Related papers: Comparison of orchard networks using their extende…
Orchards are a biologically relevant class of phylogenetic networks as they can describe treelike evolutionary histories augmented with horizontal transfer events. Moreover, the class has attractive mathematical characterizations that can…
Phylogenetic networks extend phylogenetic trees to model non-vertical inheritance, by which a lineage inherits material from multiple parents. The computational complexity of estimating phylogenetic networks from genome-wide data with…
A phylogenetic network is a directed acyclic graph that visualises an evolutionary history containing so-called reticulations such as recombinations, hybridisations or lateral gene transfers. Here we consider the construction of a simplest…
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…
Phylogenetic networks are a generalization of phylogenetic trees that allow for representation of reticulate evolution. Recently, a space of unrooted phylogenetic networks was introduced, where such a network is a connected graph in which…
Phylogenetic networks are a generalization of evolutionary or phylogenetic trees that are commonly used to represent the evolution of species which cross with one another. A special type of phylogenetic network is an {\em $X$-cactus}, which…
Phylogenetic networks which are, as opposed to trees, suitable to describe processes like hybridization and horizontal gene transfer, play a substantial role in evolutionary research. However, while non-treelike events need to be taken into…
Phylogenetic trees canonically arise as embeddings of phylogenetic networks. We recently showed that the problem of deciding if two phylogenetic networks embed the same sets of phylogenetic trees is computationally hard, \blue{in…
Phylogenetic networks are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybrid speciation and recombination. One of the most fundamental…
Phylogenetic networks are a special type of graph which generalize phylogenetic trees and that are used to model non-treelike evolutionary processes such as recombination and hybridization. In this paper, we consider {\em unrooted}…
Phylogenetic tree shapes capture fundamental signatures of evolution. We consider ``ranked'' tree shapes, which are equipped with a total order on the internal nodes compatible with the tree graph. Recent work has established an elegant…
Tree-based networks are a class of phylogenetic networks that attempt to formally capture what is meant by "tree-like" evolution. A given non-tree-based phylogenetic network, however, might appear to be very close to being tree-based, or…
Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In a recent series of papers devoted to the…
We study the problem of visualizing phylogenetic networks, which are extensions of the Tree of Life in biology. We use a space filling visualization method, called DAGmaps, in order to obtain clear visualizations using limited space. In…
In phylogenetics, phylogenetic trees are rooted binary trees, whereas phylogenetic networks are rooted arbitrary acyclic digraphs. Edges are directed away from the root and leaves are uniquely labeled with taxa in phylogenetic networks. For…
Rooted binary phylogenetic networks are extensions of rooted binary trees, adding reticulation nodes that are designed to represent evolutionary processes that involve hybridization events. Enumerative combinatorics studies have counted…
Tree-child networks are one of the most prominent network classes for modeling evolutionary processes which contain reticulation events. Several recent studies have addressed counting questions for {\it bicombining tree-child networks}…
Phylogenetic networks are a type of leaf-labelled, acyclic, directed graph used by biologists to represent the evolutionary history of species whose past includes reticulation events. A phylogenetic network is tree-child if each non-leaf…
Construction of phylogenetic trees and networks for extant species from their characters represents one of the key problems in phylogenomics. While solution to this problem is not always uniquely defined and there exist multiple methods for…
The presence of reticulate evolutionary events in phylogenies turn phylogenetic trees into phylogenetic networks. These events imply in particular that there may exist multiple evolutionary paths from a non-extant species to an extant one,…