Related papers: Making a Network Orchard by Adding Leaves

Rooted phylogenetic networks allow biologists to represent evolutionary relationships between present-day species by revealing ancestral speciation and hybridization events. A convenient and well-studied class of such networks are…

Net-trees are a general purpose data structure for metric data that have been used to solve a wide range of algorithmic problems. We give a simple randomized algorithm to construct net-trees on doubling metrics using $O(n\log n)$ time in…

A recurring theme in the least squares approach to phylogenetics has been the discovery of elegant combinatorial formulas for the least squares estimates of edge lengths. These formulas have proved useful for the development of efficient…

A classic problem in computational biology is constructing a phylogenetic tree given a set of distances between n species. In most cases, a tree structure is too constraining. We consider a circular split network, a generalization of a tree…

Automatic detection and segmentation of overlapping leaves in dense foliage can be a difficult task, particularly for leaves with strong textures and high occlusions. We present Dense-Leaves, an image dataset with ground truth segmentation…

Phylogenetic networks are generalizations of trees that allow for the modeling of non-tree like evolutionary processes. Split networks give a useful way to construct networks with intuitive distance structures induced from the associated…

The rich and varied ways that genetic material can be passed between species has motivated extensive research into the theory of phylogenetic networks. Features that align with biological processes, or with desirable mathematical…

Real-world networks evolve over time via additions or removals of vertices and edges. In current network evolution models, vertex degree varies or grows arbitrarily. A recently introduced degree-preserving network growth (DPG) family of…

Research shows that gene duplication followed by either repurposing or removal of duplicated genes is an important contributor to evolution of gene and protein interaction networks. We aim to identify which characteristics of a network can…

Phylogenetic trees represent certain species and their likely ancestors. In such a tree, present-day species are leaves and an edge from u to v indicates that u is an ancestor of v. Weights on these edges indicate the phylogenetic distance.…

Phylogenetics begins with reconstructing biological family trees from genetic data. Since Nature is not limited to tree-like histories, we use networks to organize our data, and have discovered new polytopes, metric spaces, and simplicial…

Mechanistic models can provide an intuitive and interpretable explanation of network growth by specifying a set of generative rules. These rules can be defined by domain knowledge about real-world mechanisms governing network growth or may…

Tree-child networks are a recently-described class of directed acyclic graphs that have risen to prominence in phylogenetics (the study of evolutionary trees and networks). Although these networks have a number of attractive mathematical…

The reconstruction of phylogenetic networks is an important but challenging problem in phylogenetics and genome evolution, as the space of phylogenetic networks is vast and cannot be sampled well. One approach to the problem is to solve the…

Rooted phylogenetic networks are used to describe evolutionary histories that contain non-treelike evolutionary events such as hybridization and horizontal gene transfer. In some cases, such histories can be described by a phylogenetic…

Reticulate evolution can be modelled using phylogenetic networks. Tree-based networks, which are one of the more general classes of phylogenetic networks, have recently gained eminence for its ability to represent evolutionary histories…

Phylogenetic trees are leaf-labelled trees used to model the evolution of species. In practice it is not uncommon to obtain two topologically distinct trees for the same set of species, and this motivates the use of distance measures to…

Phylogenetic networks are graphs that are used to represent evolutionary relationships between different taxa. They generalize phylogenetic trees since for example, unlike trees, they permit lineages to combine. Recently, there has been…

Introgression is an evolutionary process in which genes or other types of genetic material are introduced into a genome. It is an important evolutionary process that can, for example, play a fundamental role in speciation. Recently the…

Phylogenetic trees and networks are graphs used to model evolutionary relationships, with trees representing strictly branching histories and networks allowing for events in which lineages merge, called reticulation events. While the…