Related papers: Orienting undirected phylogenetic networks
In a previous work, we gave a metric on the class of semibinary tree-sibling time consistent phylogenetic networks that is computable in polynomial time; in particular, the problem of deciding if two networks of this kind are isomorphic is…
It was recently shown that a large class of phylogenetic networks, the `labellable' networks, is in bijection with the set of `expanding' covers of finite sets. In this paper, we show how several prominent classes of phylogenetic networks…
Phylogenetic networks generalize phylogenetic trees by representing reticulate evolution. Tree-based networks and their support trees have been extensively studied, but not all networks are tree-based. To measure how far such networks are…
Statistical inference of directed relations given some unspecified interventions (i.e., the intervention targets are unknown) is challenging. In this article, we test hypothesized directed relations with unspecified interventions. First, we…
Phylogenetic networks generalize phylogenetic trees in order to model reticulation events. Although the comparison of phylogenetic trees is well studied, and there are multiple ways to do it in an efficient way, the situation is much…
Comparative analyses of phylogenetic trees typically require identical taxon sets, however, in practice, trees often include distinct but overlapping taxa. Pruning non-shared leaves discards phylogenetic signal, whereas tree completion can…
Analyzing and characterizing the differences between networks is a fundamental and challenging problem in network science. Previously, most network comparison methods that rely on topological properties have been restricted to measuring…
We study a class of growth algorithms for directed graphs that are candidate models for the evolution of genetic regulatory networks. The algorithms involve partial duplication of nodes and their links, together with innovation of new…
Phylogenetic diversity indices are commonly used to rank the elements in a collection of species or populations for conservation purposes. The derivation of these indices is typically based on some quantitative description of the…
The search space of rooted phylogenetic trees is vast and a major research focus of recent decades has been the development of algorithms to effectively navigate this space. However this space is tiny when compared with the space of rooted…
Null models of binary phylogenetic trees are useful for testing hypotheses on real world phylogenies. In this paper we consider phylogenies as binary trees without edge lengths together with a sampling measure and encode them as algebraic…
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…
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…
We consider networks of dynamical units that evolve in time according to different laws, and are coupled to each other in highly irregular ways. Studying how to steer the dynamics of such systems towards a desired evolution is of great…
In this article we compare the known dynamical polynomial time algorithm for the game-over attack strategy, to that of the brute force approach; of checking all the ordered rooted subtrees of a given tree that represents a given computer…
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…
Polyploidization is an evolutionary process by which a species acquires multiple copies of its complete set of chromosomes. The reticulate nature of the signal left behind by it means that phylogenetic networks offer themselves as a…
Given a network of routing nodes, represented as a directed graph, we prove the following necessary and sufficient condition for the existence of deadlock-free message routing: The directed graph must contain two edge-disjoint directed…
We study the parameterized complexity of the directed variant of the classical {\sc Steiner Tree} problem on various classes of directed sparse graphs. While the parameterized complexity of {\sc Steiner Tree} parameterized by the number of…
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…