Related papers: A Duality Based 2-Approximation Algorithm for Maxi…
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…
We present efficient algorithms for computing a maximum agreement forest (MAF) of a pair of multifurcating (nonbinary) rooted trees. Our algorithms match the running times of the currently best algorithms for the binary case. The size of an…
We present a simple 4-approximation algorithm for computing a maximum agreement forest of multiple unrooted binary trees. This algorithm applies LP rounding to an extension of a recent ILP formulation of the maximum agreement forest problem…
We present new and improved fixed-parameter algorithms for computing maximum agreement forests (MAFs) of pairs of rooted binary phylogenetic trees. The size of such a forest for two trees corresponds to their subtree prune-and-regraft…
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 study approximation algorithms for the forest cover and bounded forest cover problems. A probabilistic $2+\epsilon$ approximation algorithm for the forest cover problem is given using the method of dual fitting. A deterministic algorithm…
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…
The Maximum Agreement Forest (Maf) problem is a well-studied problem in evolutionary biology, which asks for a largest common subforest of a given collection of phylogenetic trees with identical leaf label-set. However, the previous work…
Due to hybridization events in evolution, studying two different genes of a set of species may yield two related but different phylogenetic trees for the set of species. In this case, we want to measure the dissimilarity of the two trees.…
Given two rooted phylogenetic trees on the same set of taxa X, the Maximum Agreement Forest problem (MAF) asks to find a forest that is, in a certain sense, common to both trees and has a minimum number of components. The Maximum Acyclic…
Finding the most parsimonious tree inside a phylogenetic network with respect to a given character is an NP-hard combinatorial optimization problem that for many network topologies is essentially inapproximable. In contrast, if the network…
Dual-tree algorithms are a widely used class of branch-and-bound algorithms. Unfortunately, developing dual-tree algorithms for use with different trees and problems is often complex and burdensome. We introduce a four-part logical split:…
We propose the first branch-&-price algorithm for the maximum agreement forest problem on unrooted binary trees: given two unrooted X-labelled binary trees we seek to partition X into a minimum number of blocks such that the induced…
Agreement forests continue to play a central role in the comparison of phylogenetic trees since their introduction more than 25 years ago. More specifically, they are used to characterise several distances that are based on tree…
Phylogenetic trees are leaf-labelled trees used to model the evolution of species. In practice it is not uncommon to obtain two topologically distinct trees for the same set of species, and this motivates the use of distance measures to…
The ancestral maximum-likelihood and phylogeography problems are two fundamental problems involving evolutionary studies. The ancestral maximum-likelihood problem involves identifying a rooted tree alongside internal node sequences that…
We describe a kernel of size 9k-8 for the NP-hard problem of computing the Tree Bisection and Reconnect (TBR) distance k between two unrooted binary phylogenetic trees. We achieve this by extending the existing portfolio of reduction rules…
In this paper we propose and study a new complexity model for approximation algorithms. The main motivation are practical problems over large data sets that need to be solved many times for different scenarios, e.g., many multicast trees…
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…
A rearrangement operation makes a small graph-theoretical change to a phylogenetic network to transform it into another one. For unrooted phylogenetic trees and networks, popular rearrangement operations are tree bisection and reconnection…