相关论文: A quadratic kernel for computing the hybridization…

The class of graph deletion problems has been extensively studied in theoretical computer science, particularly in the field of parameterized complexity. Recently, a new notion of graph deletion problems was introduced, called deletion to…

Normal networks are an important class of phylogenetic networks that have compelling mathematical properties which align with intuition about inference from genetic data. While tools enabling widespread use of phylogenetic networks in the…

Binets and trinets are phylogenetic networks with two and three leaves, respectively. Here we consider the problem of deciding if there exists a binary level-1 phylogenetic network displaying a given set $\mathcal{T}$ of binary binets or…

In phylogenetics, the consensus problem consists in summarizing a set of phylogenetic trees that all classify the same set of species into a single tree. Several definitions of consensus exist in the literature; in this paper we focus on…

In the Maximize Phylogenetic Diversity problem, we are given a phylogenetic tree that represents the genetic proximity of species, and we are asked to select a subset of species of maximum phylogenetic diversity to be preserved through…

The propositional planning problem is a notoriously difficult computational problem. Downey et al. (1999) initiated the parameterized analysis of planning (with plan length as the parameter) and B\"ackstr\"om et al. (2012) picked up this…

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 recurring theme in the least squares approach to phylogenetics has been the discovery of elegant combinatorial formulas for the least squares estimates of edge lengths. These formulas have proved useful for the development of efficient…

The graph crossing number problem, cr(G)<=k, asks for a drawing of a graph G in the plane with at most k edge crossings. Although this problem is in general notoriously difficult, it is fixed- parameter tractable for the parameter k…

Fixed parameter tractable algorithms for bounded treewidth are known to exist for a wide class of graph optimization problems. While most research in this area has been focused on exact algorithms, it is hard to find decompositions of…

Attempting to recognize a tree inside a phylogenetic network is a fundamental undertaking in evolutionary analysis. In the last few years, therefore, tree-based phylogenetic networks, which are defined by a spanning tree called a…

Phylogenetic networks are graphs that are used to represent evolutionary relationships between different taxa. They generalize phylogenetic trees since for example, unlike trees, they permit lineages to combine. Recently, there has been…

Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…

Rooted phylogenetic networks allow biologists to represent evolutionary relationships between present-day species by revealing ancestral speciation and hybridization events. A convenient and well-studied class of such networks are…

Construction of phylogenetic trees and networks for extant species from their characters represents one of the key problems in phylogenomics. While solution to this problem is not always uniquely defined and there exist multiple methods for…

We apply classical quartet techniques to the problem of phylogenetic decisiveness and find a value $k$ such that all collections of at least $k$ quartets are decisive. Moreover, we prove that this bound is optimal and give a lower-bound on…

The Maximum Agreement Forest problem has been extensively studied in phylogenetics. Most previous work is on two binary phylogenetic trees. In this paper, we study a generalized version of the problem: the Maximum Agreement Forest problem…

We give a 2-approximation algorithm for the Maximum Agreement Forest problem on two rooted binary trees. This NP-hard problem has been studied extensively in the past two decades, since it can be used to compute the rooted Subtree…

The {\sc $k$-Leaf Out-Branching} problem is to find an out-branching (i.e. a rooted oriented spanning tree) with at least $k$ leaves in a given digraph. The problem has recently received much attention from the viewpoint of parameterized…

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…