Related papers: Unique perfect phylogeny is NP-hard
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…
Phylogenetic trees illustrate the evolutionary history of genes and species. In most cases, although genes evolve along with the species they belong to, a species tree and gene tree are not identical, because of evolutionary events at the…
We show that reconstructing a tree from order information on triples is NP-hard. This is in contrast to the case for ultra-metrics and for subtree information on quadruples which are both known to allow polynomial time reconstruction.
Several computational problems in phylogenetic reconstruction can be formulated as restrictions of the following general problem: given a formula in conjunctive normal form where the literals are rooted triples, is there a rooted binary…
Can the vertices of a graph $G$ be partitioned into $A \cup B$, so that $G[A]$ is a line-graph and $G[B]$ is a forest? Can $G$ be partitioned into a planar graph and a perfect graph? The NP-completeness of these problems are just special…
Phylogenetic networks generalize phylogenetic trees by representing reticulate evolution. Tree-based networks and their support trees have been extensively studied, but not all networks are tree-based. To measure how far such networks are…
In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$…
We consider the following basic problem in phylogenetic tree construction. Let $\mathcal{P} = \{T_1, \ldots, T_k\}$ be a collection of rooted phylogenetic trees over various subsets of a set of species. The tree compatibility problem asks…
We show that P2T - the problem of deciding whether the edge set of a simple graph can be partitioned into two trees or not - is NP-complete.
A directed phylogenetic network is tree-child if every non-leaf vertex has a child that is not a reticulation. As a class of directed phylogenetic networks, tree-child networks are very useful from a computational perspective. For example,…
Deciding whether a graph can be embedded in a grid using only unit-length edges is NP-complete, even when restricted to binary trees. However, it is not difficult to devise a number of graph classes for which the problem is polynomial, even…
We study compact straight-line embeddings of trees. We show that perfect binary trees can be embedded optimally: a tree with $n$ nodes can be drawn on a $\sqrt n$ by $\sqrt n$ grid. We also show that testing whether a given binary tree has…
The quadratic minimum spanning tree problem and its variations such as the quadratic bottleneck spanning tree problem, the minimum spanning tree problem with conflict pair constraints, and the bottleneck spanning tree problem with conflict…
We analyze the question of deciding whether a quadratic or a hyperbolic 0-1 programming instance has a unique optimal solution. Both uniqueness questions are known to be NP-hard, but are unlikely to be contained in the class NP. We…
One strategy for reconstruction of phylogenetic networks is to solve the phylogenetic network problem, which involves inferring phylogenetic trees first and subsequently computing the smallest phylogenetic network that displays all the…
We consider the polyhedral properties of two spanning tree problems with additional constraints. In the first problem, it is required to find a tree with a minimum sum of edge weights among all spanning trees with the number of leaves less…
We consider the problem of deciding, given a sequence of regions, if there is a choice of points, one for each region, such that the induced polyline is simple or weakly simple, meaning that it can touch but not cross itself. Specifically,…
Jansson and Sung showed that, given a dense set of input triplets T (representing hypotheses about the local evolutionary relationships of triplets of species), it is possible to determine in polynomial time whether there exists a level-1…
Phylogenetically decisive collections of taxon sets have the property that if trees are chosen for each of their elements, as long as these trees are compatible, the resulting supertree is unique. This means that as long as the trees…
We study the problem of constructing phylogenetic trees for a given set of species. The problem is formulated as that of finding a minimum Steiner tree on $n$ points over the Boolean hypercube of dimension $d$. It is known that an optimal…