Related papers: Minimum triplet covers of binary phylogenetic $X$-…
A binary tanglegram is a pair <S,T> of 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 or software engineering, it is required…
Let $T$ be a rooted tree, and $V(T)$ its set of vertices. A subset $X$ of $V(T)$ is called an infima closed set of $T$ if for any two vertices $u,v\in X$, the first common ancestor of $u$ and $v$ is also in $X$. This paper determines the…
A phylogenetic network is a directed acyclic graph that visualises an evolutionary history containing so-called reticulations such as recombinations, hybridisations or lateral gene transfers. Here we consider the construction of a simplest…
A multi-labeled tree, or MUL-tree, is a phylogenetic tree where two or more leaves share a label, e.g., a species name. A MUL-tree can imply multiple conflicting phylogenetic relationships for the same set of taxa, but can also contain…
A (pseudo-)metric $D$ on a finite set $X$ is said to be a `tree metric' if there is a finite tree with leaf set $X$ and non-negative edge weights so that, for all $x,y \in X$, $D(x,y)$ is the path distance in the tree between $x$ and $y$.…
A metric phylogenetic tree relating a collection of taxa induces weighted rooted triples and weighted quartets for all subsets of three and four taxa, respectively. New intertaxon distances are defined that can be calculated from these…
A phylogenetic tree is a way to organize a finite set of species, individuals or other sources of related data. The species for which we have existing DNA data make up the set of leaves of the tree. The balanced minimal evolution method of…
In order to conduct a statistical analysis on a given set of phylogenetic gene trees, we often use a distance measure between two trees. In a statistical distance-based method to analyze discordance between gene trees, it is a key to decide…
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…
In phylogenetics, tree-based networks are used to model and visualize the evolutionary history of species where reticulate events such as horizontal gene transfer have occurred. Formally, a tree-based network $N$ consists of a phylogenetic…
The distinguishing number $D(G)$ of a graph $G$ is the least integer $d$ such that $G$ has a vertex labeling with $d$ labels that is preserved only by a trivial automorphism. In this paper we characterize all trees with radius at most three…
Phylogenetic trees represent evolutionary relationships and can be uniquely defined by sets of finite-state biological characteristics. Despite prior work showing that sufficiently large trees can be determined by $r$-state character sets,…
We compare three basic kinds of discrete mathematical models used to portray phylogenetic relationships among species and higher taxa: phylogenetic trees, Hennig trees and Nelson cladograms. All three models are trees, as that term is…
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 consider problems that can be formulated as a task of finding an optimal triangulation of a graph w.r.t. some notion of optimality. We present algorithms parameterized by the size of a minimum edge clique cover ($cc$) to such problems.…
We investigate the class of the edge-shelling convex geometries of trees. The edge-shelling convex geometry of a tree is the convex geometry consisting of the sets of edges of the subtrees. For the edge-shelling convex geometry of a tree,…
A chief problem in phylogenetics and database theory is the computation of a maximum consistent tree from a set of rooted or unrooted trees. A standard input are triplets, rooted binary trees on three leaves, or quartets, unrooted binary…
We show that the expected size of the maximum agreement subtree of two $n$-leaf trees, uniformly random among all trees with the shape, is $\Theta(\sqrt{n})$. To derive the lower bound, we prove a global structural result on a decomposition…
In this work we study the interleaving distance between merge trees from a combinatorial point of view. We use a particular type of matching between trees to obtain a novel formulation of the distance. With such formulation, we tackle the…
The $c$-packedness property, proposed in 2010, is a geometric property that captures the spatial distribution of a set of edges. Despite the recent interest in $c$-packedness, its utility has so far been limited to Fr\'echet distance…