相关论文: A quadratic kernel for computing the hybridization…
Phylogenetic networks are an important way to represent evolutionary histories that involve reticulations such as hybridization or horizontal gene transfer, yet fundamental questions such as how many networks there are that satisfy certain…
Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…
We study the enumeration of spinal tree-child phylogenetic networks, a rigid family of tree-child networks in which all internal vertices lie on a single root--to--leaf path. We provide two complementary combinatorial frameworks. First, we…
A phylogenetic tree is a way to organize a finite set of species, individuals or other sources of related data. The species for which we have existing DNA data make up the set of leaves of the tree. The balanced minimal evolution method of…
Rotation distance between rooted binary trees is the minimum number of simple rotations needed to transform one tree into the other. Computing the rotation distance between a pair of rooted trees can be quickly reduced in cases where there…
Phylogenetic networks are a generalization of phylogenetic trees allowing for the representation of non-treelike evolutionary events such as hybridization. Typically, such networks have been analyzed based on their `level', i.e. based on…
Phylogenetic networks are often constructed by merging multiple conflicting phylogenetic signals into a directed acyclic graph. It is interesting to explore whether a network constructed in this way induces biologically-relevant…
Recently there has been considerable interest in the problem of finding a phylogenetic network with a minimum number of reticulation vertices which displays a given set of phylogenetic trees, that is, a network with minimum hybrid number.…
Euclidean Steiner trees are relevant to model minimal networks in real-world applications ubiquitously. In this paper, we study the feasibility of a hierarchical approach embedded with bundling operations to compute multiple and mutually…
We investigate exact crossing minimization for graphs that differ from trees by a small number of additional edges, for several variants of the crossing minimization problem. In particular, we provide fixed parameter tractable algorithms…
The Rooted Maximum Leaf Outbranching problem consists in finding a spanning directed tree rooted at some prescribed vertex of a digraph with the maximum number of leaves. Its parameterized version asks if there exists such a tree with at…
The (axis-parallel) stabbing number of a given set of line segments is the maximum number of segments that can be intersected by any one (axis-parallel) line. This paper deals with finding perfect matchings, spanning trees, or…
Working with generating functions, the combinatorics of a recurrence relation can be expressed in a way that allows for more efficient calculation of the quantity. This is true of the Catalan numbers for an ordered binary tree…
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…
A fundamental graph problem is to recognize whether the vertex set of a graph $G$ can be bipartitioned into sets $A$ and $B$ such that $G[A]$ and $G[B]$ satisfy properties $\Pi_A$ and $\Pi_B$, respectively. This so-called…
The Neighbor-Joining algorithm is a popular distance-based phylogenetic method that computes a tree metric from a dissimilarity map arising from biological data. Realizing dissimilarity maps as points in Euclidean space, the algorithm…
In the Euclidean Bottleneck Steiner Tree problem, the input consists of a set of $n$ points in $\mathbb{R}^2$ called terminals and a parameter $k$, and the goal is to compute a Steiner tree that spans all the terminals and contains at most…
An important problem in phylogenetics is the construction of phylogenetic trees. One way to approach this problem, known as the supertree method, involves inferring a phylogenetic tree with leaves consisting of a set $X$ of species from a…
Mixed-integer quadratic programming is the problem of optimizing a quadratic function over points in a polyhedral set where some of the components are restricted to be integral. In this paper, we prove that the decision version of…
We consider the Steiner tree problem on graphs where we are given a set of nodes and the goal is to find a tree sub-graph of minimum weight that contains all nodes in the given set, potentially including additional nodes. This is a…