Related papers: Tree evolution processes for bucket increasing tre…
It was recently shown that a large class of phylogenetic networks, the `labellable' networks, is in bijection with the set of `expanding' covers of finite sets. In this paper, we show how several prominent classes of phylogenetic networks…
Increasingly, biologists are constructing evolutionary trees on large numbers of overlapping sets of taxa, and then combining them into a `supertree' that classifies all the taxa. In this paper, we ask how much coverage of the total set of…
The forest of mutations associated to a multitype branching forest is obtained by merging together all vertices of its clusters and by preserving connections between them. We first show that the forest of mutations of any mulitype branching…
Plane increasing trees are rooted labeled trees embedded into the plane such that the sequence of labels is increasing on any branch starting at the root. Relaxed binary trees are a subclass of unlabeled directed acyclic graphs. We…
Trees are partial orderings where every element has a linearly ordered set of smaller elements. We define and study several natural notions of completeness of trees, extending Dedekind completeness of linear orders and Dedekind-MacNeille…
A large class of phylogenetic networks can be obtained from trees by the addition of horizontal edges between the tree edges. These networks are called tree based networks. Reticulation-visible networks and child-sibling networks are all…
A well-established model for the genealogy of a large population in equilibrium is Kingman's coalescent. For the population together with its genealogy evolving in time, this gives rise to a time-stationary tree-valued process. We study the…
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…
In this short note we discuss recent results on hook length formulas of trees unifying some earlier results, and explain hook length formulas naturally associated to families of increasingly labelled trees.
We consider the process of uncovering the vertices of a random labeled tree according to their labels. First, a labeled tree with $n$ vertices is generated uniformly at random. Thereafter, the vertices are uncovered one by one, in order of…
Staged tree models are a discrete generalization of Bayesian networks. We show that these form curved exponential families and derive their natural parameters, sufficient statistic, and cumulant-generating function as functions of their…
Bicubic maps are in bijection with \beta(0,1)-trees. We introduce two new ways of decomposing \beta(0,1)-trees. Using this we define an endofunction on \beta(0,1)-trees, and thus also on bicubic maps. We show that this endofunction is in…
The properties of randomly evolving special trees having defined and analyzed already in two earlier papers (arXiv:cond-mat/0205650 and arXiv:cond-mat/0211092) have been investigated in the case when the continuous time parameter converges…
This paper studies increasing trees on $n$ labeled vertices, in which labels increase from the root to the leaves. It is known that the number of binary increasing trees coincides with the number of alternating permutations (Euler numbers).…
The class of ranked tree-child networks, tree-child networks arising from an evolution process with a fixed embedding into the plane, has recently been introduced by Bienvenu, Lambert, and Steel. These authors derived counting results for…
Most decision tree induction algorithms are based on a greedy top-down recursive partitioning strategy for tree growth. In this paper, we propose several methods for induction of decision trees and their ensembles based on evolutionary…
We introduce the notion of evolution on sets and study several sets endowed with this structure and obtain some results about this new notion.
We give a short and direct proof of a remarkable identity that arises in the enumeration of labeled trees with respect to their indegree sequence, where all edges are oriented from the vertex with lower label towards the vertex with higher…
Rooted phylogenetic networks allow biologists to represent evolutionary relationships between present-day species by revealing ancestral speciation and hybridization events. A convenient and well-studied class of such networks are…
We give closed form expressions for the numbers of multi-rooted plane trees with specified degrees of root vertices. This results in an infinite number of integer sequences some of which are known to have an alternative interpretation. We…