Related papers: Unique perfect phylogeny is NP-hard
'Tree-based' phylogenetic networks proposed by Francis and Steel have attracted much attention of theoretical biologists in the last few years. At the heart of the definitions of tree-based phylogenetic networks is the notion of 'support…
Supertree construction is the process by which a set of phylogenetic trees, each on a subset of the overall set X of species, is combined into a tree on the full set S. The traditional use of supertree methods is the assembly of a large…
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…
We investigate the computational complexity of deciding whether a given univariate integer polynomial p(x) has a factor q(x) satisfying specific additional constraints. When the only constraint imposed on q(x) is to have a degree smaller…
We study complexity of rearrangement problems in the generalized breakpoint model and settle several open questions. The model was introduced by Tannier et al. (2009) who showed that the median problem is solvable in polynomial time in the…
Phylogenetic trees canonically arise as embeddings of phylogenetic networks. We recently showed that the problem of deciding if two phylogenetic networks embed the same sets of phylogenetic trees is computationally hard, \blue{in…
A binary matrix satisfies the consecutive ones property (COP) if its columns can be permuted such that the ones in each row of the resulting matrix are consecutive. Equivalently, a family of sets F = {Q_1,..,Q_m}, where Q_i is subset of R…
Phylogenetic Diversity(PD)is a well-regarded measure of the overall biodiversity of a set of present-day species(taxa)that indicates its ecological significance.In the Maximize Phylogenetic Diversity(Max-PD)problem one is asked to find a…
It is a well-known fact that hamiltonicity in planar cubic graphs is an NP-complete problem. This implies that the existence of an A-trail in plane eulerian graphs is also an NP-complete problem even if restricted to planar 3-connected…
This article concerns the following question arising in computational evolutionary biology. For a given subclass of phylogenetic networks, what is the maximum value of 0 <= p <= 1 such that for every input set T of rooted triplets, there…
We prove that computing an evolutionary ordering of a family of sets, i.e. an ordering where each set intersects with --but is not included in-- the union earlier sets, is NP-hard.
I consider the problem of learning an optimal path graphical model from data and show the problem to be NP-hard for the maximum likelihood and minimum description length approaches and a Bayesian approach. This hardness result holds despite…
Some classical graph problems such as finding minimal spanning tree, shortest path or maximal flow can be done efficiently. We describe slight variations of such problems which are shown to be NP-complete. Our proofs use straightforward…
For a graph property $\Pi$, Subgraph Complementation to $\Pi$ is the problem to find whether there is a subset $S$ of vertices of the input graph $G$ such that modifying $G$ by complementing the subgraph induced by $S$ results in a graph…
We prove that certain problems naturally arising in knot theory are NP--hard or NP--complete. These are the problems of obtaining one diagram from another one of a link in a bounded number of Reidemeister moves, determining whether a link…
In the rectilinear Steiner arborescence problem the task is to build a shortest rectilinear Steiner tree connecting a given root and a set of terminals which are placed in the plane such that all root-terminal-paths are shortest paths. This…
The problem of constructing an optimal rooted phylogenetic network from a set of rooted triplets is an NP-hard problem. In this paper, we present a heuristic algorithm called TripNet which tries to construct an optimal rooted phylogenetic…
We show that three natural decision problems about links and 3-manifolds are computationally hard, assuming some conjectures in complexity theory. The first problem is determining whether a link in the 3-sphere bounds a Seifert surface with…
In this paper, we study the complexity of two types of digraph packing problems: perfect out-forests problem and Steiner cycle packing problem. For the perfect out-forest problem, we prove that it is NP-hard to decide whether a given strong…
We study the uniform query reliability problem, which asks, for a fixed Boolean query Q, given an instance I, how many subinstances of I satisfy Q. Equivalently, this is a restricted case of Boolean query evaluation on tuple-independent…