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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 . -
Active@ Livecd User Guide Copyright © 1999-2015, LSOFT TECHNOLOGIES INC
Active@ LiveCD User Guide Copyright © 1999-2015, LSOFT TECHNOLOGIES INC. All rights reserved. No part of this documentation may be reproduced in any form or by any means or used to make any derivative work (such as translation, transformation, or adaptation) without written permission from LSOFT TECHNOLOGIES INC. LSOFT TECHNOLOGIES INC. reserves the right to revise this documentation and to make changes in content from time to time without obligation on the part of LSOFT TECHNOLOGIES INC. to provide notification of such revision or change. LSOFT TECHNOLOGIES INC. provides this documentation without warranty of any kind, either, implied or expressed, including, but not limited to, the implied warranties of merchantability and fitness for a particular purpose. LSOFT may make improvements or changes in the product(s) and/or the program(s) described in this documentation at any time. All technical data and computer software is commercial in nature and developed solely at private expense. As the User, or Installer/Administrator of this software, you agree not to remove or deface any portion of any legend provided on any licensed program or documentation contained in, or delivered to you in conjunction with, this User Guide. LSOFT.NET logo is a trademark of LSOFT TECHNOLOGIES INC. Other brand and product names may be registered trademarks or trademarks of their respective holders. 2 Active@ LiveCD User Guide Contents 1 Product Overview................................................................................................................ 4 1.1 About Active@ LiveCD .................................................................................................. 4 1.2 Requirements for Using Active@ Boot Disk .................................................................... 6 1.3 Downloading and Creating Active@ LiveCD.................................................................... 6 1.4 Booting from a CD, DVD or USB Media ......................................................................... -
Amphibian Ark Number 43 Keeping Threatened Amphibian Species Afloat June 2018
AArk Newsletter NewsletterNumber 43, June 2018 amphibian ark Number 43 Keeping threatened amphibian species afloat June 2018 In this issue... Reintroduction of the Northern Pool Frog to the UK - Progress Report, April 2018 ............... 2 ® Establishment of a captive breeding program for the Kroombit Tinkerfrog .............................. 4 In situ conservation of the Lemur Leaf Frog through habitat improvement and forest management practices in the Guayacán Rainforest Reserve in Costa Rica .................... 6 Neotropical amphibian biology, management and conservation course .................................. 8 Donation provides for equipment upgrades within the Biogeos Foundation facilities, at the Rescue of Endangered Venezuelan Amphibians program in Venezuela ................... 9 New AArk Conservation Grants program, and call for applications .................................. 10 Amphibian Advocates - José Alfredo Hernández Díaz, Africam Safari, Mexico ........ 11 Amphibian Advocates - Dr. Phil Bishop, Co-Chair IUCN SSC ASG............................... 12 AArk Newsletter - Instructions for authors ...... 13 A private donation helps the Valcheta Frog program in Argentina ...................................... 14 A rich food formula to raise tadpoles in captivity........................................................... 16 Vibicaria Conservation Program: creation of an ex situ model for a rediscovered species in Costa Rica ...................................................... 18 Reproduction of Dendropsophus padreluna at -
Community Report 2Nd Quarter 2012 | Issue 22
COMMUNITY REPORT 2ND QUARTER 2012 | ISSUE 22 WELCOME MESSAGE Dear KDE members, contributors, night only to return after few hours of raised. A Pledgie campaign users, supporters, patrons, sponsors sleep to continue working from where (http://pledgie.com/campaigns/18045) and friends, they left off. Since then, a lot has is available to help achieve this goal. changed. We now have regular sprints Please spread the word about this We are coming back from a successful pretty much all year around. campaign and donate if you can. Akademy 2012 in Tallinn, Estonia. The event commenced with a befitting talk One such sprint is the Randa meeting. Speaking of changing times, a very “Freedom of Expression” by Mathias In fact, it has become the most important one is the upcoming new Klang; “freedom of expression” is a intense and largest KDE sprint. In 2011, ownership of Qt. Recently Nokia trait that has embodied KDE since its the event saw participation by 40 KDE announced that it is selling its Qt beginning. It was followed by an contributors from around the world business to Digia. Congratulations to excellent two day line-up of talks. The coming together to plan, design, KDE e.V. supporting member Digia on main conference was followed by a create and work on their favorite KDE acquiring Qt Software. We wish them diverse and interesting array of BoF projects. The Randa sprint is being all the best in taking Qt to even sessions and workshops. The KDE e.V. organized by our own KDE hero higher levels of success and adoption. -
Download the Index
41_067232945x_index.qxd 10/5/07 1:09 PM Page 667 Index NUMBERS 3D video, 100-101 10BaseT Ethernet NIC (Network Interface Cards), 512 64-bit processors, 14 100BaseT Ethernet NIC (Network Interface Cards), 512 A A (Address) resource record, 555 AbiWord, 171-172 ac command, 414 ac patches, 498 access control, Apache web server file systems, 536 access times, disabling, 648 Accessibility module (GNOME), 116 ACPI (Advanced Configuration and Power Interface), 61-62 active content modules, dynamic website creation, 544 Add a New Local User screen, 44 add command (CVS), 583 address books, KAddressBook, 278 Administrator Mode button (KDE Control Center), 113 Adobe Reader, 133 AFPL Ghostscript, 123 41_067232945x_index.qxd 10/5/07 1:09 PM Page 668 668 aggregators aggregators, 309 antispam tools, 325 aKregator (Kontact), 336-337 KMail, 330-331 Blam!, 337 Procmail, 326, 329-330 Bloglines, 338 action line special characters, 328 Firefox web browser, 335 recipe flags, 326 Liferea, 337 special conditions, 327 Opera web browser, 335 antivirus tools, 331-332 RSSOwl, 338 AP (Access Points), wireless networks, 260, 514 aKregator webfeeder (Kontact), 278, 336-337 Apache web server, 529 album art, downloading to multimedia dynamic websites, creating players, 192 active content modules, 544 aliases, 79 CGI programming, 542-543 bash shell, 80 SSI, 543 CNAME (Canonical Name) resource file systems record, 555 access control, 536 local aliases, email server configuration, 325 authentication, 536-538 allow directive (Apache2/httpd.conf), 536 installing Almquist shells -
What's New in KDE SC
RevieWs KDE SC 4.4 What’s new in KDE SC 4.4 FOUR-IN-HAND fmatte, photocase.com fmatte, Version 4.4 sees the KDE Software Compilation reach a status on par puzzle bench lets you create your own puzzles, giving you a free choice of the with the user friendliness and stability of good old KDE 3.5. On top of number of parts (Figure 3). Palapeli au- tomatically remembers your progress in this, many features are new. BY MARCEL HILZINGER completing the puzzles. You can thus work on multiple puzzles, or new puzzle f you have not looked at an open line feature allows users to compose designs, concurrently. source operating system for a year, postings at any time. iyou probably won’t recognize any- The KDE-Edu educational set includes New system Components thing. Projects disappear and new ones two new programs: Cantor and Rocs. KDE always had an address book, but take their place; a tool or library that is The Cantor math tool (Figure 2) lets you the tool that comes with KDE SC 4.4 is today’s buzz can be obsolete tomorrow. compose math worksheets. By default, practically a new program. Its author is KDE users experienced this situation Cantor relies on the internal KAlgebra KDE PIM developer Tobias König, who is when the desktop warped from version back end, although it 3.x to 4.x. Early 4.x releases showed supports the free Maxima promise, but none could achieve the sta- [3] and Sage [4] educa- Online. Easy. Secure. Reliable bility and versatility of the late 3.x se- tional systems. -
Release Notes
LispWorks® Release Notes and Installation Guide Version 5.1 Copyright and Trademarks LispWorks Release Notes and Installation Guide Version 5.1 March 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. -
Getting Started with Ubuntu and Kubuntu
Getting Started With Ubuntu and Kubuntu IN THIS PART Chapter 1 The Ubuntu Linux Project Chapter 2 Installing Ubuntu and Kubuntu Chapter 3 Installing Ubuntu and Kubuntu on Special-Purpose Systems COPYRIGHTED MATERIAL 94208c01.indd 1 3/16/09 11:43:23 PM 94208c01.indd 2 3/16/09 11:43:24 PM The Ubuntu Linux Project ersonal computers and their operating systems have come a long way since the late 1970s, when the first home computer hit the market. At IN THIS cHAPTER that time, you could only toggle in a program by flipping switches on the P Introducing Ubuntu Linux front of the machine, and the machine could then run that program and only that program until you manually loaded another, at which time the first program Choosing Ubuntu was kicked off the system. Today’s personal computers provide powerful graph- ics and a rich user interface that make it easy to select and run a wide variety of Reviewing hardware and software concurrently. software requirements The first home computer users were a community of interested people who just Using Ubuntu CDs wanted to do something with these early machines. They formed computer clubs and published newsletters to share their interests and knowledge — and often the Getting help with Ubuntu Linux software that they wrote for and used on their machines. Sensing opportunities and a growing market, thousands of computer companies sprang up to write and Getting more information sell specific applications for the computer systems of the day. This software ranged about Ubuntu from applications such as word processors, spreadsheets, and games to operating systems that made it easier to manage, load, and execute different programs. -
Pclinuxos Magazine
Proje cts: PCLinuxOS Sm all Bus ine s s Edition H ow To: Se tup a Printe r in a W indow s W ork group Conne ct to AOL Us ing a Dialup Mode m Issue 4 D ecem ber, 2006 h ttp://w w w.pclinuxos.com Add a Me nu Ite m H elpful Link s Netw ork File System by PCLinuxO S Forum M e m be rs by jaydot Music Players: Th e Good, Th e Bad and Th e Ugly by Joh n "Papaw oob" Paxton Creating Th um bnail Galleries of Your Pictures by Tim Robins on Exce pt w h e re oth e rw is e note d, conte nt of th is m agaz ine is lice ns e d unde r a Cre ative Com m ons Atrribution-NonCom m e rcial-NoD e rvis 2.5 Lice ns e PCLinuxOS Magaz ine is a com m unity From th e Desk of th e Ch ief Editor proje ct of MyPCLinuxOS.com to provide an additional m e ans of com m unication to th e PCLinuxOS com m unity. W e ll, h e re w e are w ith is s ue #4, and I be lie ve w e h ave an e ve n be tte r m agaz ine for you th is m onth . Proje ct Coordinator: De rrick De vine Publis h e r: MyPCLinuxOS.com Th e re are re vie w s of th re e m us ic m anage m e nt applications , an ope n s ource Contact: m ag@ m ypclinuxos .com re place m e nt for AOL's inte rface , and a colle ction of link s th at s h ould prove us e ful for ne w bie s and e xpe rts alik e . -
Software Studies: a Lexicon, Edited by Matthew Fuller, 2008
fuller_jkt.qxd 4/11/08 7:13 AM Page 1 ••••••••••••••••••••••••••••••••••••• •••• •••••••••••••••••••••••••••••••••• S •••••••••••••••••••••••••••••••••••••new media/cultural studies ••••software studies •••••••••••••••••••••••••••••••••• ••••••••••••••••••••••••••••••••••••• •••• •••••••••••••••••••••••••••••••••• O ••••••••••••••••••••••••••••••••••••• •••• •••••••••••••••••••••••••••••••••• ••••••••••••••••••••••••••••••••••••• •••• •••••••••••••••••••••••••••••••••• F software studies\ a lexicon ••••••••••••••••••••••••••••••••••••• •••• •••••••••••••••••••••••••••••••••• ••••••••••••••••••••••••••••••••••••• •••• •••••••••••••••••••••••••••••••••• T edited by matthew fuller Matthew Fuller is David Gee Reader in ••••••••••••••••••••••••••••••••••••• •••• •••••••••••••••••••••••••••••••••• This collection of short expository, critical, Digital Media at the Centre for Cultural ••••••••••••••••••••••••••••••••••••• •••• •••••••••••••••••••••••••••••••••• W and speculative texts offers a field guide Studies, Goldsmiths College, University of to the cultural, political, social, and aes- London. He is the author of Media ••••••••••••••••••••••••••••••••••••• •••• •••••••••••••••••••••••••••••••••• thetic impact of software. Computing and Ecologies: Materialist Energies in Art and A digital media are essential to the way we Technoculture (MIT Press, 2005) and ••••••••••••••••••••••••••••••••••••• •••• •••••••••••••••••••••••••••••••••• work and live, and much has been said Behind the Blip: Essays on the Culture of ••••••••••••••••••••••••••••••••••••• -
Das Handbuch Zu Krusader Das Handbuch Zu Krusader
Das Handbuch zu Krusader Das Handbuch zu Krusader 2 Inhaltsverzeichnis 1 Einführung 14 1.1 Paketbeschreibung . 14 1.2 Willkommen zu Krusader! . 14 2 Funktionen 17 3 Die Benutzerschnittstelle 21 3.1 Benutzerschnittstelle mit zwei Dateifenstern . 21 3.2 Das Hauptfenster von Krusader . 21 3.3 Werkzeugleisten . 21 3.3.1 Haupt-Werkzeugleiste . 21 3.3.2 Aufgaben-Werkzeugleiste . 23 3.3.3 Aktionen-Werkzeugleiste . 23 3.3.4 Adressleiste . 23 3.3.5 Dateifenster-Werkzeugleiste . 24 3.4 Dateifenster . 24 3.4.1 Dateifenster . 24 3.4.2 Seitenleiste . 26 3.4.3 Ordnerverlauf . 27 3.5 Befehlszeile / Terminal-Emulator . 27 3.5.1 Befehlszeile . 27 3.5.2 Terminal-Emulator . 27 3.6 Funktionstasten (F1-F12) . 28 3.7 Unterfenster für Ordner . 28 3.8 Knöpfe . 29 4 Grundlegende Funktionen 30 4.1 Bedienelemente . 30 4.1.1 Allgemein . 30 4.1.2 Navigation . 30 4.1.3 Auswahl . 31 4.1.4 Befehle ausführen . 31 4.1.5 Schnellsuche . 32 Das Handbuch zu Krusader 4.1.6 Schnellfilter . 32 4.1.7 Schnellauswahl . 32 4.1.8 Kontextmenü . 32 4.2 Grundlegende Dateiverwaltung . 33 4.2.1 Dateien ausführen . 33 4.2.2 Kopieren und Verschieben . 33 4.2.3 Warteschlangenverwaltung . 34 4.2.4 Löschen - in den Plasma-Papierkorb verschieben . 34 4.2.5 Dateien in den Reißwolf werfen . 34 4.2.6 Dateien umbenennen, Ordner erstellen und Verknüpfungen verwalten . 34 4.2.7 Dateien anzeigen und bearbeiten . 35 4.3 Archiv-Verwaltung . 35 4.3.1 Archive durchsuchen . 35 4.3.2 Dateien entpacken . 35 4.3.3 Dateien packen . -
Release Notes for Fedora 17
Fedora 17 Release Notes Release Notes for Fedora 17 Edited by The Fedora Docs Team Copyright © 2012 Fedora Project Contributors. 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.