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

A cubic-time algorithm for computing the trinet distance between level-1 networks

In evolutionary biology, phylogenetic networks are constructed to represent the evolution of species in which reticulate events are thought to have occurred, such as recombination and hybridization. It is therefore useful to have efficiently computable metrics with which to systematically compare such networks. Through developing an optimal algorithm to enumerate all trinets displayed by a level-1 network (a type of network that is slightly more general than an evolutionary tree), here we propose a cubic-time algorithm to compute the trinet distance between two level-1 networks. Employing simulations, we also present a comparison between the trinet metric and the so-called Robinson-Foulds phylogenetic network metric restricted to level-1 networks. The algorithms described in this paper have been implemented in JAVA and are freely available at (https://www.uea.ac.uk/computing/TriLoNet

Reconstructing phylogenetic level-1 networks from nondense binet and trinet sets

Binets and trinets are phylogenetic networks with two and three leaves, respectively. Here we consider the problem of deciding if there exists a binary level-1 phylogenetic network displaying a given set T of binary binets or trinets over a taxon set X, and constructing such a network whenever it exists. We show that this is NP-hard for trinets but polynomial-time solvable for binets. Moreover, we show that the problem is still polynomial-time solvable for inputs consisting of binets and trinets as long as the cycles in the trinets have size three. Finally, we present an O(3^{|X|} poly(|X|)) time algorithm for general sets of binets and trinets. The latter two algorithms generalise to instances containing level-1 networks with arbitrarily many leaves, and thus provide some of the first supernetwork algorithms for computing networks from a set of rooted 1 phylogenetic networks

Network and Algebraic Topology of Influenza Evolution

Evolution is a force that has molded human existence since its divergence from chimpanzees about 5.4 million years ago. In that same amount of time, an influenza virus, which replicates every six hours, would have undergone an equivalent number of generations over only a hundred years. The fast replication times of influenza, coupled with its high mutation rate, make the virus a perfect model to study real-time evolution at a mega-Darwin scale, more than a million times faster than human evolution. While recent developments in high-throughput sequencing provide an optimal opportunity to dissect their genetic evolution, a concurrent growth in computational tools is necessary to analyze the large influx of complex genomic data. In my thesis, I present novel computational methods to examine different aspects of influenza evolution. I first focus on seasonal influenza, particularly the problems that hamper public health initiatives to combat the virus. I introduce two new approaches: 1. The q2-coefficient, a method of quantifying pathogen surveillance, and 2. FluGraph, a technique that employs network topology to track the spread of seasonal influenza around the world. The second chapter of my thesis examines how mutations and reassortment combine to alter the course of influenza evolution towards pandemic formation. I highlight inherent deficiencies in the current phylogenetic paradigm for analyzing evolution and offer a novel methodology based on algebraic topology that comprehensively reconstructs both vertical and horizontal evolutionary events. I apply this method to viruses, with emphasis on influenza, but foresee broader application to cancer cells, bacteria, eukaryotes, and other taxa

Superseded: Grammatical theory: From transformational grammar to constraint-based approaches. Second revised and extended edition.

This book is superseded by the third edition, available at http://langsci-press.org/catalog/book/255. This book introduces formal grammar theories that play a role in current linguistic theorizing (Phrase Structure Grammar, Transformational Grammar/Government & Binding, Generalized Phrase Structure Grammar, Lexical Functional Grammar, Categorial Grammar, Head-​Driven Phrase Structure Grammar, Construction Grammar, Tree Adjoining Grammar). The key assumptions are explained and it is shown how the respective theory treats arguments and adjuncts, the active/passive alternation, local reorderings, verb placement, and fronting of constituents over long distances. The analyses are explained with German as the object language. The second part of the book compares these approaches with respect to their predictions regarding language acquisition and psycholinguistic plausibility. The nativism hypothesis, which assumes that humans posses genetically determined innate language-specific knowledge, is critically examined and alternative models of language acquisition are discussed. The second part then addresses controversial issues of current theory building such as the question of flat or binary branching structures being more appropriate, the question whether constructions should be treated on the phrasal or the lexical level, and the question whether abstract, non-visible entities should play a role in syntactic analyses. It is shown that the analyses suggested in the respective frameworks are often translatable into each other. The book closes with a chapter showing how properties common to all languages or to certain classes of languages can be captured. The book is a translation of the German book Grammatiktheorie, which was published by Stauffenburg in 2010. The following quotes are taken from reviews: With this critical yet fair reflection on various grammatical theories, Müller fills what was a major gap in the literature. Karen Lehmann, Zeitschrift für Rezen­sio­nen zur ger­man­is­tis­chen Sprach­wis­senschaft, 2012 Stefan Müller’s recent introductory textbook, Gram­matik­the­o­rie, is an astonishingly comprehensive and insightful survey for beginning students of the present state of syntactic theory. Wolfgang Sternefeld und Frank Richter, Zeitschrift für Sprach­wissen­schaft, 2012 This is the kind of work that has been sought after for a while [...] The impartial and objective discussion offered by the author is particularly refreshing. Werner Abraham, Germanistik, 2012   This book is a new edition of http://langsci-press.org/catalog/book/25

Superseded: Grammatical theory: From transformational grammar to constraint-based approaches. Second revised and extended edition.

This book is superseded by the third edition, available at http://langsci-press.org/catalog/book/255. This book introduces formal grammar theories that play a role in current linguistic theorizing (Phrase Structure Grammar, Transformational Grammar/Government & Binding, Generalized Phrase Structure Grammar, Lexical Functional Grammar, Categorial Grammar, Head-​Driven Phrase Structure Grammar, Construction Grammar, Tree Adjoining Grammar). The key assumptions are explained and it is shown how the respective theory treats arguments and adjuncts, the active/passive alternation, local reorderings, verb placement, and fronting of constituents over long distances. The analyses are explained with German as the object language. The second part of the book compares these approaches with respect to their predictions regarding language acquisition and psycholinguistic plausibility. The nativism hypothesis, which assumes that humans posses genetically determined innate language-specific knowledge, is critically examined and alternative models of language acquisition are discussed. The second part then addresses controversial issues of current theory building such as the question of flat or binary branching structures being more appropriate, the question whether constructions should be treated on the phrasal or the lexical level, and the question whether abstract, non-visible entities should play a role in syntactic analyses. It is shown that the analyses suggested in the respective frameworks are often translatable into each other. The book closes with a chapter showing how properties common to all languages or to certain classes of languages can be captured. The book is a translation of the German book Grammatiktheorie, which was published by Stauffenburg in 2010. The following quotes are taken from reviews: With this critical yet fair reflection on various grammatical theories, Müller fills what was a major gap in the literature. Karen Lehmann, Zeitschrift für Rezen­sio­nen zur ger­man­is­tis­chen Sprach­wis­senschaft, 2012 Stefan Müller’s recent introductory textbook, Gram­matik­the­o­rie, is an astonishingly comprehensive and insightful survey for beginning students of the present state of syntactic theory. Wolfgang Sternefeld und Frank Richter, Zeitschrift für Sprach­wissen­schaft, 2012 This is the kind of work that has been sought after for a while [...] The impartial and objective discussion offered by the author is particularly refreshing. Werner Abraham, Germanistik, 2012   This book is a new edition of http://langsci-press.org/catalog/book/25

Superseded: Grammatical theory: From transformational grammar to constraint-based approaches. Second revised and extended edition.

This book is superseded by the third edition, available at http://langsci-press.org/catalog/book/255. This book introduces formal grammar theories that play a role in current linguistic theorizing (Phrase Structure Grammar, Transformational Grammar/Government & Binding, Generalized Phrase Structure Grammar, Lexical Functional Grammar, Categorial Grammar, Head-​Driven Phrase Structure Grammar, Construction Grammar, Tree Adjoining Grammar). The key assumptions are explained and it is shown how the respective theory treats arguments and adjuncts, the active/passive alternation, local reorderings, verb placement, and fronting of constituents over long distances. The analyses are explained with German as the object language. The second part of the book compares these approaches with respect to their predictions regarding language acquisition and psycholinguistic plausibility. The nativism hypothesis, which assumes that humans posses genetically determined innate language-specific knowledge, is critically examined and alternative models of language acquisition are discussed. The second part then addresses controversial issues of current theory building such as the question of flat or binary branching structures being more appropriate, the question whether constructions should be treated on the phrasal or the lexical level, and the question whether abstract, non-visible entities should play a role in syntactic analyses. It is shown that the analyses suggested in the respective frameworks are often translatable into each other. The book closes with a chapter showing how properties common to all languages or to certain classes of languages can be captured. The book is a translation of the German book Grammatiktheorie, which was published by Stauffenburg in 2010. The following quotes are taken from reviews: With this critical yet fair reflection on various grammatical theories, Müller fills what was a major gap in the literature. Karen Lehmann, Zeitschrift für Rezen­sio­nen zur ger­man­is­tis­chen Sprach­wis­senschaft, 2012 Stefan Müller’s recent introductory textbook, Gram­matik­the­o­rie, is an astonishingly comprehensive and insightful survey for beginning students of the present state of syntactic theory. Wolfgang Sternefeld und Frank Richter, Zeitschrift für Sprach­wissen­schaft, 2012 This is the kind of work that has been sought after for a while [...] The impartial and objective discussion offered by the author is particularly refreshing. Werner Abraham, Germanistik, 2012   This book is a new edition of http://langsci-press.org/catalog/book/25

Grammatical theory

This book introduces formal grammar theories that play a role in current linguistic theorizing (Phrase Structure Grammar, Transformational Grammar/Government & Binding, Generalized Phrase Structure Grammar, Lexical Functional Grammar, Categorial Grammar, Head-​Driven Phrase Structure Grammar, Construction Grammar, Tree Adjoining Grammar). The key assumptions are explained and it is shown how the respective theory treats arguments and adjuncts, the active/passive alternation, local reorderings, verb placement, and fronting of constituents over long distances. The analyses are explained with German as the object language. The second part of the book compares these approaches with respect to their predictions regarding language acquisition and psycholinguistic plausibility. The nativism hypothesis, which assumes that humans posses genetically determined innate language-specific knowledge, is critically examined and alternative models of language acquisition are discussed. The second part then addresses controversial issues of current theory building such as the question of flat or binary branching structures being more appropriate, the question whether constructions should be treated on the phrasal or the lexical level, and the question whether abstract, non-visible entities should play a role in syntactic analyses. It is shown that the analyses suggested in the respective frameworks are often translatable into each other. The book closes with a chapter showing how properties common to all languages or to certain classes of languages can be captured. The book is a translation of the German book Grammatiktheorie, which was published by Stauffenburg in 2010. The following quotes are taken from reviews: With this critical yet fair reflection on various grammatical theories, Müller fills what was a major gap in the literature. Karen Lehmann, Zeitschrift für Rezen­sio­nen zur ger­man­is­tis­chen Sprach­wis­senschaft, 2012 Stefan Müller’s recent introductory textbook, Gram­matik­the­o­rie, is an astonishingly comprehensive and insightful survey for beginning students of the present state of syntactic theory. Wolfgang Sternefeld und Frank Richter, Zeitschrift für Sprach­wissen­schaft, 2012 This is the kind of work that has been sought after for a while [...] The impartial and objective discussion offered by the author is particularly refreshing. Werner Abraham, Germanistik, 201

The Open Anthology of Earlier American Literature

This is an anthology of public domain texts from earlier American literature, collected by students, faculty, and alumnae of Plymouth State University as an OER alternative to expensive commercial anthologies. In addition to content from earlier editions, the 2018 edition adds four new sections: Where is American Literature Now?: Contemporary Connections, Earlier American Literature in Music, Female American (1767) Supplementary Readings, and Letters from an American Farmer (1767) Supplementary Readings. This file represents the state of the work at the end of 2018. Visit to see new and updated material visit https://openeal.pressbooks.com