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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. -
PC-BSD Quick Guide.Pdf
PC-BSD Quick Guide file:///E:/Documents%20and%20Settings/Owner/Desktop/PC-BSD%20Q... PC-BSD Quick Guide This quick start guide is aimed at users new to PC-BSD, FreeBSD and Unix in general. It is under constant development, and you will probably find mistakes in this guide. Whenever you find errors, feel free to report them on the documentation forum. For the latest and most up-to-date version please visit the Quick Guide online. Alternatively you can also download this file as PDF. We hope this guide is both simple and useful and make using PC-BSD an enjoyable experience. If you have suggestions for PC-BSD, you can either let us know on the forum, or send us an e-mail to: [email protected] , we value your opinion. Thank you for your support. Table of contents 1. Introduction 1.1. Welcome to PC-BSD 1.2. Differences between PC-BSD and FreeBSD 1.3. Microsoft Windows vs PC-BSD 1.4. PC-BSD's goals 1.5. Reasons for using PC-BSD 1.6. PC-BSD's cutting-edge features 1.7. Package Management 1.8. Summary of PC-BSD's features 1.9. More features (advanced/technical) 1.10. PC-BSD Releases 1.11. Where can I get help? 1.12. Additional resources 2. Installation 2.1. Requirements 2.2. Creation of the CD-ROM 2.3. Installation 2.4. Starting up PC-BSD 2.5. Network configuration 2.6. Post-installation 2.7. Windows Software 2.8. Troubleshooting 3. Workspace 3.1. Applications 3.2. -
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. -
Manuel De Juk
Manuel de JuK Lauri Watts Michael Pyne Scott Wheeler Traduction française : Robert Jacolin Traduction française : Ludovic Grossard Relecture de la documentation française : Ludovic Grossard Manuel de JuK 2 Table des matières 1 Introduction 5 2 Utiliser JuK 6 2.1 La liste des chansons . .7 2.2 Listes de lecture de JuK . .9 2.3 L’éditeur d’étiquettes de JuK . 10 2.3.1 Modifier les étiquettes d’un unique fichier . 10 2.3.2 Modification d’étiquettes dans plusieurs fichiers . 11 2.4 La boîte de dialogue pour renommer les fichiers . 12 2.5 La boîte de dialogue de configuration du devineur d’étiquettes . 13 2.6 La boîte de dialogue de recherche avancée . 14 3 La barre d’outils de JuK 15 3.1 La barre principale . 15 3.2 La barre de recherche . 16 4 Référence du menu et des commandes 17 4.1 Menus . 17 4.1.1 Menu Fichier . 17 4.1.2 Menu Édition . 18 4.1.3 Menu Affichage . 18 4.1.4 Menu Lecteur . 19 4.1.5 Menu Éditeur d’en-tête . 19 4.1.6 Menu Configuration . 20 4.2 Référence des raccourcis clavier . 21 5 Remerciements et licence 22 Résumé JuK est un juke-box, un éditeur d’étiquettes et un gestionnaire de discothèque. Manuel de JuK Chapitre 1 Introduction JuK est un vrai juke-box. Comme la plupart des applications juke-box, JuK vous permet de mo- difier les “étiquettes” de vos fichiers audio et de gérer votre collection et vos listes de lecture. 5 Manuel de JuK Chapitre 2 Utiliser JuK JuK maintient une liste de tous les fichiers qu’il connaît. -
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, -
Why Be a KDE Project? Martin Klapetek David Edmundson
Why be a KDE Project? Martin Klapetek David Edmundson What is KDE? KDE is not a desktop, it's a community „Community of technologists, designers, writers and advocates who work to ensure freedom for all people through our software“ --The KDE Manifesto What is a KDE Project? Project needs more than just good code What will you get as a KDE Project? Git repository Git repository plus „scratch repos“ (your personal playground) Creating a scratch repo git push –all kde:scratch/username/reponame Git repository plus web interface (using GitPHP) Git repository plus migration from Gitorious.org Bugzilla (the slightly prettier version) Review Board Integration of git with Bugzilla and Review Board Integration of git with Bugzilla and Review Board Using server-side commit hooks ● BUG: 24578 ● CCBUG: 29456 ● REVIEW: 100345 ● CCMAIL: [email protected] Communication tools Mailing lists Wiki pages Forums Single sign-on to all services Official IRC channels #kde-xxxxx (on Freenode) IRC cloak me@kde/developer/mklapetek [email protected] email address Support from sysadmin team Community support Development support Translations (71 translation teams) Testing support (Active Jenkins and EBN servers, plus Quality Team) Project continuation (when you stop developing it) KDE e.V. support Financial and organizational help Trademark security Project's licence defense via FLA Promo support Stories in official KDE News site (Got the Dot?) Your blog aggregated at Planet KDE Promo through social channels Web hosting under kde.org domain Association with one of the best -
KDE Galaxy 4.13
KDE Galaxy 4.13 - Devaja Shah About Me ●3rd Year Alienatic Student at DA- !"# Gandhinagar ●Dot-editor %or KDE &romo "ea' ●Member of KDE e.(. ●&a))ion for Technology# Literature ●+un the Google Developer Group in !olle$e ●-rganizin$ Tea' of KDE Meetup# con%./de.in 14 -/ay, sooooo....... ●Ho1 many of you are %an) of Science Fiction3 ●Astronomy3 ● 0o1 is it Related to KDE3 ●That i) precisely 1hat the talk is about. ●Analogy to $et you to kno1 everythin$ that you should about ● “Galaxy KDE 4.13” 4ait, isn't it 4.14? ●KDE5) late)t ver)ion S! 4.14 6 7ove'ber 8914 ●KDE Soft1are !o',ilation ::.xx ●Significance o% +elea)e) ●- -r$ani.ed# )y)te'atic co',ilation o% %eature) < develo,'ent) ●- 2ive )erie) of relea)e) till date. ●7o Synchronized +elea)e) Any lon$er: ● - KDE 2ra'e1ork) > ?'onthly@ ● - KDE &la)'a > ?3 'onth)@ ● - KDE Ap,lication) ?date ba)ed@ ●Au)t *i/e Ap, (er)ion) But, 1hat am I to do o% the Galaxy 7umber? ●4ork in a "eam ●4ork acros) a Deadline ●-%;ce Space Si'ulation ●Added 'petus %or Deliverin$ your 2eature) ●You 1ork a) a ,art of the C!oreD Developer "ea' ● nstils Discipline ●Better +e),onse# Better 2eedbac/ ●Better Deliverance ●Synchronized 1ork with other C)ea)onedD developer) Enough of the bore....... ●Ho1 do $et started3 ● - Hope you didn't )nooze yesterday ● +!# Subscribe to Mailing Lists ●Mentoring Progra') ●GsoC# Season of KDE, O2W Progra') ●Bootstra,pin$ Training Session) Strap yourself onto the Rocket ●And Blast O%%......... ● ● ● Entered A 4ormhole and Ea,ped into the KDE Galaxy ●No1 what? ●Pick a Planet to nhabit ●But.... -
Linux: Come E Perchх
ÄÒÙÜ Ô ©2007 mcz 12 luglio 2008 ½º I 1. Indice II ½º Á ¾º ¿º ÈÖÞÓÒ ½ º È ÄÒÙÜ ¿ º ÔÔÖÓÓÒÑÒØÓ º ÖÒÞ ×Ó×ØÒÞÐ ÏÒÓÛ× ¾½ º ÄÒÙÜ ÕÙÐ ×ØÖÙÞÓÒ ¾ º ÄÒÙÜ ÀÖÛÖ ×ÙÔÔ ÓÖØØÓ ¾ º È Ð ÖÒÞ ØÖ ÖÓ ÓØ Ù×Ö ¿½ ½¼º ÄÒÙÜ × Ò×ØÐÐ ¿¿ ½½º ÓÑ × Ò×ØÐÐÒÓ ÔÖÓÖÑÑ ¿ ½¾º ÒÓÒ ØÖÓÚÓ ÒÐ ×ØÓ ÐÐ ×ØÖÙÞÓÒ ¿ ½¿º Ó׳ ÙÒÓ ¿ ½º ÓÑ × Ð ××ØÑ ½º ÓÑ Ð ½º Ð× Ñ ½º Ð Ñ ØÐ ¿ ½º ÐÓ ½º ÓÑ × Ò×ØÐÐ Ð ×ØÑÔÒØ ¾¼º ÓÑ ÐØØÖ¸ Ø×Ø ÐÖ III Indice ¾½º ÓÑ ÚÖ Ð ØÐÚ×ÓÒ ¿ 21.1. Televisioneanalogica . 63 21.2. Televisione digitale (terrestre o satellitare) . ....... 64 ¾¾º ÐÑØ ¾¿º Ä 23.1. Fotoritocco ............................. 67 23.2. Grafica3D.............................. 67 23.3. Disegnovettoriale-CAD . 69 23.4.Filtricoloreecalibrazionecolori . .. 69 ¾º ×ÖÚ Ð ½ 24.1.Vari.................................. 72 24.2. Navigazionedirectoriesefiles . 73 24.3. CopiaCD .............................. 74 24.4. Editaretesto............................. 74 24.5.RPM ................................. 75 ¾º ×ÑÔ Ô ´ËÐе 25.1.Montareundiscoounapenna . 77 25.2. Trovareunfilenelsistema . 79 25.3.Vedereilcontenutodiunfile . 79 25.4.Alias ................................. 80 ¾º × ÚÓÐ×× ÔÖÓÖÑÑÖ ½ ¾º ÖÓÛ×Ö¸ ÑÐ ººº ¿ ¾º ÖÛÐРгÒØÚÖÙ× Ð ÑØØÑÓ ¾º ÄÒÙÜ ½ ¿¼º ÓÑ ØÖÓÚÖ ÙØÓ ÖÖÑÒØ ¿ ¿½º Ð Ø×ØÙÐ Ô Ö Ð ×ØÓÔ ÄÒÙÜ ¿¾º ´ÃµÍÙÒØÙ¸ ÙÒ ×ØÖÙÞÓÒ ÑÓÐØÓ ÑØ ¿¿º ËÙÜ ÙÒ³ÓØØÑ ×ØÖÙÞÓÒ ÄÒÙÜ ½¼½ ¿º Á Ó Ò ÄÒÙÜ ½¼ ¿º ÃÓÒÕÙÖÓÖ¸ ÕÙ×ØÓ ½¼ ¿º ÃÓÒÕÙÖÓÖ¸ Ñ ØÒØÓ Ô Ö ½½¿ 36.1.Unaprimaocchiata . .114 36.2.ImenudiKonqueror . .115 36.3.Configurazione . .116 IV Indice 36.4.Alcuniesempidiviste . 116 36.5.Iservizidimenu(ServiceMenu) . 119 ¿º ÃÓÒÕÙÖÓÖ Ø ½¾¿ ¿º à ÙÒ ÖÖÒØ ½¾ ¿º à ÙÒ ÐÙ×ÓÒ ½¿½ ¼º ÓÒÖÓÒØÓ Ò×ØÐÐÞÓÒ ÏÒÓÛ×È ÃÍÙÒØÙ º½¼ ½¿¿ 40.1. -
Dolphin Power Tools User's Guide Rev E
Dolphin® Power Tools For Windows Mobile® 5.0 Windows Mobile® 2003 Second Edition Windows® CE 5.0 (Dolphin 6100, 6500, 7600) User’s Guide Disclaimer Honeywell International Inc. (“HII”) reserves the right to make changes in specifications and other information contained in this document without prior notice, and the reader should in all cases consult HII to determine whether any such changes have been made. The information in this publication does not represent a commitment on the part of HII. HII shall not be liable for technical or editorial errors or omissions contained herein; nor for incidental or consequential damages resulting from the furnishing, performance, or use of this material. This document contains proprietary information that is protected by copyright. All rights are reserved. No part of this document may be photocopied, reproduced, or translated into another language without the prior written consent of HII. ©2007–2010 Honeywell International Inc. All rights reserved. Web Address: www.honeywellaidc.com Trademarks Dolphin, Dolphin RF, HomeBase, Mobile Base, and QuadCharger are trademarks or registered trademarks of Hand Held Products, Inc. or Honeywell International Inc. Microsoft, Windows, Windows Mobile, Windows CE, Windows NT, Windows 2000, Windows ME, Windows XP, ActiveSync, Outlook, and the Windows logo are trademarks or registered trademarks of Microsoft Corporation. Other product names mentioned in this manual may be trademarks or registered trademarks of their respective companies and are the property of their respective owners. Patents Please refer to the product packaging for a list of patents. Other Trademarks The Bluetooth trademarks are owned by Bluetooth SIG, Inc. U.S.A.