Related papers: Two metrics for general phylogenetic networks

We prove that Nakhleh's latest dissimilarity measure for phylogenetic networks is a metric on the classes of tree-child phylogenetic networks, of semi-binary time consistent tree-sibling phylogenetic networks, and of multi-labeled…

Galled networks, directed acyclic graphs that model evolutionary histories with reticulation cycles containing only tree nodes, have become very popular due to both their biological significance and the existence of polynomial time…

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…

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,…

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 this paper, we present and study a new…

Dissimilarity measures for (possibly weighted) phylogenetic trees based on the comparison of their vectors of path lengths between pairs of taxa, have been present in the systematics literature since the early seventies. But, as far as…

In phylogenetics, it is important for the phylogenetic network model parameters to be identifiable so that the evolutionary histories of a group of species can be consistently inferred. However, as the complexity of the phylogenetic network…

We define a special network that exhibits the large embeddings in any class of similar algebras. With the aid of this network, we introduce a notion of distance that conceivably counts the minimum number of dissimilarities, in a sense,…

Semidirected networks have received interest in evolutionary biology as the appropriate generalization of unrooted trees to networks, in which some but not all edges are directed. Yet these networks lack proper theoretical study. We define…

Phylogenetic networks are useful in representing the evolutionary history of taxa. In certain scenarios, one requires a way to compare different networks. In practice, this can be rather difficult, except within specific classes of…

The search for similarity and dissimilarity measures on phylogenetic trees has been motivated by the computation of consensus trees, the search by similarity in phylogenetic databases, and the assessment of clustering results in…

Phylogenetic networks are a type of directed acyclic graph that represent how a set $X$ of present-day species are descended from a common ancestor by processes of speciation and reticulate evolution. In the absence of reticulate evolution,…

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…

A phylogenetic network is a graph-theoretical tool that is used by biologists to represent the evolutionary history of a collection of species. One potential way of constructing such networks is via a distance-based approach, where one is…

In phylogenetic networks, it is desirable to estimate edge lengths in substitutions per site or calendar time. Yet, there is a lack of scalable methods that provide such estimates. Here we consider the problem of obtaining edge length…

Phylogenetic trees summarize evolutionary relationships between organisms, and tools to analyze collections of phylogenetic trees enable contrasts between different genes' ancestry. The BHV metric space has enabled the analysis of…

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…

Inferring the phylogenetic relationships among a sample of organisms is a fundamental problem in modern biology. While distance-based hierarchical clustering algorithms achieved early success on this task, these have been supplanted by…

Many classes of phylogenetic networks have been proposed in the literature. A feature of several of these classes is that if one restricts a network in the class to a subset of its leaves, then the resulting network may no longer lie within…

The inference of phylogenetic networks, which model complex evolutionary processes including hybridization and gene flow, remains a central challenge in evolutionary biology. Until now, statistically consistent inference methods have been…