Related papers: Decks of rooted binary trees
In evolutionary biology, phylogenetic trees are commonly inferred from a set of characters (partitions) of a collection of biological entities (e.g., species or individuals in a population). Such characters naturally arise from molecular…
We study an abstract notion of tree structure which lies at the common core of various tree-like discrete structures commonly used in combinatorics: trees in graphs, order trees, nested subsets of a set, tree-decompositions of graphs and…
This paper investigates some properties of the number of subtrees of a tree with given degree sequence. These results are used to characterize trees with the given degree sequence that have the largest number of subtrees, which generalizes…
Phylogenetic networks are a generalization of phylogenetic trees allowing for the representation of non-treelike evolutionary events such as hybridization. Typically, such networks have been analyzed based on their `level', i.e. based on…
We prove polynomial upper and lower bounds on the expected size of the maximum agreement subtree of two random binary phylogenetic trees under both the uniform distribution and Yule-Harding distribution. This positively answers a question…
Tanglegrams are a special class of graphs appearing in applications concerning cospeciation and coevolution in biology and computer science. They are formed by identifying the leaves of two rooted binary trees. We give an explicit formula…
A compacted binary tree is a graph created from a binary tree such that repeatedly occurring subtrees in the original tree are represented by pointers to existing ones, and hence every subtree is unique. Such representations form a special…
This is a survey article on trees, with a modest number of proofs to give a flavor of the way these topologies can be efficiently handled. Trees are defined in set-theorist fashion as partially ordered sets in which the elements below each…
We study a partially ordered set of planar labeled rooted trees by use of combinatorial objects called Dyck tilings. A generating function of the poset is factorized when the minimum element of the poset is $312$-avoiding and satisfies some…
A fringe subtree of a rooted tree is a subtree induced by one of the vertices and all its descendants. We consider the problem of estimating the number of distinct fringe subtrees in two types of random trees: simply generated trees and…
Frequent tree mining asks us to enumerate tree patterns that occur frequently in a database of rooted trees. This problem is motivated by tree-structured data in bioinformatics, such as glycans and pseudoknot-free RNA secondary structures.…
We study the bounded regions in a generic slice of the hyperplane arrangement in $\mathbb{R}^n$ consisting of the hyperplanes defined by $x_i$ and $x_i+x_j$. The bounded regions are in bijection with several classes of combinatorial…
Phylogenetic (evolutionary) trees and networks are leaf-labeled graphs that are widely used to represent the evolutionary relationships between entities such as species, languages, cancer cells, and viruses. To reconstruct and analyze…
Attempting to recognize a tree inside a phylogenetic network is a fundamental undertaking in evolutionary analysis. In the last few years, therefore, tree-based phylogenetic networks, which are defined by a spanning tree called a…
We introduce tree dimension and its leveled variant in order to measure the complexity of leaf sets in binary trees. We then provide a tight upper bound on the size of such sets using leveled tree dimension. This, in turn, implies both the…
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…
This extended abstract is dedicated to the analysis of the height of non-plane unlabelled rooted binary trees. The height of such a tree chosen uniformly among those of size $n$ is proved to have a limiting theta distribution, both in a…
Let $T$ be a weighted tree. The weight of a subtree $T_1$ of $T$ is defined as the product of weights of vertices and edges of $T_1$. We obtain a linear-time algorithm to count the sum of weights of subtrees of $T$. As applications, we…
We consider the problem of embedding the Steiner points of a Steiner tree with given topology into the rectilinear plane. Thereby, the length of the path between a distinguished terminal and each other terminal must not exceed given length…
Reconstructing a parsimonious phylogenetic network that displays multiple phylogenetic trees is an important problem in theory of phylogenetics, where the complexity of the inferred networks is measured by reticulation numbers. The…