Related papers: On Determining if Tree-based Networks Contain Fixe…
Rooted acyclic graphs appear naturally when the phylogenetic relationship of a set $X$ of taxa involves not only speciations but also recombination, horizontal transfer, or hybridization, that cannot be captured by trees. A variety of…
Highly dynamic networks are characterized by frequent changes in the availability of communication links. These networks are often partitioned into several components, which split and merge unpredictably. We present a distributed algorithm…
The structure of an evolving network contains information about its past. Extracting this information efficiently, however, is, in general, a difficult challenge. We formulate a fast and efficient method to estimate the most likely history…
In the NP-hard Optimizing PD with Dependencies (PDD) problem, the input consists of a phylogenetic tree $T$ over a set of taxa $X$, a food-web that describes the prey-predator relationships in $X$, and integers $k$ and $D$. The task is to…
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…
A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called…
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…
We consider network design problems with deadline or delay. All previous results for these models are based on randomized embedding of the graph into a tree (HST) and then solving the problem on this tree. We show that this is not…
For a given set $\mathcal{L}$ of species and a set $\mathcal{T}$ of triplets on $\mathcal{L}$, one wants to construct a phylogenetic network which is consistent with $\mathcal{T}$, i.e which represents all triplets of $\mathcal{T}$. The…
Phylogenetic networks are rooted acyclic directed graphs in which the leaves are identified with members of a set X of species. The cluster of a vertex is the set of leaves that are descendants of the vertex. A network is "distinct-cluster"…
Phylogenetic trees are a central tool in understanding evolution. They are typically inferred from sequence data, and capture evolutionary relationships through time. It is essential to be able to compare trees from different data sources…
We prove that finding a rooted subtree with at least $k$ leaves in a digraph is a fixed parameter tractable problem. A similar result holds for finding rooted spanning trees with many leaves in digraphs from a wide family $\cal L$ that…
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 used to represent the evolutionary history of species. They are versatile when compared to traditional phylogenetic trees, as they capture more complex evolutionary events such as hybridization and horizontal gene…
The evolutionary relationships among organisms have traditionally been represented using rooted phylogenetic trees. However, due to reticulate processes such as hybridization or lateral gene transfer, evolution cannot always be adequately…
Inference of species networks from genomic data under the Network Multispecies Coalescent Model is currently severely limited by heavy computational demands. It also remains unclear how complicated networks can be for consistent inference…
Phylogenetic networks are leaf-labelled directed acyclic graphs that are used to describe non-treelike evolutionary histories and are thus a generalization of phylogenetic trees. The hybridization number of a phylogenetic network is the sum…
Given a dense triplet set $\mathcal{T}$, there arise two interesting questions: Does there exists any phylogenetic network consistent with $\mathcal{T}$? And if so, can we find an effective algorithm to construct one? For cases of networks…
Here we present a new fixed parameter tractable algorithm to compute the hybridization number r of two rooted, not necessarily binary phylogenetic trees on taxon set X in time (6^r.r!).poly(n)$, where n=|X|. The novelty of this approach is…
Rooted phylogenetic networks are used by biologists to infer and represent complex evolutionary relationships between species that cannot be accurately explained by a phylogenetic tree. Tree-child networks are a particular class of rooted…