Related papers: Rooted Almost-binary Phylogenetic Networks for whi…
Pattern matching can be used to calculate the support of patterns, and is a key issue in sequential pattern mining (or sequence pattern mining). Nonoverlapping pattern matching means that two occurrences cannot use the same character in the…
For a phylogenetic tree, the phylogenetic diversity of a set A of taxa is the total weight of edges on paths to A. Finding small sets of maximal diversity is crucial for conservation planning, as it indicates where limited resources can be…
The maximum agreement forest (MAF) problem in phylogenetics takes as input a set t >= 2 of binary phylogenetic trees T on the same set of taxa X. It asks for a partition of X into the smallest number of blocks such that the subtrees induced…
A phylogenetic network is a directed acyclic graph that visualises an evolutionary history containing so-called reticulations such as recombinations, hybridisations or lateral gene transfers. Here we consider the construction of a simplest…
Interpreting three-leaf binary trees or {\em rooted triples} as constraints yields an entailment relation, whereby binary trees satisfying some rooted triples must also thus satisfy others, and thence a closure operator, which is known to…
Phylogenetic networks which are, as opposed to trees, suitable to describe processes like hybridization and horizontal gene transfer, play a substantial role in evolutionary research. However, while non-treelike events need to be taken into…
In the classical (min-cost) Steiner tree problem, we are given an edge-weighted undirected graph and a set of terminal nodes. The goal is to compute a min-cost tree S which spans all terminals. In this paper we consider the min-power…
Phylogenetic networks generalize evolutionary trees, and are commonly used to represent evolutionary histories of species that undergo reticulate evolutionary processes such as hybridization, recombination and lateral gene transfer.…
Along with the development of manufacture and services, the problem of distribution network optimization has been growing in importance, thus receiving much attention from the research community. One of the most recently introduced network…
Popular methods for exploring the space of rooted phylogenetic trees use rearrangement moves such as rNNI (rooted Nearest Neighbour Interchange) and rSPR (rooted Subtree Prune and Regraft). Recently, these moves were generalized to rooted…
A contemporary and fundamental problem faced by many evolutionary biologists is how to puzzle together a collection $\mathcal P$ of partial trees (leaf-labelled trees whose leaves are bijectively labelled by species or, more generally,…
Mutations of genetic sequences are often accompanied by their recombinations, known as phylogenetic networks. These networks are typically reconstructed from coalescent processes that may arise from optimal merging or fitting together a…
In comparison to phylogenetic trees, phylogenetic networks are more suitable to represent complex evolutionary histories of species whose past includes reticulation such as hybridisation or lateral gene transfer. However, the reconstruction…
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…
Phylogenetic networks are a special type of graph which generalize phylogenetic trees and that are used to model non-treelike evolutionary processes such as recombination and hybridization. In this paper, we consider {\em unrooted}…
Due to its broad applications in practice, the minimum spanning tree problem and its all kinds of variations have been studied extensively during the last decades, for which a host of efficient exact and heuristic algorithms have been…
In Francis and Steel (2015), it was shown that there exists non-trivial networks on $4$ leaves upon which the distance metric affords a metric on a tree which is not the base tree of the network. In this paper we extend this result in two…
In the context of algorithm theory, various studies have been conducted on spanning trees with desirable properties. In this paper, we consider the \textsc{Minimum Cover Spanning Tree} problem (MCST for short). Given a graph $G$ and a…
Suppose N is a phylogenetic network indicating a complicated relationship among individuals and taxa. Often of interest is a much simpler network, for example, a species tree T, that summarizes the most fundamental relationships. The…
Rooted phylogenetic networks provide an explicit representation of the evolutionary history of a set $X$ of sampled species. In contrast to phylogenetic trees which show only speciation events, networks can also accommodate reticulate…