相关论文: A note on efficient computation of hybridization n…

Phylogenetic trees are leaf-labelled trees used to model the evolution of species. Here we explore the practical impact of kernelization (i.e. data reduction) on the NP-hard problem of computing the TBR distance between two unrooted binary…

Phylogenetic trees are leaf-labelled trees, where the leaves correspond to extant species (taxa), and the internal vertices represent ancestral species. The evolutionary history of a set of species can be explained by more than one…

Billey et al. [arXiv:1507.04976] have recently discovered a surprisingly simple formula for the number $a_n(\sigma)$ of leaf-labelled rooted non-embedded binary trees (also known as phylogenetic trees) with $n\geq 1$ leaves, fixed (for the…

We address an open question of Francis and Steel about phylogenetic networks and trees. They give a polynomial time algorithm to decide if a phylogenetic network, N, is tree-based and pose the problem: given a fixed tree T and network N, is…

Reticulate events play an important role in determining evolutionary relationships. The problem of computing the minimum number of such events to explain discordance between two phylogenetic trees is a hard computational problem. Even for…

Tree structures appear in many fields of the life sciences, including phylogenetics, developmental biology and nucleic acid structures. Trees can be used to represent RNA secondary structures, which directly relate to the function of…

Rotation distance between rooted binary trees measures the number of simple operations it takes to transform one tree into another. There are no known polynomial-time algorithms for computing rotation distance. We give an efficient,…

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 $X$…

Here we show that, given a set of clusters C on a set of taxa X, where |X|=n, it is possible to determine in time f(k).poly(n) whether there exists a level-<= k network (i.e. a network where each biconnected component has reticulation…

We propose a hybrid tree algorithm for reducing calculation and communication cost of collision-less N-body simulations. The concept of our algorithm is that we split interaction force into two parts: hard-force from neighbor particles and…

Nowadays hybrid evolutionary algorithms, i.e, heuristic search algorithms combining several mutation operators some of which are meant to implement stochastically a well known technique designed for the specific problem in question while…

Binary jumbled pattern matching asks to preprocess a binary string $S$ in order to answer queries $(i,j)$ which ask for a substring of $S$ that is of length $i$ and has exactly $j$ 1-bits. This problem naturally generalizes to…

We consider the tree consensus problem, an important problem in bioinformatics. Given a rooted tree $t$ and another tree $T$, one would like to incorporate compatible information from $T$ to $t$. This problem is a subproblem in the tree…

Motivated by an application in computational topology, we consider a novel variant of the problem of efficiently maintaining dynamic rooted trees. This variant requires merging two paths in a single operation. In contrast to the standard…

An alphabetic binary tree formulation applies to problems in which an outcome needs to be determined via alphabetically ordered search prior to the termination of some window of opportunity. Rather than finding a decision tree minimizing…

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…

Nowadays, multiprocessing is mainstream with exponentially increasing number of processors. Load balancing is, therefore, a critical operation for the efficient execution of parallel algorithms. In this paper we consider the fundamental…

In this paper, we study factorizations of cycles. The main result is that under certain condition, the number of ways to factor a $d$-cycle into a product of cycles of prescribed lengths is $d^{r-2}.$ To prove our result, we first define a…

Mathematical modeling is a standard approach to solve many real-world problems and {\em diversity} of solutions is an important issue, emerging in applying solutions obtained from mathematical models to real-world problems. Many studies…

The supertree construction problem is about combining several phylogenetic trees with possibly conflicting information into a single tree that has all the leaves of the source trees as its leaves and the relationships between the leaves are…