Related papers: Phylogenetic flexibility via Hall-type inequalitie…
We present the first sub-quadratic time algorithm that with high probability correctly reconstructs phylogenetic trees for short sequences generated by a Markov model of evolution. Due to rapid expansion in sequence databases, such very…
We define a new balance index for rooted phylogenetic trees based on the symmetry of the evolutive history of every set of 4 leaves. This index makes sense for multifurcating trees and it can be computed in time linear in the number of…
Phylogenetic networks are a generalization of phylogenetic trees to leaf-labeled directed acyclic graphs that represent ancestral relationships between species whose past includes non-tree-like events such as hybridization and horizontal…
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…
We systematically explore the self-assembly of semi-flexible polymers in deformable spherical confinement across a wide regime of chain stiffness, contour lengths and packing fractions by means of coarse-grained molecular dynamics…
Phylogenetic networks play an important role in evolutionary biology as, other than phylogenetic trees, they can be used to accommodate reticulate evolutionary events such as horizontal gene transfer and hybridization. Recent research has…
By providing a framework of accounting for the shared ancestry inherent to all life, phylogenetics is becoming the statistical foundation of biology. The importance of model choice continues to grow as phylogenetic models continue to…
The inference of phylogenetic networks, which model complex evolutionary processes including hybridization and gene flow, remains a central challenge in evolutionary biology. Until now, statistically consistent inference methods have been…
In computational phylogenetics, the problem of constructing a supertree of a given set of rooted input trees can be formalized in different ways, to cope with contradictory information in the input. We consider the Minimum Flip Supertree…
Tree Containment is a fundamental problem in phylogenetics useful for verifying a proposed phylogenetic network, representing the evolutionary history of certain species. Tree Containment asks whether the given phylogenetic tree (for…
Phylogenetic networks are a flexible model of evolution that can represent reticulate evolution and handle complex data. Tree-based networks, which are phylogenetic networks that have a spanning tree with the same root and leaf-set as the…
The first part of this paper ( arXiv:1607.02114 ) introduced splitting trees, those chronological trees admitting the self-similarity property where individuals give birth, at constant rate, to iid copies of themselves. It also established…
Rare events have played an increasing role in molecular phylogenetics as potentially homoplasy-poor characters.In this contribution we analyze the phylogenetic information content from a combinatorial point of view by consid-ering the…
We introduce the package PhylogeneticTrees for Macaulay2 which allows users to compute phylogenetic invariants for group-based tree models. We provide some background information on phylogenetic algebraic geometry and show how the package…
Phylogenetic networks are an extension of phylogenetic trees which are used to represent evolutionary histories in which reticulation events (such as recombination and hybridization) have occurred. A central question for such networks is…
Rooted phylogenetic networks are used to describe evolutionary histories that contain non-treelike evolutionary events such as hybridization and horizontal gene transfer. In some cases, such histories can be described by a phylogenetic…
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…
A recurring theme in the least squares approach to phylogenetics has been the discovery of elegant combinatorial formulas for the least squares estimates of edge lengths. These formulas have proved useful for the development of efficient…
Phylogenetic networks extend phylogenetic trees to allow for modeling reticulate evolutionary processes such as hybridization. They take the shape of a rooted, directed, acyclic graph, and when parameterized with evolutionary parameters,…
Distance-based phylogenetic algorithms attempt to solve the NP-hard least squares phylogeny problem by mapping an arbitrary dissimilarity map representing biological data to a tree metric. The set of all dissimilarity maps is a Euclidean…