Related papers: Distinguishing Phylogenetic Networks
Markov chain Monte Carlo algorithms play a key role in the Bayesian approach to phylogenetic inference. In this paper, we present the first theoretical work analyzing the rate of convergence of several Markov chains widely used in…
Galled networks, directed acyclic graphs that model evolutionary histories with reticulation cycles containing only tree nodes, have become very popular due to both their biological significance and the existence of polynomial time…
We study the problem of visualizing phylogenetic networks, which are extensions of the Tree of Life in biology. We use a space filling visualization method, called DAGmaps, in order to obtain clear visualizations using limited space. In…
We describe Galois connections which arise between two kinds of combinatorial structures, both of which generalize trees with labelled leaves, and then apply those connections to a family of polytopes. The graphs we study can be imbued with…
Ranked tree-child networks are a recently introduced class of rooted phylogenetic networks in which the evolutionary events represented by the network are ordered so as to respect the flow of time. This class includes the well-studied…
When hybridization or other forms of lateral gene transfer have occurred, evolutionary relationships of species are better represented by phylogenetic networks than by trees. While inference of such networks remains challenging, several…
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…
There are diverse mechanisms driving the evolution of social networks. A key open question dealing with understanding their evolution is: How various preferential linking mechanisms produce networks with different features? In this paper we…
We explore a simple mathematical model of network computation, based on Markov chains. Similar models apply to a broad range of computational phenomena, arising in networks of computers, as well as in genetic, and neural nets, in social…
Phylogenetic trees describe the relationships between species in the evolutionary process, and provide information about the rates of diversification. To understand the mechanisms behind macroevolution, we consider a class of multitype…
Phylogenetic networks are a special type of graph which generalize phylogenetic trees and that are used to model non-treelike evolutionary processes such as recombination and hybridization. In this paper, we consider {\em unrooted}…
Rapid developments in genetics and biology have led to phylogenetic methods becoming an important direction in the study of cancer and viral evolution. Although our understanding of gene biology and biochemistry has increased and is…
More than ever, today we are left with the abundance of molecular data outpaced by the advancements of the phylogenomic methods. Especially in the case of presence of many genes over a set of species under the phylogeny question, more…
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…
Recent genomic and bioinformatic advances have motivated the development of numerous random network models purporting to describe graphs of biological, technological, and sociological origin. The success of a model has been evaluated by how…
The aim of this review is to present and analyze the probabilistic models of mathematical phylogenetics which have been intensively used in recent years in biology as the cornerstone of attempts to infer and reconstruct the ancestral…
Systems as diverse as genetic networks or the world wide web are best described as networks with complex topology. A common property of many large networks is that the vertex connectivities follow a scale-free power-law distribution. This…
Genealogical networks, also known as family trees or population pedigrees, are commonly studied by genealogists wanting to know about their ancestry, but they also provide a valuable resource for disciplines such as digital demography,…
Phylogenetic trees canonically arise as embeddings of phylogenetic networks. We recently showed that the problem of deciding if two phylogenetic networks embed the same sets of phylogenetic trees is computationally hard, \blue{in…
Phylogenetic networks are a generalization of phylogenetic trees that allow for representation of reticulate evolution. Recently, a space of unrooted phylogenetic networks was introduced, where such a network is a connected graph in which…