Related papers: Deciding the Closure of Inconsistent Rooted Triple…
We systematically study the computational complexity of a broad class of computational problems in phylogenetic reconstruction. The class contains for example the rooted triple consistency problem, forbidden subtree problems, the quartet…
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…
Given an order, a commutative ring whose additive group is free of finite rank, a natural computational question is whether a fixed univariate polynomial $f \in \mathbb{Z}[X]$ has a root in this ring. In this paper, we show that the…
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…
Here we show that deciding whether two rooted binary phylogenetic trees on the same set of taxa permit a cherry-picking sequence, a special type of elimination order on the taxa, is NP-complete. This improves on an earlier result which…
We study the problem of decomposing (clustering) a tree with respect to costs attributed to pairs of nodes, so as to minimize the sum of costs for those pairs of nodes that are in the same component (cluster). For the general case and for…
We show that deciding whether a sparse univariate polynomial has a p-adic rational root can be done in NP for most inputs. We also prove a polynomial-time upper bound for trinomials with suitably generic p-adic Newton polygon. We thus…
Recently, the minimum number of reticulation events that is required to simultaneously embed a collection P of rooted binary phylogenetic trees into a so-called temporal network has been characterized in terms of cherry-picking sequences.…
In graph realization problems one is given a degree sequence and the task is to decide whether there is a graph whose vertex degrees match to the given sequence. This realization problem is known to be polynomial-time solvable when the…
This paper solves a long standing open problem of whether NP-complete problems could be solved in polynomial time on a deterministic Turing machine by showing that the indistinguishable binomial decision tree can be formed in a 3-SAT…
A classical problem in phylogenetic tree analysis is to decide whether there is a phylogenetic tree $T$ that contains all information of a given collection $\cP$ of phylogenetic trees. If the answer is "yes" we say that $\cP$ is compatible…
We convert, within polynomial-time and sequential processing, NP-Complete Problems into a problem of deciding feasibility of a given system S of linear equations with constants and coefficients of binary-variables that are 0, 1, or -1. S is…
Rooted triples, rooted binary phylogenetic trees on three leaves, are sufficient to encode rooted binary phylogenetic trees. That is, if $\mathcal T$ and $\mathcal T'$ are rooted binary phylogenetic $X$-trees that infers the same set of…
Phylogenetic trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a…
Tree containment problem is a fundamental problem in phylogenetic study, as it is used to verify a network model. It asks whether a given network contain a subtree that resembles a binary tree. The problem is NP-complete in general, even in…
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…
This is the latest in a series of articles aimed at exploring the relationship between the complexity classes of P and NP. In the previous papers, we have proved that the sat CNF problem is polynomially reduced to the problem of finding a…
In phylogenetics, phylogenetic trees are rooted binary trees, whereas phylogenetic networks are rooted arbitrary acyclic digraphs. Edges are directed away from the root and leaves are uniquely labeled with taxa in phylogenetic networks. For…
It has recently been shown that the NP-hard problem of calculating the minimum number of hybridization events that is needed to explain a set of rooted binary phylogenetic trees by means of a hybridization network is fixed-parameter…
In this work, we answer an open problem in the study of phylogenetic networks. Phylogenetic trees are rooted binary trees in which all edges are directed away from the root, whereas phylogenetic networks are rooted acyclic digraphs. For the…