Related papers: Universal rooted phylogenetic tree shapes and univ…

A \emph{binary tanglegram} is a drawing of a pair of rooted binary trees whose leaf sets are in one-to-one correspondence; matching leaves are connected by inter-tree edges. For applications, for example, in phylogenetics, it is essential…

In this article, we construct explicit examples of pairs of non-isomorphic trees with the same restricted $U$-polynomial for every $k$; by this we mean that the polynomials agree on terms with degree at most $k+1$. The main tool for this…

Imitating a recently introduced invariant of trees, we initiate the study of the inducibility of $d$-ary trees (rooted trees whose vertex outdegrees are bounded from above by $d\geq 2$) with a given number of leaves. We determine the exact…

We prove that one can perfectly pack degenerate graphs into complete or dense $n$-vertex quasirandom graphs, provided that all the degenerate graphs have maximum degree $o(\frac{n}{\log n})$, and in addition $\Omega(n)$ of them have at most…

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…

Let $\Omega_n$ be the family of binary trees on $n$ vertices obtained by identifying the root of an rgood binary tree with a vertex of maximum eccentricity of a binary caterpillar. In the paper titled "On different middle parts of a tree…

It is a known fact that, given two rooted binary phylogenetic trees, the concept of maximum acyclic agreement forests is sufficient to compute hybridization networks with minimum hybridization number. In this work, we demonstrate by first…

We prove that finding a rooted subtree with at least $k$ leaves in a digraph is a fixed parameter tractable problem. A similar result holds for finding rooted spanning trees with many leaves in digraphs from a wide family $\cal L$ that…

We consider root-finding algorithms for random rooted trees grown by uniform attachment. Given an unlabeled copy of the tree and a target accuracy $\varepsilon > 0$, such an algorithm outputs a set of nodes that contains the root with…

The inducibility of a graph represents its maximum density as an induced subgraph over all possible sequences of graphs of size growing to infinity. This invariant of graphs has been extensively studied since its introduction in $1975$ by…

Rooted triples, rooted binary phylogenetic trees on three leaves, are sufficient to encode rooted binary phylogenetic trees. That is, if $\mathcal T$ and $\mathcal T'$ are rooted binary phylogenetic $X$-trees that infers the same set of…

In the study of extensions of polytopes of combinatorial optimization problems, a notorious open question is that for the size of the smallest extended formulation of the Minimum Spanning Tree problem on a complete graph with $n$ nodes. The…

A tanglegram consists of two rooted binary trees and a perfect matching between their leaves, and a planar tanglegram is one that admits a layout with no crossings. We show that the problem of generating planar tanglegrams uniformly at…

We extend the theory of minimal absent words to (rooted and unrooted) trees, having edges labeled by letters from an alphabet $\Sigma$ of cardinality $\sigma$. We show that the set $\text{MAW}(T)$ of minimal absent words of a rooted (resp.…

Trees with labelled leaves and with all other vertices of degree three play an important role in systematic biology and other areas of classification. A classical combinatorial result ensures that such trees can be uniquely reconstructed…

We show that a tree of order $n$ has at most $O(5^{n/4})$ nonisomorphic subtrees, and that this bound is best possible. We also prove an analogous result for the number of nonisomorphic rooted subtrees of a rooted tree.

For every $n\in \mathbb{N}$, we present a set $S_n$ of $O(n^{3/2}\log n)$ points in the plane such that every planar 3-tree with $n$ vertices has a straight-line embedding in the plane in which the vertices are mapped to a subset of $S_n$.…

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…

Three standard subtree transfer operations for binary trees, used in particular for phylogenetic trees, are: tree bisection and reconnection ($TBR$), subtree prune and regraft ($SPR$) and rooted subtree prune and regraft ($rSPR$). For a…

A normal network is uniquely determined by the set of phylogenetic trees that it displays. Given a set $\mathcal{P}$ of rooted binary phylogenetic trees, this paper presents a polynomial-time algorithm that reconstructs the unique binary…