On Finding the Adams Consensus Tree

This paper presents a fast algorithm for finding the Adams consensus tree of a set of conflicting phylogenetic trees with identical leaf labels, for the first time improving the time complexity of a widely used algorithm invented by Adams in 1972 [1]. Our algorithm applies the centroid path decomposition technique [9] in a new way to traverse the input trees\u27 centroid paths in unison, and runs in O(k n log n) time, where k is the number of input trees and n is the size of the leaf label set. (In comparison, the old algorithm from 1972 has a worst-case running time of O(k n^2).) For the special case of k = 2, an even faster algorithm running in O(n cdot frac{log n}{loglog n}) time is provided, which relies on an extension of the wavelet tree-based technique by Bose et al. [6] for orthogonal range counting on a grid. Our extended wavelet tree data structure also supports truncated range maximum queries efficiently and may be of independent interest to algorithm designers

Polyhedral computational geometry for averaging metric phylogenetic trees

This paper investigates the computational geometry relevant to calculations of the Frechet mean and variance for probability distributions on the phylogenetic tree space of Billera, Holmes and Vogtmann, using the theory of probability measures on spaces of nonpositive curvature developed by Sturm. We show that the combinatorics of geodesics with a specified fixed endpoint in tree space are determined by the location of the varying endpoint in a certain polyhedral subdivision of tree space. The variance function associated to a finite subset of tree space has a fixed $C^\infty$ algebraic formula within each cell of the corresponding subdivision, and is continuously differentiable in the interior of each orthant of tree space. We use this subdivision to establish two iterative methods for producing sequences that converge to the Frechet mean: one based on Sturm's Law of Large Numbers, and another based on descent algorithms for finding optima of smooth functions on convex polyhedra. We present properties and biological applications of Frechet means and extend our main results to more general globally nonpositively curved spaces composed of Euclidean orthants.Comment: 43 pages, 6 figures; v2: fixed typos, shortened Sections 1 and 5, added counter example for polyhedrality of vistal subdivision in general CAT(0) cubical complexes; v1: 43 pages, 5 figure

ViCTree: an automated framework for taxonomic classification from protein sequences

Motivation: The increasing rate of submission of genetic sequences into public databases is providing a growing resource for classifying the organisms that these sequences represent. To aid viral classification, we have developed ViCTree, which automatically integrates the relevant sets of sequences in NCBI GenBank and transforms them into an interactive maximum likelihood phylogenetic tree that can be updated automatically. ViCTree incorporates ViCTreeView, which is a JavaScript-based visualisation tool that enables the tree to be explored interactively in the context of pairwise distance data. Results: To demonstrate utility, ViCTree was applied to subfamily Densovirinae of family Parvoviridae. This led to the identification of six new species of insect virus. Availability: ViCTree is open-source and can be run on any Linux- or Unix-based computer or cluster. A tutorial, the documentation and the source code are available under a GPL3 license, and can be accessed at http://bioinformatics.cvr.ac.uk/victree_web/

Characterization of newly isolated lytic bacteriophages active against Acinetobacter baumannii

Based on genotyping and host range, two newly isolated lytic bacteriophages, myovirus vB_AbaM_Acibel004 and podovirus vB_AbaP_Acibel007, active against Acinetobacter baumannii clinical strains, were selected from a new phage library for further characterization. The complete genomes of the two phages were analyzed. Both phages are characterized by broad host range and essential features of potential therapeutic phages, such as short latent period (27 and 21 min, respectively), high burst size (125 and 145, respectively), stability of activity in liquid culture and low frequency of occurrence of phage-resistant mutant bacterial cells. Genomic analysis showed that while Acibel004 represents a novel bacteriophage with resemblance to some unclassified Pseudomonas aeruginosa phages, Acibel007 belongs to the well-characterized genus of the Phikmvlikevirus. The newly isolated phages can serve as potential candidates for phage cocktails to control A. baumannii infections

Extracting Build Changes with BUILDDIFF

Build systems are an essential part of modern software engineering projects. As software projects change continuously, it is crucial to understand how the build system changes because neglecting its maintenance can lead to expensive build breakage. Recent studies have investigated the (co-)evolution of build configurations and reasons for build breakage, but they did this only on a coarse grained level. In this paper, we present BUILDDIFF, an approach to extract detailed build changes from MAVEN build files and classify them into 95 change types. In a manual evaluation of 400 build changing commits, we show that BUILDDIFF can extract and classify build changes with an average precision and recall of 0.96 and 0.98, respectively. We then present two studies using the build changes extracted from 30 open source Java projects to study the frequency and time of build changes. The results show that the top 10 most frequent change types account for 73% of the build changes. Among them, changes to version numbers and changes to dependencies of the projects occur most frequently. Furthermore, our results show that build changes occur frequently around releases. With these results, we provide the basis for further research, such as for analyzing the (co-)evolution of build files with other artifacts or improving effort estimation approaches. Furthermore, our detailed change information enables improvements of refactoring approaches for build configurations and improvements of models to identify error-prone build files.Comment: Accepted at the International Conference of Mining Software Repositories (MSR), 201

Landowners' liability? is perception of the risk of liability for visitors accidents a barrier to countryside access?

The study seeks to analyse both the perception and reality of liability risk for owners of countryside land for injuries suffered by recreational visitors. The study starts by evaluating the relevant legislation and case law in England, Wales, Scotland and Northern Ireland on countryside access and liability in tort for injury suffered by visitors to such places. In doing so it reviews legislation such as Health &amp; Safety at Work Act 1974, Countryside &amp; Rights of Way Act 2000, Land Reform (Scotland) Act 2003, Occupiers' Liability Acts 1957 &amp; 1984, Animals Act 1971 and the Compensation Act 2006. Through appraisal of this legislation and key cases such as Tomlinson -v- Congleton Borough Council (2004) the actual level of liability risk is assessed to be low. The study then investigates the rise of a pervasive discourse amongst policy makers, judiciary and senior business figures asserting the need to avoid further development of a risk adverse culture within the UK and/or to tackle a growth in the perceived "compensation culture". A link to deregulation and pro-entrepreneurship interests is shown. The reality of compensation claim rates and associated behaviours is then examined. Issues of liability risk perception are then addressed by reviewing in detail the limited available UK literature on liability perception by landowners and comparing this with evidence from the United States and New Zealand. Case studies of alleged risk adverse land management are then examined to test the evidence base for common assertions of excess regulation and/or withdrawal of access to land or facilities through fear of liability. Finally, the study explores (via interviews of 21 land managers and representative bodies) how liability risks are actually perceived by land owners and the extent of awareness of recent changes in discourse and case law regarding public safety issues. In doing so the study reveals the ways in which land managers in large pro-access agencies and utilities develop common standards and understandings around the level of "reasonably practicable" safety provision. The study concludes with recommendations for further research to investigate the way in which liability risk perceptions are formed by smaller landowners who are more remote from such "interpretive communities" (Fish 1980).</p