Related papers: Unique perfect phylogeny is NP-hard
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…
A secure set $S$ in a graph is defined as a set of vertices such that for any $X\subseteq S$ the majority of vertices in the neighborhood of $X$ belongs to $S$. It is known that deciding whether a set $S$ is secure in a graph is…
The computational complexity of the partition, 0-1 subset sum, unbounded subset sum, 0-1 knapsack and unbounded knapsack problems and their multiple variants were studied in numerous papers in the past where all the weights and profits were…
Phylogenetic Diversity (PD) is a measure of the overall biodiversity of a set of present-day species (taxa) within a phylogenetic tree. In Maximize Phylogenetic Diversity (MPD) one is asked to find a set of taxa (of bounded size/cost) for…
We study the Steiner Tree problem on unit disk graphs. Given a $n$ vertex unit disk graph $G$, a subset $R\subseteq V(G)$ of $t$ vertices and a positive integer $k$, the objective is to decide if there exists a tree $T$ in $G$ that spans…
A fundamental problem in the study of phylogenetic networks is to determine whether or not a given phylogenetic network contains a given phylogenetic tree. We develop a quadratic-time algorithm for this problem for binary nearly-stable…
The decision problems of the existence of a Hamiltonian cycle or of a Hamiltonian path in a given graph, and of the existence of a truth assignment satisfying a given Boolean formula $C$, are well-known {\it NP}-complete problems. Here we…
We consider the problem of constructing an an optimal-weight tree from the 3*(n choose 4) weighted quartet topologies on n objects, where optimality means that the summed weight of the embedded quartet topologiesis optimal (so it can be the…
An evolutionary tree (phylogenetic tree) is a binary, rooted, unordered tree that models the evolutionary history of currently living species in which leaves are labeled by species. In this paper, we investigate the problem of finding the…
Given a tree $T$ on $n$ vertices, and $k, b, s_1, \ldots, s_b \in N$, the Tree Partitioning problem asks if at most $k$ edges can be removed from $T$ so that the resulting components can be grouped into $b$ groups such that the number of…
Phylogenetic Diversity (PD) is a prominent quantitative measure of the biodiversity of a collection of present-day species (taxa). This measure is based on the evolutionary distance among the species in the collection. Loosely speaking, if…
We show that the problem of finding a set with maximum cohesion in an undirected network is NP-hard.
IV-matching is a generalization of perfect bipartite matching. The complexity of finding IV-matching in a graph was posted as an open problem at the ICALP 2014 conference. In this note, we resolve the question and prove that, contrary to…
Given a finite set $X$, a collection $\mathcal{T}$ of rooted phylogenetic trees on $X$ and an integer $k$, the Hybridization Number problem asks if there exists a phylogenetic network on $X$ that displays all trees from $\mathcal{T}$ and…
We introduce a new -as far as we know- problem, according to which we are asked to match sequences of two digits in matrices having entries among those two digits (but others too) and prove that this problem is NP-complete
The inference of new information on the relatedness of species by phylogenetic trees based on DNA data is one of the main challenges of modern biology. But despite all technological advances, DNA sequencing is still a time-consuming and…
Disjoint-Set forests, consisting of Union-Find trees are data structures having a widespread practical application due to their efficiency. Despite them being well-known, no exact structural characterization of these trees is known (such a…
A Supertree synthesizes the topologies of a set of phylogenetic trees carrying overlapping taxa set. In process, conflicts in the tree topologies are aimed to be resolved with the consensus clades. Such a problem is proved to be NP-hard.…
The binary perfect phylogeny model is too restrictive to model biological events such as back mutations. In this paper we consider a natural generalization of the model that allows a special type of back mutation. We investigate the problem…
It has remained an open question for some time whether, given a set of not necessarily binary (i.e. "nonbinary") trees T on a set of taxa X, it is possible to determine in time f(r).poly(m) whether there exists a phylogenetic network that…