Algorithms for Visualizing Phylogenetic Networks

We study the problem of visualizing phylogenetic networks, which are extensions of the Tree of Life in biology. We use a space filling visualization method, called DAGmaps, in order to obtain clear visualizations using limited space. In this paper, we restrict our attention to galled trees and galled networks and present linear time algorithms for visualizing them as DAGmaps.Comment: Appears in the Proceedings of the 24th International Symposium on Graph Drawing and Network Visualization (GD 2016

Parking functions, labeled trees and DCJ sorting scenarios

In genome rearrangement theory, one of the elusive questions raised in recent years is the enumeration of rearrangement scenarios between two genomes. This problem is related to the uniform generation of rearrangement scenarios, and the derivation of tests of statistical significance of the properties of these scenarios. Here we give an exact formula for the number of double-cut-and-join (DCJ) rearrangement scenarios of co-tailed genomes. We also construct effective bijections between the set of scenarios that sort a cycle and well studied combinatorial objects such as parking functions and labeled trees.Comment: 12 pages, 3 figure

A Survey of Combinatorial Methods for Phylogenetic Networks

The evolutionary history of a set of species is usually described by a rooted phylogenetic tree. Although it is generally undisputed that bifurcating speciation events and descent with modifications are major forces of evolution, there is a growing belief that reticulate events also have a role to play. Phylogenetic networks provide an alternative to phylogenetic trees and may be more suitable for data sets where evolution involves significant amounts of reticulate events, such as hybridization, horizontal gene transfer, or recombination. In this article, we give an introduction to the topic of phylogenetic networks, very briefly describing the fundamental concepts and summarizing some of the most important combinatorial methods that are available for their computation

Insertion Magnets

Chapter 3 in High-Luminosity Large Hadron Collider (HL-LHC) : Preliminary Design Report. The Large Hadron Collider (LHC) is one of the largest scientific instruments ever built. Since opening up a new energy frontier for exploration in 2010, it has gathered a global user community of about 7,000 scientists working in fundamental particle physics and the physics of hadronic matter at extreme temperature and density. To sustain and extend its discovery potential, the LHC will need a major upgrade in the 2020s. This will increase its luminosity (rate of collisions) by a factor of five beyond the original design value and the integrated luminosity (total collisions created) by a factor ten. The LHC is already a highly complex and exquisitely optimised machine so this upgrade must be carefully conceived and will require about ten years to implement. The new configuration, known as High Luminosity LHC (HL-LHC), will rely on a number of key innovations that push accelerator technology beyond its present limits. Among these are cutting-edge 11-12 tesla superconducting magnets, compact superconducting cavities for beam rotation with ultra-precise phase control, new technology and physical processes for beam collimation and 300 metre-long high-power superconducting links with negligible energy dissipation. The present document describes the technologies and components that will be used to realise the project and is intended to serve as the basis for the detailed engineering design of HL-LHC.Comment: 19 pages, Chapter 3 in High-Luminosity Large Hadron Collider (HL-LHC) : Preliminary Design Repor