Related papers: Encoding and ordering X-cactuses
The C-Orientation problem asks whether it is possible to orient an undirected graph to a directed phylogenetic network of a desired network class C. This problem arises, for example, when visualising evolutionary data, as popular methods…
We introduce new methods for phylogenetic tree quartet construction by using machine learning to optimize the power of phylogenetic invariants. Phylogenetic invariants are polynomials in the joint probabilities which vanish under a model of…
'Tree-based' phylogenetic networks proposed by Francis and Steel have attracted much attention of theoretical biologists in the last few years. At the heart of the definitions of tree-based phylogenetic networks is the notion of 'support…
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…
A network can be analyzed by means of many graph theoretical parameters. In the context of networks analysis, closeness is a structural metric that evaluates a node's significance inside a network. A cactus is a connected graph in which any…
Species networks generalize the notion of species trees to allow for hybridization or other lateral gene transfer. Under the Network Multispecies Coalescent Model, individual gene trees arising from a network can have any topology, but…
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…
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set 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…
For a phylogenetic tree, the phylogenetic diversity of a set A of taxa is the total weight of edges on paths to A. Finding small sets of maximal diversity is crucial for conservation planning, as it indicates where limited resources can be…
Methods that generate networks sharing a given degree distribution and global clustering can induce changes in structural properties other than that controlled for. Diversity in structural properties, in turn, can affect the outcomes of…
We describe the conditions under which a set of continuous variables or characters can be described as an X-tree or a split network. A distance matrix corresponds exactly to a split network or a valued X-tree if, after ordering of the taxa,…
Network representations of systems from various scientific and societal domains are neither completely random nor fully regular, but instead appear to contain recurring structural building blocks. These features tend to be shared by…
Construction of phylogenetic trees has traditionally focused on binary trees where all species appear on leaves, a problem for which numerous efficient solutions have been developed. Certain application domains though, such as viral…
Motivation: The abundance of gene flow in the Tree of Life challenges the notion that evolution can be represented with a fully bifurcating process, as this process cannot capture important biological realities like hybridization,…
We compare three basic kinds of discrete mathematical models used to portray phylogenetic relationships among species and higher taxa: phylogenetic trees, Hennig trees and Nelson cladograms. All three models are trees, as that term is…
Discovering evolutionary traits that are heritable across species on the tree of life (also referred to as a phylogenetic tree) is of great interest to biologists to understand how organisms diversify and evolve. However, the measurement of…
The appearance of mathematical regularities in the disposition of leaves on a stem, scales on a pine-cone and spines on a cactus has puzzled scholars for millennia; similar so-called phyllotactic patterns are seen in self-organized growth,…
Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…
In this paper, we lay the groundwork on the comparison of phylogenetic networks based on edge contractions and expansions as edit operations, as originally proposed by Robinson and Foulds to compare trees. We prove that these operations…