylogenetic networks

Commonly, the evolutionary history of a set of taxa is described by a phylogenetic tree. However, in certain cases, evolution can best be described by a phylogenetic network. In previous research, the term tree-based was introduced for a phylogenetic network, meaning that it can be drawn as a phylogenetic tree with additional horizontal arcs. In...