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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 . -
Visual Component Library VCL Autor: I
Visual Component Library VCL Autor: I. Stepanenko Fecha: Monday 27th of September 2021 04:09:10 PM VCL (Visual Component Library) es un marco de trabajo desarrollado por Borland basado en objetos visuales que tienen como finalidad diseñarframes para las aplicaciones que se han programado para Windows y diseñada bajo el concepto de componente: propiedades, métodos y eventos. Está estructuralmente y visualmente sincronizado con Windows, pues el aspecto de las ventanas, los botones o los accesos a internet, etc. son similares. Actualmente es propiedad de CodeGear, de Embarcadero Technologies. Está escrita en Object Pascal (orientado a objetos) por lo que la VCL es una librería usada por los entornos de desarrollo Delphi y C++ Builder. Al hablar de este tipo de bibliotecas o toolkits, se hace mención implícitamente a la programación orientada a objetos, pues los componentes son clases predeterminadas, haciendo su uso más sencillo, visual y cómodo. Se diferencian dos tipos de componentes. Componentes visuales Entre los visuales se distinguen los botones, las etiquetas, las formas y demás elementos visibles. Componentes no visuales Entre los no visuales están los temporizadores, las conexiones a bases de datos y demás elementos sin interfaz gráfica. Clases más importantes Aunque no todas las clases hacen referencia a componentes concretos algunas realizan tareas de gestión interna y se utilizan como clases bases de las cuales derivan otras clases mediante la herencia. VCL es bastante profundo y complicado; no obstante, las clases que forman la parte superior jerárquica son clases abstractas y son: Artículo descargado de www.masterhacks.net | 1 Visual Component Library VCL Autor: I. -
Rapid Application Development Software | Codegear RAD Studio
RAD Studio 2010 Product Review Guide August 2009 Corporate Headquarters EMEA Headquarters Asia-Pacific Headquarters 100 California Street, 12th Floor York House L7. 313 La Trobe Street San Francisco, California 94111 18 York Road Melbourne VIC 3000 Maidenhead, Berkshire Australia SL6 1SF, United Kingdom RAD Studio 2010 Reviewer Guide TABLE OF CONTENTS Table of Contents ............................................................................................................................ - 1 - Introduction ...................................................................................................................................... - 3 - General Overview of RAD Studio 2010 ...................................................................................... - 3 - What is New in RAD Studio 2010 ............................................................................................... - 3 - A Word on Delphi Prism ............................................................................................................. - 6 - Prerequisites ................................................................................................................................ - 7 - Minimum System Requirements ................................................................................................. - 7 - Internationalizations .................................................................................................................... - 7 - Editions ........................................................................................................................................ -
An Implementation of Python for Racket
An Implementation of Python for Racket Pedro Palma Ramos António Menezes Leitão INESC-ID, Instituto Superior Técnico, INESC-ID, Instituto Superior Técnico, Universidade de Lisboa Universidade de Lisboa Rua Alves Redol 9 Rua Alves Redol 9 Lisboa, Portugal Lisboa, Portugal [email protected] [email protected] ABSTRACT Keywords Racket is a descendent of Scheme that is widely used as a Python; Racket; Language implementations; Compilers first language for teaching computer science. To this end, Racket provides DrRacket, a simple but pedagogic IDE. On the other hand, Python is becoming increasingly popular 1. INTRODUCTION in a variety of areas, most notably among novice program- The Racket programming language is a descendent of Scheme, mers. This paper presents an implementation of Python a language that is well-known for its use in introductory for Racket which allows programmers to use DrRacket with programming courses. Racket comes with DrRacket, a ped- Python code, as well as adding Python support for other Dr- agogic IDE [2], used in many schools around the world, as Racket based tools. Our implementation also allows Racket it provides a simple and straightforward interface aimed at programs to take advantage of Python libraries, thus signif- inexperienced programmers. Racket provides different lan- icantly enlarging the number of usable libraries in Racket. guage levels, each one supporting more advanced features, that are used in different phases of the courses, allowing Our proposed solution involves compiling Python code into students to benefit from a smoother learning curve. Fur- semantically equivalent Racket source code. For the run- thermore, Racket and DrRacket support the development of time implementation, we present two different strategies: additional programming languages [13]. -
POWEROPT. Power Engineering Optimization Techniques Educational Software Library
Available online at www.sciencedirect.com ScienceDirect Procedia - Social and Behavioral Sciences 191 ( 2015 ) 1790 – 1795 WCES 2014 POWEROPT. Power Engineering Optimization Techniques Educational Software Library Stefan Kilyenia, Constantin Barbulescua* aPolitehnica University Timisoara, Power Systems Department, 2 Bd. V, Parvan, 300223 Timisoara, Romania Abstract The power engineering field uses classic operational research methods and the most recent ones are based on artificial intelligence to solve a large number of optimization problems. In this context, this paper presents an optimization technique dedicated to an educational software library. It focuses on solving several optimization applications from the power engineering field. The software library is designed for students involved within the electrical power engineering field, at BSc and MSc levels. © 20152014 TheThe Authors. Authors. Published Published by by Elsevier Elsevier Ltd. Ltd This. is an open access article under the CC BY-NC-ND license (Selectionhttp://creativecommons.org/licenses/by-nc-nd/4.0/ and peer-review under responsibility of). the Organizing Committee of WCES 2014. Selection and peer-review under responsibility of the Organizing Committee of WCES 2014 Keywords:optimization techniques, educational software, power engineering. 1. Introduction The power engineering domain uses both models and classic methods of operational research and the most recent ones are based on artificial intelligence for solving a large number of optimization problems. In this context, this paper presents an optimization software library for the power engineering domain, to solve several applications. The programs use classic operational research methods dedicated for linear and nonlinear optimization problem solving and those specific to graphs theory. The software library synthesizes the experience accumulated in this field at the Politehnica University of Timisoara, Power Systems Department in Romania. -
Common Lispworks User Guide
LispWorks® for the Windows® Operating System Common LispWorks User Guide Version 5.1 Copyright and Trademarks Common LispWorks User Guide (Windows version) Version 5.1 February 2008 Copyright © 2008 by LispWorks Ltd. All Rights Reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording, or otherwise, without the prior written permission of LispWorks Ltd. The information in this publication is provided for information only, is subject to change without notice, and should not be construed as a commitment by LispWorks Ltd. LispWorks Ltd assumes no responsibility or liability for any errors or inaccuracies that may appear in this publication. The software described in this book is furnished under license and may only be used or copied in accordance with the terms of that license. LispWorks and KnowledgeWorks are registered trademarks of LispWorks Ltd. Adobe and PostScript are registered trademarks of Adobe Systems Incorporated. Other brand or product names are the registered trade- marks or trademarks of their respective holders. The code for walker.lisp and compute-combination-points is excerpted with permission from PCL, Copyright © 1985, 1986, 1987, 1988 Xerox Corporation. The XP Pretty Printer bears the following copyright notice, which applies to the parts of LispWorks derived therefrom: Copyright © 1989 by the Massachusetts Institute of Technology, Cambridge, Massachusetts. Permission to use, copy, modify, and distribute this software and its documentation for any purpose and without fee is hereby granted, pro- vided that this copyright and permission notice appear in all copies and supporting documentation, and that the name of M.I.T. -
IDE User Guide Version 7.1 Copyright and Trademarks Lispworks IDE User Guide (Unix Version) Version 7.1 September 2017 Copyright © 2017 by Lispworks Ltd
LispWorks® IDE User Guide Version 7.1 Copyright and Trademarks LispWorks IDE User Guide (Unix version) Version 7.1 September 2017 Copyright © 2017 by LispWorks Ltd. All Rights Reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording, or otherwise, without the prior written permission of LispWorks Ltd. The information in this publication is provided for information only, is subject to change without notice, and should not be construed as a commitment by LispWorks Ltd. LispWorks Ltd assumes no responsibility or liability for any errors or inaccuracies that may appear in this publication. The software described in this book is furnished under license and may only be used or copied in accordance with the terms of that license. LispWorks and KnowledgeWorks are registered trademarks of LispWorks Ltd. Adobe and PostScript are registered trademarks of Adobe Systems Incorporated. Other brand or product names are the registered trade- marks or trademarks of their respective holders. The code for walker.lisp and compute-combination-points is excerpted with permission from PCL, Copyright © 1985, 1986, 1987, 1988 Xerox Corporation. The XP Pretty Printer bears the following copyright notice, which applies to the parts of LispWorks derived therefrom: Copyright © 1989 by the Massachusetts Institute of Technology, Cambridge, Massachusetts. Permission to use, copy, modify, and distribute this software and its documentation for any purpose and without fee is hereby granted, pro- vided that this copyright and permission notice appear in all copies and supporting documentation, and that the name of M.I.T. -
Omnipresent and Low-Overhead Application Debugging
Omnipresent and low-overhead application debugging Robert Strandh [email protected] LaBRI, University of Bordeaux Talence, France ABSTRACT application programmers as opposed to system programmers. The state of the art in application debugging in free Common The difference, in the context of this paper, is that the tech- Lisp implementations leaves much to be desired. In many niques that we suggest are not adapted to debugging the cases, only a backtrace inspector is provided, allowing the system itself, such as the compiler. Instead, throughout this application programmer to examine the control stack when paper, we assume that, as far as the application programmer an unhandled error is signaled. Most such implementations do is concerned, the semantics of the code generated by the not allow the programmer to set breakpoints (unconditional compiler corresponds to that of the source code. or conditional), nor to step the program after it has stopped. In this paper, we are mainly concerned with Common Furthermore, even debugging tools such as tracing or man- Lisp [1] implementations distributed as so-called FLOSS, i.e., ually calling break are typically very limited in that they do \Free, Libre, and Open Source Software". While some such not allow the programmer to trace or break in important sys- implementations are excellent in terms of the quality of the tem functions such as make-instance or shared-initialize, code that the compiler generates, most leave much to be simply because these tools impact all callers, including those desired when it comes to debugging tools available to the of the system itself, such as the compiler. -
Delphi XE2 Feature Matrix
Delphi® XE2 The fastest way to build native applications for Windows, Mac and iOS Feature Matrix Feature Architect Ultimate Enterprise Professional Starter INTEGRATED COMPILERS Enhanced in XE2! High-performance 32-bit optimizing Delphi® native code compiler 23.0 (dcc32), including High performance x86 Assembler – 32-bit inline assembler supporting the Intel® x86 instruction set (including Intel Pentium® Pro, Pentium III, X X X X X Pentium 4, Intel MMX™, SIMD, Streaming SIMD Extensions, SSE, SSE2, SSE3, SSE 4.1, SSE 4.2, AMD SSE4A and AMD® 3DNow!® New in XE2! Delphi 64-bit compiler X X X X New in XE2! Delphi OS X compiler X X X X Delphi command line compiler (dcc32.exe) X X X X Enhanced in XE2! Create 32-bit optimized Delphi native executables that can run X X X X X on both 32 and 64-bit Windows operating systems APPLICATION PLATFORMS, INTEGRATED FRAMEWORKS, DESIGNERS, SDKS AND INSTALLERS New in XE2! FireMonkey Platform for creating 32-bit Windows applications for X X X X X Windows 7, Windows Vista and XP; Server 2003 and 2008. New in XE2! FireMonkey Platform for creating 64-bit Windows applications for X X X X Windows 7, Windows Vista and XP; Server 2003 and 2008. New in XE2! FireMonkey Platform for creating OS X 10.6 and 10.7 applications X X X X New in XE2! FireMonkey Platform for creating applications for iOS 4.2 and higher X X X X New in XE2! VCL (Visual Component Library) for rapidly building 64-bit applications X X X X for Windows 7,Windows Vista and XP; Server 2003 and 2008. -
RAD Studio XE6 Feature Matrix
RAD Studio XE6 The complete app development suite for Windows, Mac, iOS and Android Personality: D = Delphi® C = C++Builder® Feature Matrix H = HTML5 Builder Feature Personality Architect Ultimate Enterprise Professional INTEGRATED COMPILERS AND TOOLCHAINS High-performance 32-bit optimizing Delphi® native code compiler D X X X X (dcc32), including high performance x86 Assembler Delphi 64-bit compiler D X X X X Delphi command line toolchains for Windows (dcc32, dcc64) D X X X X Delphi OS X compiler D X X X X Delphi command line toolchains for Mac OS X (dccosx) D X X X X Introduced in XE4! Delphi iOS ARM Compiler and Delphi iOS D X X X X Compiler for iOS Simulator Introduced in XE4! Delphi command line toolchains for iOS D X X X X (dccios32, dcciosarm) Enhanced in XE5! Embarcadero C++ Compiler for Win64 (bcc64) C X X X X Enhanced in XE5! Embarcadero C++ Compiler for Win32 (bcc32) C X X X X C++ command line toolchains for Windows C X X X X C++ OS X compiler (bccosx) C X X X X C++ command line toolchains for OS X C X X X X Introduced in XE5! C++Builder iOS ARM Compiler C X X X X Introduced in XE5! C++Builder command line toolchain for iOS C X X X X (bcciosarm) New in XE6! C++Builder Android ARM Compiler C X X X X New in XE6! C++Builder command line toolchain for Android C X X X X (bccaarm) APPLICATION PLATFORMS, INTEGRATED FRAMEWORKS, DESIGNERS AND SDKS FMX Application Platform for creating 32-bit Windows applications for Windows 8 and 8.1, Windows 7, and Windows Vista; Server C D X X X X 2008 and 2012. -
Installation Iraf
INSTALLATION IRAF o IRAF: IMAGE REDUCTION AND ANALYSIS FACILITY (NOAO, TUCSON) SCISOFT (IRAF + DS9 + ...) MAC http://scisoftosx.dyndns.org/ LINUX http://www.eso.org/sci/software/scisoft/ P. OCVIRK - COURS DE REDUCTION DES DONNEES - M2 OBSERVATOIRE ASTRONOMIQUE DE STRASBOURG IRAF UBUNTU o DEPENDANCES o IRAF o CONFIG IRAF P. OCVIRK - COURS DE REDUCTION DES DONNEES - M2 OBSERVATOIRE ASTRONOMIQUE DE STRASBOURG INSTALLATION IRAF UBUNTU OCTOBRE 2012 Dependances (a installer avant iraf) o C’est peut-etre la premiere fois que vous devez installer des dependances. Vous aurez peut-etre l’impression de ne pas tout comprendre. Peu importe!! Le but c’est d’avoir iraf qui tourne! o Certaines sont deja presentes. Pour tester leur existence sur votre systeme: locate <ma dependance> o En general elles s’installent grace a apt-get: sudo apt-get install <ma dependance> o En cas de probleme avec une dependance, google est votre ami: faire une recherche “install SDL_image ubuntu” par exemple o Toutes les commandes de cette aide se lancent dans un terminal (ou xterm), la plupart (mais pas toutes!!) en mode super-user. Elles debutent alors par sudo (super-user do). P. OCVIRK - COURS DE REDUCTION DES DONNEES - M2 OBSERVATOIRE ASTRONOMIQUE DE STRASBOURG INSTALLATION IRAF UBUNTU OCTOBRE 2012 Dependances 1 o csh: sudo apt-get install csh o tcsh: sudo apt-get install tcsh o emacs (editeur de textes): sudo apt-get install emacs o SDL_image, SDL_ttf, libgfortran: deja installees? (me contacter si elles n’apparaissent pas avec un locate) P. OCVIRK - COURS DE REDUCTION DES DONNEES - M2 OBSERVATOIRE ASTRONOMIQUE DE STRASBOURG INSTALLATION IRAF UBUNTU OCTOBRE 2012 Dependances 2: le cas particuler de compat-libf2c-34. -
Proceedings of the 8Th European Lisp Symposium Goldsmiths, University of London, April 20-21, 2015 Julian Padget (Ed.) Sponsors
Proceedings of the 8th European Lisp Symposium Goldsmiths, University of London, April 20-21, 2015 Julian Padget (ed.) Sponsors We gratefully acknowledge the support given to the 8th European Lisp Symposium by the following sponsors: WWWLISPWORKSCOM i Organization Programme Committee Julian Padget – University of Bath, UK (chair) Giuseppe Attardi — University of Pisa, Italy Sacha Chua — Toronto, Canada Stephen Eglen — University of Cambridge, UK Marc Feeley — University of Montreal, Canada Matthew Flatt — University of Utah, USA Rainer Joswig — Hamburg, Germany Nick Levine — RavenPack, Spain Henry Lieberman — MIT, USA Christian Queinnec — University Pierre et Marie Curie, Paris 6, France Robert Strandh — University of Bordeaux, France Edmund Weitz — University of Applied Sciences, Hamburg, Germany Local Organization Christophe Rhodes – Goldsmiths, University of London, UK (chair) Richard Lewis – Goldsmiths, University of London, UK Shivi Hotwani – Goldsmiths, University of London, UK Didier Verna – EPITA Research and Development Laboratory, France ii Contents Acknowledgments i Messages from the chairs v Invited contributions Quicklisp: On Beyond Beta 2 Zach Beane µKanren: Running the Little Things Backwards 3 Bodil Stokke Escaping the Heap 4 Ahmon Dancy Unwanted Memory Retention 5 Martin Cracauer Peer-reviewed papers Efficient Applicative Programming Environments for Computer Vision Applications 7 Benjamin Seppke and Leonie Dreschler-Fischer Keyboard? How quaint. Visual Dataflow Implemented in Lisp 15 Donald Fisk P2R: Implementation of