Related papers: Lassoing and corraling rooted phylogenetic trees

An evolutionary tree is a cascade of bifurcations starting from a single common root, generating a growing set of daughter species as time goes by. Species here is a general denomination for biological species, spoken languages or any other…

In molecular systematics, evolutionary trees are reconstructed from sequences at the tips under simple models of site substitution. A central question is how much sequence data is required to reconstruct a tree accurately? The answer…

Phylogenetically decisive collections of taxon sets have the property that if trees are chosen for each of their elements, as long as these trees are compatible, the resulting supertree is unique. This means that as long as the trees…

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}…

Phylogenetic trees play a key role in the reconstruction of evolutionary relationships. Typically, they are derived from aligned sequence data (like DNA, RNA, or proteins) by using optimization criteria like, e.g., maximum parsimony (MP).…

We address an open question of Francis and Steel about phylogenetic networks and trees. They give a polynomial time algorithm to decide if a phylogenetic network, N, is tree-based and pose the problem: given a fixed tree T and network N, is…

Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…

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…

We consider a discrete-time Markov chain, called fragmentation process, that describes a specific way of successively removing objects from a linear arrangement. The process arises in population genetics and describes the ancestry of the…

The tree-metric theorem provides a necessary and sufficient condition for a dissimilarity matrix to be a tree metric, and has served as the foundation for numerous distance-based reconstruction methods in phylogenetics. Our main result is…

Recently, so-called treebased phylogenetic networks have gained considerable interest in the literature, where a treebased network is a network that can be constructed from a phylogenetic tree, called the base tree, by adding additional…

Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…

Phylogenetic networks are a generalization of evolutionary or phylogenetic trees that are commonly used to represent the evolution of species which cross with one another. A special type of phylogenetic network is an {\em $X$-cactus}, which…

The {\sc Directed Maximum Leaf Out-Branching} problem is to find an out-branching (i.e. a rooted oriented spanning tree) in a given digraph with the maximum number of leaves. In this paper, we improve known parameterized algorithms and…

Three-way dissimilarities are a generalization of (two-way) dissimilarities which can be used to indicate the lack of homogeneity or resemblance between any three objects. Such maps have applications in cluster analysis, and have been used…

Robertson and Seymour constructed for every graph $G$ a tree-decomposition that efficiently distinguishes all the tangles in $G$. While all previous constructions of these decompositions are either iterative in nature or not canonical, we…

This paper outlines a method to determine whether two label-regular directed trees, are isomorphic and when they are almost isomorphic. The approach involves reinterpreting label-regular directed trees as universal covers of rooted graphs.…

Semidirected networks have received interest in evolutionary biology as the appropriate generalization of unrooted trees to networks, in which some but not all edges are directed. Yet these networks lack proper theoretical study. We define…

The evolution of aligned DNA sequence sites is generally modeled by a Markov process operating along the edges of a phylogenetic tree. It is well known that the probability distribution on the site patterns at the tips of the tree…

Phylogenetic trees are leaf-labelled trees used to model the evolution of species. In practice it is not uncommon to obtain two topologically distinct trees for the same set of species, and this motivates the use of distance measures to…