Related papers: Quarnet inference rules for level-1 networks
The reliability of a phylogenetic inference method from genomic sequence data is ensured by its statistical consistency. Bayesian inference methods produce a sample of phylogenetic trees from the posterior distribution given sequence data.…
In molecular phylogeny, relationships among organisms are reconstructed using DNA or protein sequences and are displayed as trees. A linear increase in the number of sequences results in an exponential increase of possible trees. Thus,…
Phylogenetic networks are increasingly being considered as better suited to represent the complexity of the evolutionary relationships between species. One class of phylogenetic networks that has received a lot of attention recently is the…
Quartet Reconstruction, the task of recovering a phylogenetic tree from smaller trees on four species called \textit{quartets}, is a well-studied problem in theoretical computer science with far-reaching connections to statistics, graph…
Deciding whether there is a single tree -a supertree- that summarizes the evolutionary information in a collection of unrooted trees is a fundamental problem in phylogenetics. We consider two versions of this question: agreement and…
A classical problem in phylogenetic tree analysis is to decide whether there is a phylogenetic tree $T$ that contains all information of a given collection $\cP$ of phylogenetic trees. If the answer is "yes" we say that $\cP$ is compatible…
Latent space models for network data characterize each node through a vector of latent features whose pairwise similarities define the edge probabilities among the pairs of nodes. Although this formulation has led to successful…
The algebraic properties of flattenings and subflattenings provide direct methods for identifying edges in the true phylogeny -- and by extension the complete tree -- using pattern counts from a sequence alignment. The relatively small…
The amount of completely sequenced chloroplast genomes increases rapidly every day, leading to the possibility to build large scale phylogenetic trees of plant species. Considering a subset of close plant species defined according to their…
Galled trees are studied as a recombination model in population genetics. This class of phylogenetic networks is generalized into tree-child, galled and reticulation-visible network classes by relaxing a structural condition imposed on…
Phylogenetic networks are an important way to represent evolutionary histories that involve reticulations such as hybridization or horizontal gene transfer, yet fundamental questions such as how many networks there are that satisfy certain…
Phylogenetic reconstruction aims at finding plausible hypotheses of the evolutionary history of genes or species based on genomic sequence information. The distinction of orthologous genes (genes that having a common ancestry and diverged…
Interest in the inference of evolutionary networks relating species or populations has grown with the increasing recognition of the importance of hybridization, gene flow and admixture, and the availability of large-scale genomic data.…
Phylogenetic inference, the task of reconstructing how related sequences evolved from common ancestors, is a central objective in evolutionary genomics. The current state-of-the-art methods exploit probabilistic models of sequence evolution…
In biology, a phylogenetic tree is a tool to represent the evolutionary relationship between species. Unfortunately, the classical Schr\"oder tree model is not adapted to take into account the chronology between the branching nodes. In…
A Supertree synthesizes the topologies of a set of phylogenetic trees carrying overlapping taxa set. In process, conflicts in the tree topologies are aimed to be resolved with the consensus clades. Such a problem is proved to be NP-hard.…
A common problem in phylogenetics is to try to infer a species phylogeny from gene trees. We consider different variants of this problem. The first variant, called Unrestricted Minimal Episodes Inference, aims at inferring a species tree…
We consider species tree estimation under a standard stochastic model of gene tree evolution that incorporates incomplete lineage sorting (as modeled by a coalescent process) and gene duplication and loss (as modeled by a branching…
Increasingly, biologists are constructing evolutionary trees on large numbers of overlapping sets of taxa, and then combining them into a `supertree' that classifies all the taxa. In this paper, we ask how much coverage of the total set of…
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…