Related papers: Which Phylogenetic Networks are Level-k Networks w…

Rooted phylogenetic networks are often used to represent conflicting phylogenetic signals. Given a set of clusters, a network is said to represent these clusters in the "softwired" sense if, for each cluster in the input set, at least one…

Unrooted phylogenetic networks are graphs used to represent evolutionary relationships. Accurately reconstructing such networks is of great relevance for evolutionary biology. It has recently been conjectured that all phylogenetic networks…

Galled trees are studied as a recombination model in theoretic population genetics. This class of phylogenetic networks has been generalized to tree-child networks, normal networks and tree-based networks by relaxing a structural condition.…

Phylogenetic networks are a generalization of phylogenetic trees that are used in biology to represent reticulate or non-treelike evolution. Recently, several algorithms have been developed which aim to construct phylogenetic networks from…

Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…

Phylogenetic networks are mathematical structures for modeling and visualization of reticulation processes in the study of evolution. Galled networks, reticulation visible networks, nearly-stable networks and stable-child networks are the…

In phylogenetics, evolution is traditionally represented in a tree-like manner. However, phylogenetic networks can be more appropriate for representing evolutionary events such as hybridization, horizontal gene transfer, and others. 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…

The evolution of molecular and phenotypic traits is commonly modelled using Markov processes along a phylogeny. This phylogeny can be a tree, or a network if it includes reticulations, representing events such as hybridization or admixture.…

Phylogenetic networks are an extension of phylogenetic trees which are used to represent evolutionary histories in which reticulation events (such as recombination and hybridization) have occurred. A central question for such networks is…

One strategy for reconstruction of phylogenetic networks is to solve the phylogenetic network problem, which involves inferring phylogenetic trees first and subsequently computing the smallest phylogenetic network that displays all the…

Combining a set of phylogenetic trees into a single phylogenetic network that explains all of them is a fundamental challenge in evolutionary studies. Existing methods are computationally expensive and can either handle only small numbers…

Orthologous genes, which arise through speciation, play a key role in comparative genomics and functional inference. In particular, graph-based methods allow for the inference of orthology estimates without prior knowledge of the underlying…

Balanced minimum evolution is a distance-based criterion for the reconstruction of phylogenetic trees. Several algorithms exist to find the optimal tree with respect to this criterion. One approach is to minimize a certain linear functional…

Reticulate evolutionary processes result in phylogenetic histories that cannot be modeled using a tree topology. Here, we apply methods from topological data analysis to molecular sequence data with reticulations. Using a simple example, we…

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…

A normal network is uniquely determined by the set of phylogenetic trees that it displays. Given a set $\mathcal{P}$ of rooted binary phylogenetic trees, this paper presents a polynomial-time algorithm that reconstructs the unique binary…

Phylogenetic networks are often constructed by merging multiple conflicting phylogenetic signals into a directed acyclic graph. It is interesting to explore whether a network constructed in this way induces biologically-relevant…

A fundamental problem in the study of phylogenetic networks is to determine whether or not a given phylogenetic network contains a given phylogenetic tree. We develop a quadratic-time algorithm for this problem for binary nearly-stable…

Normal networks are an important class of phylogenetic networks that have compelling mathematical properties which align with intuition about inference from genetic data. While tools enabling widespread use of phylogenetic networks in the…