Related papers: On the elusiveness of clusters

Reconstructing a parsimonious phylogenetic network that displays multiple phylogenetic trees is an important problem in theory of phylogenetics, where the complexity of the inferred networks is measured by reticulation numbers. The…

Here we show that deciding whether two rooted binary phylogenetic trees on the same set of taxa permit a cherry-picking sequence, a special type of elimination order on the taxa, is NP-complete. This improves on an earlier result which…

We propose a novel method to cluster gene networks. Based on a dissimilarity built using correlation structures, we consider networks that connect all the genes based on the strength of their dissimilarity. The large number of genes require…

Evolutionary scenarios displaying reticulation events are often represented by rooted phylogenetic networks. Due to biological reasons, those events occur very rarely, and, thus, networks containing a minimum number of such events,…

Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…

Phylogenetic networks are a generalization of phylogenetic trees allowing for the representation of non-treelike evolutionary events such as hybridization. Typically, such networks have been analyzed based on their `level', i.e. based on…

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…

Several computational problems in phylogenetic reconstruction can be formulated as restrictions of the following general problem: given a formula in conjunctive normal form where the literals are rooted triples, is there a rooted binary…

It is required to find an optimal order of constructing the edges of a network so as to minimize the sum of the weighted connection times of relevant pairs of vertices. Construction can be performed anytime anywhere in the network, with a…

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…

Tree-child networks, one of the prominent network classes in phylogenetics, have been introduced for the purpose of modeling reticulate evolution. Recently, the first author together with Gittenberger and Mansouri (2019) showed that the…

Inference of phylogenetic networks is of increasing interest in the genomic era. However, the extent to which phylogenetic networks are identifiable from various types of data remains poorly understood, despite its crucial role in…

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…

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 notoriously difficult to reconstruct. Here we suggest that it can be useful to view unknown genetic distance along edges in phylogenetic networks as analogous to unknown resistance in electric circuits. This…

This article concerns the following question arising in computational evolutionary biology. For a given subclass of phylogenetic networks, what is the maximum value of 0 <= p <= 1 such that for every input set T of rooted triplets, there…

In mathematical phylogenetics, evolutionary relationships are often represented by trees and networks. The latter are typically used whenever the relationships cannot be adequately described by a tree, which happens when so-called…

Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…

Clustering is often a challenging problem because of the inherent ambiguity in what the "correct" clustering should be. Even when the number of clusters $K$ is known, this ambiguity often still exists, particularly when there is variation…

A phylogenetic tree is a graphical representation of an evolutionary history of taxa in which the leaves correspond to the taxa and the non-leaves correspond to speciations. One of important problems in phylogenetic analysis is to assemble…