Related papers: Constructing level-2 phylogenetic networks from tr…
In this paper we study two problems related to the drawing of level graphs, that is, T-LEVEL PLANARITY and CLUSTERED-LEVEL PLANARITY. We show that both problems are NP-complete in the general case and that they become polynomial-time…
Phylogenetic (evolutionary) trees and networks are leaf-labeled graphs that are widely used to represent the evolutionary relationships between entities such as species, languages, cancer cells, and viruses. To reconstruct and analyze…
In phylogenetics, evolution is traditionally represented in a tree-like manner. However, phylogenetic networks can be more appropriate for representing evolutionary events such as hybridization, horizontal gene transfer, and others. In…
We consider the polyhedral properties of two spanning tree problems with additional constraints. In the first problem, it is required to find a tree with a minimum sum of edge weights among all spanning trees with the number of leaves less…
A contemporary and fundamental problem faced by many evolutionary biologists is how to puzzle together a collection $\mathcal P$ of partial trees (leaf-labelled trees whose leaves are bijectively labelled by species or, more generally,…
Phylogenetic trees illustrate the evolutionary history of genes and species. In most cases, although genes evolve along with the species they belong to, a species tree and gene tree are not identical, because of evolutionary events at the…
Phylogenetic networks generalize phylogenetic trees by allowing reticulate evolutionary events such as horizontal gene transfer and hybridization. Among the many subclasses of phylogenetic networks, orchard networks have attracted…
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…
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…
In a complex network, different groups of nodes may have existed for different amounts of time. To detect the evolutionary history of a network is of great importance. We present a general method based on spectral analysis to address this…
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…
Phylogenetic networks model reticulate evolutionary histories. The last two decades have seen an increased interest in establishing mathematical results and developing computational methods for inferring and analyzing these networks. A…
The supertree problem asking for a tree displaying a set of consistent input trees has been largely considered for the reconstruction of species trees. Here, we rather explore this framework for the sake of reconstructing a gene tree from a…
We perform a refined complexity-theoretic analysis of three classical problems in the context of Hierarchical Task Network Planning: the verification of a provided plan, whether an executable plan exists, and whether a given state can be…
While every rooted binary phylogenetic tree is determined by its set of displayed rooted triples, such a result does not hold for an arbitrary rooted binary phylogenetic network. In particular, there exist two non-isomorphic rooted binary…
Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains…
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 are an important network class which are used in phylogenetics to model reticulate evolution. In a recent paper, Pons and Batle (2021) conjectured a relation between tree-child networks and certain words. In this short…
The Tree of Life is the graphical structure that represents the evolutionary process from single-cell organisms at the origin of life to the vast biodiversity we see today. Reconstructing this tree from genomic sequences is challenging due…
Galled trees are studied as a recombination model in theoretic population genetics. This class of phylogenetic networks has been generalized to tree-child networks, normal networks and tree-based networks by relaxing a structural condition.…