Related papers: Tree-based unrooted phylogenetic networks

Orchards are a biologically relevant class of phylogenetic networks as they can describe treelike evolutionary histories augmented with horizontal transfer events. Moreover, the class has attractive mathematical characterizations that can…

Phylogenetic tree shapes capture fundamental signatures of evolution. We consider ``ranked'' tree shapes, which are equipped with a total order on the internal nodes compatible with the tree graph. Recent work has established an elegant…

Arboreal networks are multi-rooted phylogenetic networks whose underlying graph is a tree. We give an encoding of stack-free arboreal networks in terms of triplets and the novel concept of a duet. This yields a polynomial time algorithm to…

Phylogenetics is now fundamental in life sciences, providing insights into the earliest branches of life and the origins and spread of epidemics. However, finding suitable phylogenies from the vast space of possible trees remains…

Phylogenetic networks are becoming increasingly popular in phylogenetics since they have the ability to describe a wider range of evolutionary events than their tree counterparts. In this paper, we study Markov models on phylogenetic…

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 networks extend phylogenetic trees to model non-vertical inheritance, by which a lineage inherits material from multiple parents. The computational complexity of estimating phylogenetic networks from genome-wide data with…

Recently, there has been a growing interest in the relationships between unrooted and rooted phylogenetic networks. In this context, a natural question to ask is if an unrooted phylogenetic network U can be oriented as a rooted phylogenetic…

Arboreal networks are a generalization of rooted trees, defined by keeping the tree-like structure, but dropping the requirement for a single root. Just as the class of cographs is precisely the class of undirected graphs that can be…

Phylogenetic networks are generalizations of trees that allow for the modeling of non-tree like evolutionary processes. Split networks give a useful way to construct networks with intuitive distance structures induced from the associated…

Two genes are xenologs in the sense of Fitch if they are separated by at least one horizontal gene transfer event. Horizonal gene transfer is asymmetric in the sense that the transferred copy is distinguished from the one that remains…

Ultametrics are an important class of distances used in applications such as phylogenetics, clustering and classification theory. Ultrametrics are essentially distances that can be represented by an edge-weighted rooted tree so that all of…

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.…

Phylogenetic networks generalize evolutionary trees, and are commonly used to represent evolutionary histories of species that undergo reticulate evolutionary processes such as hybridization, recombination and lateral gene transfer.…

Orthologous genes, which arise through speciation, play a key role in comparative genomics and functional inference. In particular, graph-based methods allow for the inference of orthology estimates without prior knowledge of the underlying…

In phylogenetics, phylogenetic trees are rooted binary trees, whereas phylogenetic networks are rooted arbitrary acyclic digraphs. Edges are directed away from the root and leaves are uniquely labeled with taxa in phylogenetic networks. For…

The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…

In this work, we answer an open problem in the study of phylogenetic networks. Phylogenetic trees are rooted binary trees in which all edges are directed away from the root, whereas phylogenetic networks are rooted acyclic digraphs. For the…

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…

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…