Related papers: On symmetries in phylogenetic trees

Given any regularly varying dislocation measure, we identify a natural self-similar fragmentation tree as scaling limit of discrete fragmentation trees with unit edge lengths. As an application, we obtain continuum random tree limits of…

Given a rooted, binary phylogenetic network and a rooted, binary phylogenetic tree, can the tree be embedded into the network? This problem, called \textsc{Tree Containment}, arises when validating networks constructed by phylogenetic…

Here we present a new fixed parameter tractable algorithm to compute the hybridization number r of two rooted binary phylogenetic trees on taxon set X in time (6r)^r.poly(n), where n=|X|. The novelty of this approach is that it avoids the…

Metrics on rooted phylogenetic trees are integral to a number of areas of phylogenetic analysis. Cluster-similarity metrics have recently been introduced in order to limit skew in the distribution of distances, and to ensure that trees in…

An involution is a permutation that is its own inverse. Given a permutation $\sigma$ of $[n],$ let $\mathbf{N}_{n}(\sigma)$ denote the number of ways to write $\sigma$ as a product of two involutions of $[n].$ If we endow the symmetric…

Phylogenetic inference, the task of reconstructing how related sequences evolved from common ancestors, is a central objective in evolutionary genomics. The current state-of-the-art methods exploit probabilistic models of sequence evolution…

A classic problem in computational biology is constructing a phylogenetic tree given a set of distances between n species. In most cases, a tree structure is too constraining. We consider a circular split network, a generalization of a tree…

This paper finally fully elaborates the tree pulldown method used by one of us (Harrington) to settle McLaughlin's conjecture. This method enables the construction of a computable tree $T_0$ whose paths are incomparable over $0^{(\alpha)}$…

Connected acyclic graphs (trees) are data objects that hierarchically organize categories. Collections of trees arise in a diverse variety of fields, including evolutionary biology, public health, machine learning, social sciences and…

In the context of reconstructing phylogenetic networks from a collection of phylogenetic trees, several characterisations and subsequently algorithms have been established to reconstruct a phylogenetic network that collectively embeds all…

Evolutionary scenarios displaying reticulation events are often represented by rooted phylogenetic networks. Due to biological reasons, those events occur very rarely, and, thus, networks containing a minimum number of such events,…

A new tree model is introduced based on ordered trees, by distinguishing exactly one child of each node that \emph{has} children. The basic enumeration leads to a cubic equation of the generating function. The extraction of its coefficients…

A major task of evolutionary biology is the reconstruction of phylogenetic trees from molecular data. The evolutionary model is given by a Markov chain on a tree. Given samples from the leaves of the Markov chain, the goal is to reconstruct…

In the critical beta-splitting model of a random $n$-leaf rooted tree, clades are recursively (from the root) split into sub-clades, and a clade of $m$ leaves is split into sub-clades containing $i$ and $m-i$ leaves with probabilities…

Sturmian words are infinite binary words with many equivalent definitions: They have a minimal factor complexity among all aperiodic sequences; they are balanced sequences (the labels 0 and 1 are as evenly distributed as possible) and they…

Here we show that deciding whether two rooted binary phylogenetic trees on the same set of taxa permit a cherry-picking sequence, a special type of elimination order on the taxa, is NP-complete. This improves on an earlier result which…

We consider finite trees with edges labeled by letters on a finite alphabet $\varSigma$. Each pair of nodes defines a unique labeled path whose trace is a word of the free monoid $\varSigma^*$. The set of all such words defines the language…

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…

Normal networks are an important class of phylogenetic networks that have compelling mathematical properties which align with intuition about inference from genetic data. While tools enabling widespread use of phylogenetic networks in the…

The rooted subtree prune and regraft (rSPR) distance between two rooted binary phylogenetic trees is a well-studied measure of topological dissimilarity that is NP-hard to compute. Here we describe an improved linear kernel for the problem.…