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Lecture Notes: the Mathematics of Phylogenetics
Lecture Notes: The Mathematics of Phylogenetics Elizabeth S. Allman, John A. Rhodes IAS/Park City Mathematics Institute June-July, 2005 University of Alaska Fairbanks Spring 2009, 2012, 2016 c 2005, Elizabeth S. Allman and John A. Rhodes ii Contents 1 Sequences and Molecular Evolution 3 1.1 DNA structure . .4 1.2 Mutations . .5 1.3 Aligned Orthologous Sequences . .7 2 Combinatorics of Trees I 9 2.1 Graphs and Trees . .9 2.2 Counting Binary Trees . 14 2.3 Metric Trees . 15 2.4 Ultrametric Trees and Molecular Clocks . 17 2.5 Rooting Trees with Outgroups . 18 2.6 Newick Notation . 19 2.7 Exercises . 20 3 Parsimony 25 3.1 The Parsimony Criterion . 25 3.2 The Fitch-Hartigan Algorithm . 28 3.3 Informative Characters . 33 3.4 Complexity . 35 3.5 Weighted Parsimony . 36 3.6 Recovering Minimal Extensions . 38 3.7 Further Issues . 39 3.8 Exercises . 40 4 Combinatorics of Trees II 45 4.1 Splits and Clades . 45 4.2 Refinements and Consensus Trees . 49 4.3 Quartets . 52 4.4 Supertrees . 53 4.5 Final Comments . 54 4.6 Exercises . 55 iii iv CONTENTS 5 Distance Methods 57 5.1 Dissimilarity Measures . 57 5.2 An Algorithmic Construction: UPGMA . 60 5.3 Unequal Branch Lengths . 62 5.4 The Four-point Condition . 66 5.5 The Neighbor Joining Algorithm . 70 5.6 Additional Comments . 72 5.7 Exercises . 73 6 Probabilistic Models of DNA Mutation 81 6.1 A first example . 81 6.2 Markov Models on Trees . 87 6.3 Jukes-Cantor and Kimura Models . -
Organizace a Vybavení Vojska V 15. Století: Paralelní Vývoj Ve Francii, Burgundsku a St Řední Evrop Ě
UNIVERZITA KARLOVA V PRAZE FILOZOFICKÁ FAKULTA ÚSTAV ČESKÝCH D ĚJIN HISTORICKÉ V ĚDY Jan Biederman Organizace a vybavení vojska v 15. století: paralelní vývoj ve Francii, Burgundsku a st řední Evrop ě Organization and equipment of the army in 15 th century: parallel development in France, Burgundy and in the Central Europe DISERTA ČNÍ PRÁCE VEDOUCÍ DISERTA ČNÍ PRÁCE: doc. PhDr. Martin Nejedlý, Dr. PRAHA 2015 Prohlašuji, že jsem diserta ční práci napsal samostatn ě s využitím uvedených a řádn ě citovaných pramen ů a literatury a že práce nebyla využita v rámci jiného vysokoškolského studia či k získání jiného nebo stejného titulu. V Praze, dne 28. července 2015 ................................................. Klí čová slova ( česky) organizace vojska – zásobování – zbrojní výroba a výzbroj – palné zbran ě – transport Klí čová slova (anglicky) military organization – food supply – weapons production and armament – firearms – transport Abstrakt Organizace a vybavení vojska v 15. století: paralelní vývoj ve Francii, Burgundsku a st řední Evrop ě Tak jako v jiných epochách, i v pozdním st ředov ěku m ěla na kvalitách vojska klí čový podíl forma vojenské organizace, zajišt ění zásobování, technické možnosti a podmínky transportu a samoz řejm ě i povaha výzbroje. V této souvislosti byly d ůležité také dobové technické možnosti zbrojní výroby, obchodu se zbran ěmi a v neposlední řad ě též p řístup k progresivn ě se rozvíjející složce výzbroje, jíž p ředstavovaly palné zbran ě. Zám ěrem této práce je vzhledem ke zmín ěným tematickým okruh ům komparace oblasti st řední Evropy s důrazem na české zem ě a frankofonního západu Evropy, zastoupeného francouzským královstvím spolu s burgundským vévodstvím. -
Red Hat Enterprise Linux 6 Developer Guide
Red Hat Enterprise Linux 6 Developer Guide An introduction to application development tools in Red Hat Enterprise Linux 6 Dave Brolley William Cohen Roland Grunberg Aldy Hernandez Karsten Hopp Jakub Jelinek Developer Guide Jeff Johnston Benjamin Kosnik Aleksander Kurtakov Chris Moller Phil Muldoon Andrew Overholt Charley Wang Kent Sebastian Red Hat Enterprise Linux 6 Developer Guide An introduction to application development tools in Red Hat Enterprise Linux 6 Edition 0 Author Dave Brolley [email protected] Author William Cohen [email protected] Author Roland Grunberg [email protected] Author Aldy Hernandez [email protected] Author Karsten Hopp [email protected] Author Jakub Jelinek [email protected] Author Jeff Johnston [email protected] Author Benjamin Kosnik [email protected] Author Aleksander Kurtakov [email protected] Author Chris Moller [email protected] Author Phil Muldoon [email protected] Author Andrew Overholt [email protected] Author Charley Wang [email protected] Author Kent Sebastian [email protected] Editor Don Domingo [email protected] Editor Jacquelynn East [email protected] Copyright © 2010 Red Hat, Inc. and others. The text of and illustrations in this document are licensed by Red Hat under a Creative Commons Attribution–Share Alike 3.0 Unported license ("CC-BY-SA"). An explanation of CC-BY-SA is available at http://creativecommons.org/licenses/by-sa/3.0/. In accordance with CC-BY-SA, if you distribute this document or an adaptation of it, you must provide the URL for the original version. Red Hat, as the licensor of this document, waives the right to enforce, and agrees not to assert, Section 4d of CC-BY-SA to the fullest extent permitted by applicable law. -
Ubuntu Kung Fu
Prepared exclusively for Alison Tyler Download at Boykma.Com What readers are saying about Ubuntu Kung Fu Ubuntu Kung Fu is excellent. The tips are fun and the hope of discov- ering hidden gems makes it a worthwhile task. John Southern Former editor of Linux Magazine I enjoyed Ubuntu Kung Fu and learned some new things. I would rec- ommend this book—nice tips and a lot of fun to be had. Carthik Sharma Creator of the Ubuntu Blog (http://ubuntu.wordpress.com) Wow! There are some great tips here! I have used Ubuntu since April 2005, starting with version 5.04. I found much in this book to inspire me and to teach me, and it answered lingering questions I didn’t know I had. The book is a good resource that I will gladly recommend to both newcomers and veteran users. Matthew Helmke Administrator, Ubuntu Forums Ubuntu Kung Fu is a fantastic compendium of useful, uncommon Ubuntu knowledge. Eric Hewitt Consultant, LiveLogic, LLC Prepared exclusively for Alison Tyler Download at Boykma.Com Ubuntu Kung Fu Tips, Tricks, Hints, and Hacks Keir Thomas The Pragmatic Bookshelf Raleigh, North Carolina Dallas, Texas Prepared exclusively for Alison Tyler Download at Boykma.Com Many of the designations used by manufacturers and sellers to distinguish their prod- ucts are claimed as trademarks. Where those designations appear in this book, and The Pragmatic Programmers, LLC was aware of a trademark claim, the designations have been printed in initial capital letters or in all capitals. The Pragmatic Starter Kit, The Pragmatic Programmer, Pragmatic Programming, Pragmatic Bookshelf and the linking g device are trademarks of The Pragmatic Programmers, LLC. -
Resumen Los Widgets, Pequeñas Aplicaciones De Escritorio, Se Han Convertido En Objeto De Estudio Para Este Trabajo
Resumen Los widgets, pequeñas aplicaciones de escritorio, se han convertido en objeto de estudio para este trabajo. Se ha analizado y estudiado su entorno, funcionamiento y estructura. Como resultado se ha obtenido una definición del concepto de widget, con diferentes ejemplos prácticos, y una comparativa entre las compañías más destacadas que ofrecen widgets (Apple, Microsoft, Yahoo!, Google y Opera) así como de las diferencias a nivel de estructura e implementación que se encuentran entre sus widgets. En el apartado de estudio también se ha dado atención a los usuarios de estas aplicaciones, explicando cuáles son sus necesidades, costumbres y posibilidades de elección en este campo. Otro de los apartados trata de cubrir algunas de las tecnologías más relevantes implicadas en la creación posterior de un widget, la aplicación Dashcode, el lenguaje de programación JavaScript, y los canales RSS. El tema de los widgets también ha dado lugar a todo un apartado de desarrollo. Se ha creado un widget para la plataforma de Apple, Macintosh. El widget proporciona al usuario las últimas noticias y resultados del mundo deportivo, concretamente de dos deportes, fútbol y baloncesto. Todas las fases del proceso de creación del widget han sido descritas de principio a fin, desde los bocetos iniciales a la puesta en funcionamiento, pasando por el prototipado e implementación. De manera adicional, también se ha incluido un apartado dedicado al diseño de widgets, con algunas y consejos a tener en cuenta al diseñar widgets en general. Por último se han vertido diferentes conclusiones fruto del presente trabajo y de la reflexión sobre la situación actual de este campo, sin olvidar los aspectos a mejorar, las áreas en que se está trabajando y las perspectivas de futuro. -
106 INKSCAPE – FREE VECTOR GRAPHICS EDITOR Grabareva A
INKSCAPE – FREE VECTOR GRAPHICS EDITOR Grabareva A. Supervisor: Voevodina M. E-mail: [email protected], [email protected] Kharkiv, О.М. Beketov National University of Urban Economy in Kharkiv Inkscape is a cross-platform, powerful enough and in many ways competitive free vector graphics editor with open source code, and in which the SVG format is used as the main standard for work. It is convenient for creating both artistic and technical illustrations. Inkscape is an analogue of such graphic editors as Corel Draw, Adobe Illustrator, Xara X and Freehand. Intended use: - illustrations for office circulars, presentations, creation of logos, business cards, posters; - technical illustrations (diagrams, graphics, etc.); - vector graphics for high-quality printing (with preliminary import of SVG into Scribus); - web graphics – from banners to site layouts, icons for applications and website buttons, - graphics for games. Main characteristics of Inkscape: - the program is free and distributed under the GNU General Public License; - cross-platform; - the program supports the following document formats: import – almost all popular and frequently used formats: SVG, JPEG, GIF, BMP, EPS, PDF, PNG, ICO, and many additional ones, such as SVGZ, EMF, PostScript, AI, Dia, Sketch, TIFF, XPM, WMF, WPG, GGR, ANI, CUR, PCX, PNM, RAS, TGA, WBMP, XBM, XPM; export – the main formats are PNG and SVG and many additional EPS, PostScript, PDF, Dia, AI, Sketch, POV-Ray, LaTeX, OpenDocument Draw, GPL, EMF, POV, DXF; - there is support for layers; - -
The GNOME Census: Who Writes GNOME?
The GNOME Census: Who writes GNOME? Dave Neary & Vanessa David, Neary Consulting © Neary Consulting 2010: Some rights reserved Table of Contents Introduction.........................................................................................3 What is GNOME?.............................................................................3 Project governance...........................................................................3 Why survey GNOME?.......................................................................4 Scope and methodology...................................................................5 Tools and Observations on Data Quality..........................................7 Results and analysis...........................................................................10 GNOME Project size.......................................................................10 The Long Tail..................................................................................11 Effects of commercialisation..........................................................14 Who does the work?.......................................................................15 Who maintains GNOME?................................................................17 Conclusions........................................................................................22 References.........................................................................................24 Appendix 1: Modules included in survey...........................................25 2 Introduction What -
Release Notes for Fedora 15
Fedora 15 Release Notes Release Notes for Fedora 15 Edited by The Fedora Docs Team Copyright © 2011 Red Hat, Inc. and others. The text of and illustrations in this document are licensed by Red Hat under a Creative Commons Attribution–Share Alike 3.0 Unported license ("CC-BY-SA"). An explanation of CC-BY-SA is available at http://creativecommons.org/licenses/by-sa/3.0/. The original authors of this document, and Red Hat, designate the Fedora Project as the "Attribution Party" for purposes of CC-BY-SA. In accordance with CC-BY-SA, if you distribute this document or an adaptation of it, you must provide the URL for the original version. Red Hat, as the licensor of this document, waives the right to enforce, and agrees not to assert, Section 4d of CC-BY-SA to the fullest extent permitted by applicable law. Red Hat, Red Hat Enterprise Linux, the Shadowman logo, JBoss, MetaMatrix, Fedora, the Infinity Logo, and RHCE are trademarks of Red Hat, Inc., registered in the United States and other countries. For guidelines on the permitted uses of the Fedora trademarks, refer to https:// fedoraproject.org/wiki/Legal:Trademark_guidelines. Linux® is the registered trademark of Linus Torvalds in the United States and other countries. Java® is a registered trademark of Oracle and/or its affiliates. XFS® is a trademark of Silicon Graphics International Corp. or its subsidiaries in the United States and/or other countries. MySQL® is a registered trademark of MySQL AB in the United States, the European Union and other countries. All other trademarks are the property of their respective owners. -
How-To Gnome-Look Guide
HHOOWW--TTOO Written by David D Lowe GGNNOOMMEE--LLOOOOKK GGUUIIDDEE hen I first joined the harddisk, say, ~/Pictures/Wallpapers. right-clicking on your desktop Ubuntu community, I and selecting the appropriate You may have noticed that gnome- button (you know which one!). Wwas extremely look.org separates wallpapers into impressed with the amount of different categories, according to the customization Ubuntu had to size of the wallpaper in pixels. For Don't let acronyms intimidate offer. People posted impressive the best quality, you want this to you; you don't have to know screenshots, and mentioned the match your screen resolution. If you what the letters stand for to themes they were using. They don't know what your screen know what it is. Basically, GTK is soon led me to gnome-look.org, resolution is, click System > the system GNOME uses to the number one place for GNOME Preferences > Screen Resolution. display things like buttons and visual customization. The However, Ubuntu stretches controls. GNOME is Ubuntu's screenshots there looked just as wallpapers quite nicely if you picked default desktop environment. I impressive, but I was very the wrong size, so you needn't fret will only be dealing with GNOME confused as to what the headings about it. on the sidebar meant, and I had customization here--sorry no idea how to use the files I SVG is a special image format that Kubuntu and Xubuntu folks! downloaded. Hopefully, this guide doesn't use pixels; it uses shapes Gnome-look.org distinguishes will help you learn what I found called vectors, which means you can between two versions of GTK: out the slow way. -
Kde-Guide-De-Developpement.Web.Pdf
KDE Published : 2017-06-26 License : GPLv2+ 1 KDE DU POINT DE VUE D'UN DÉVELOPPEUR 1. AVEZ-VOUS BESOIN DE CE LIVRE ? 2. LA PHILOSOPHIE DE KDE 3. COMMENT OBTENIR DE L'AIDE 2 1. AVEZ-VOUS BESOIN DE CE LIVRE ? Vous devriez lire ce livre si vous voulez développer pour KDE. Nous utilisons le terme développement très largement pour couvrir tout ce qui peut conduire à un changement dans le code source, ce qui inclut : Soumettre une correction de bogue Écrire une nouvelle application optimisée par la technologie KDE Contribuer à un projet existant Ajouter de la fonctionnalité aux bibliothèques de développement de KDE Dans ce livre, nous vous livrerons les bases dont vous avez besoin pour être un développeur productif. Nous décrirons les outils que vous devrez installer, montrer comment lire la documentation (et écrire la vôtre propre, une fois que vous aurez créé la nouvelle fonctionnalité !) et comment obtenir de l'aide par d'autres moyens. Nous vous présenterons la communauté KDE, qui est essentielle pour comprendre KDE parce que nous sommes un projet « open source », libre (gratuit). Les utilisateurs finaux du logiciel n'ont PAS besoin de ce livre ! Cependant, ils pourraient le trouver intéressant pour les aider à comprendre comment les logiciels complexes et riches en fonctionnalités qu'ils utilisent ont vu le jour. 3 2. LA PHILOSOPHIE DE KDE Le succès de KDE repose sur une vue globale, que nous avons trouvée à la fois pratique et motivante. Les éléments de cette philosophie de développement comprennent : L'utilisation des outils disponibles plutôt que de ré-inventer ceux existants : beaucoup des bases dont vous avez besoin pour travailler font déjà partie de KDE, comme les bibliothèques principales ou les « Kparts », et sont tout à fait au point. -
The Glib/GTK+ Development Platform
The GLib/GTK+ Development Platform A Getting Started Guide Version 0.8 Sébastien Wilmet March 29, 2019 Contents 1 Introduction 3 1.1 License . 3 1.2 Financial Support . 3 1.3 Todo List for this Book and a Quick 2019 Update . 4 1.4 What is GLib and GTK+? . 4 1.5 The GNOME Desktop . 5 1.6 Prerequisites . 6 1.7 Why and When Using the C Language? . 7 1.7.1 Separate the Backend from the Frontend . 7 1.7.2 Other Aspects to Keep in Mind . 8 1.8 Learning Path . 9 1.9 The Development Environment . 10 1.10 Acknowledgments . 10 I GLib, the Core Library 11 2 GLib, the Core Library 12 2.1 Basics . 13 2.1.1 Type Definitions . 13 2.1.2 Frequently Used Macros . 13 2.1.3 Debugging Macros . 14 2.1.4 Memory . 16 2.1.5 String Handling . 18 2.2 Data Structures . 20 2.2.1 Lists . 20 2.2.2 Trees . 24 2.2.3 Hash Tables . 29 2.3 The Main Event Loop . 31 2.4 Other Features . 33 II Object-Oriented Programming in C 35 3 Semi-Object-Oriented Programming in C 37 3.1 Header Example . 37 3.1.1 Project Namespace . 37 3.1.2 Class Namespace . 39 3.1.3 Lowercase, Uppercase or CamelCase? . 39 3.1.4 Include Guard . 39 3.1.5 C++ Support . 39 1 3.1.6 #include . 39 3.1.7 Type Definition . 40 3.1.8 Object Constructor . 40 3.1.9 Object Destructor . -
Metadata Track Akonadi the Independent Solution for PIM Data
Akonadi – The independent solution for PIM GCDS 2009 data Metadata track Akonadi the independent solution for PIM data Will Stephenson Will Stephenson Akonadi – The independent solution for PIM GCDS 2009 data Akonadi Topics Akona-what? Design Overview What we give you What you give us Will Stephenson Akonadi – The independent solution for PIM GCDS 2009 data Akonadi The story so far Monolithic apps Own data storage Limited if any external interfaces E-D-S Data storage service Limited range of types supported Will Stephenson Akonadi – The independent solution for PIM GCDS 2009 data Why? Limitations of KDE3 KResource framework limitations: Data is not shared Designed for synchronous access Hard to extend to other data types Basically no shared common code KMail limitations: Only limited backend abstraction Designed for small amounts of local data Will Stephenson Akonadi – The independent solution for PIM GCDS 2009 data Scalability with KDE 3 |Data| = small Contact applet KAddressBook l l KMail Kopete Will Stephenson Akonadi – The independent solution for PIM GCDS 2009 data Scalability in KDE 3 |Data| = large Contact applet KAddressBook l l KMail Kopete Will Stephenson Akonadi – The independent solution for PIM GCDS 2009 data Why? Goals As much as possible shared, type independent functionality Easy to extend to new data types Unified API to access PIM data, independent of the actual data source Scalability Will Stephenson Akonadi – The independent solution for PIM GCDS 2009 data Why? Goals One synchronization point for mobile devices Reliable,