Related papers: On Finding Directed Trees with Many Leaves
Let $\T_{n}$ be the set of rooted labeled trees on $\set{0,...,n}$. A maximal decreasing subtree of a rooted labeled tree is defined by the maximal subtree from the root with all edges being decreasing. In this paper, we study a new…
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…
A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called…
Given a directed graph $G$ with non negative cost on the arcs, a directed tree cover of $G$ is a rooted directed tree such that either head or tail (or both of them) of every arc in $G$ is touched by $T$. The minimum directed tree cover…
An out-branching and an in-branching of a digraph $D$ are called $k$-distinct if each of them has $k$ arcs absent in the other. Bang-Jensen, Saurabh and Simonsen (2016) proved that the problem of deciding whether a strongly connected…
Phylogenetic trees are leaf-labelled trees used to model the evolution of species. In practice it is not uncommon to obtain two topologically distinct trees for the same set of species, and this motivates the use of distance measures to…
Tree Containment is a fundamental problem in phylogenetics useful for verifying a proposed phylogenetic network, representing the evolutionary history of certain species. Tree Containment asks whether the given phylogenetic tree (for…
The recursive removal of leaves (dead end vertices) and their neighbors from an undirected network results, when this pruning algorithm stops, in a so-called core of the network. This specific subgraph should be distinguished from…
The Edge Multicut problem is a classical cut problem where given an undirected graph $G$, a set of pairs of vertices $\mathcal{P}$, and a budget $k$, the goal is to determine if there is a set $S$ of at most $k$ edges such that for each…
A tree with at most $k$ leaves is called a $k$-ended tree. A spanning 2-ended tree is a Hamilton path. A Hamilton cycle can be considered as a spanning 1-ended tree. The earliest result concerning spanning trees with few leaves states that…
Finding a maximum clique in a given graph is one of the fundamental NP-hard problems. We compare two multi-core thread-parallel adaptations of a state-of-the-art branch and bound algorithm for the maximum clique problem, and provide a novel…
As a generalization of the Edmonds arborescence packing theorem, Kamiyama--Katoh--Takizawa (2009) gave a good characterization of directed graphs that contain arc-disjoint arborescences spanning the set of vertices reachable from each root.…
An evolutionary tree is a rooted tree where each internal vertex has at least two children and where the leaves are labeled with distinct symbols representing species. Evolutionary trees are useful for modeling the evolutionary history of…
Tree-based phylogenetic networks, which may be roughly defined as leaf-labeled networks built by adding arcs only between the original tree edges, have elegant properties for modeling evolutionary histories. We answer an open question of…
We consider the following problem: Given an undirected (mixed) network and a set of ordered source-target, or cause-effect pairs, direct all edges so as to maximize the number of pairs that admit a directed source-target path. This is…
Over some types of trees with a given number of vertices, which trees minimize or maximize the total number of subtrees or leaf containing subtrees are studied. Here are some of the main results:\ (1)\, Sharp upper bound on the total number…
Rooted binary perfect phylogenies provide a generalization of rooted binary unlabeled trees in which each leaf is assigned a positive integer value that corresponds in a biological setting to the count of the number of indistinguishable…
Designing well-connected graphs is a fundamental problem that frequently arises in various contexts across science and engineering. The weighted number of spanning trees, as a connectivity measure, emerges in numerous problems and plays a…
This paper tightens the best known analysis of Hein's 1989 algorithm to infer the topology of a weighted tree based on the lengths of paths between its leaves. It shows that the number of length queries required for a degree-$k$ tree of $n$…
Let $T$ be a tree, a vertex of degree one is a leaf of $T$ and a vertex of degree at least three is a branch vertex of $T$. For two distinct vertices $u,v$ of $T$, let $P_T[u,v]$ denote the unique path in $T$ connecting $u$ and $v.$ For a…