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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 . -
Red Hat Enterprise Linux 8 Installing, Managing, and Removing User-Space Components
Red Hat Enterprise Linux 8 Installing, managing, and removing user-space components An introduction to AppStream and BaseOS in Red Hat Enterprise Linux 8 Last Updated: 2021-06-25 Red Hat Enterprise Linux 8 Installing, managing, and removing user-space components An introduction to AppStream and BaseOS in Red Hat Enterprise Linux 8 Legal Notice Copyright © 2021 Red Hat, Inc. 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. Red Hat, Red Hat Enterprise Linux, the Shadowman logo, the Red Hat logo, JBoss, OpenShift, Fedora, the Infinity logo, and RHCE are trademarks of Red Hat, Inc., registered in the United States and other countries. 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. -
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. -
Schon Mal Dran Gedacht,Linux Auszuprobieren? Von G. Schmidt
Schon mal dran gedacht, Linux auszuprobieren? Eine Einführung in das Betriebssystem Linux und seine Distributionen von Günther Schmidt-Falck Das Magazin AUSWEGE wird nun schon seit 2010 mit Hilfe des Computer-Betriebs- system Linux erstellt: Texte layouten, Grafiken und Fotos bearbeiten, Webseiten ge- stalten, Audio schneiden - alles mit freier, unabhängiger Software einer weltweiten Entwicklergemeinde. Aufgrund der guten eigenen Erfahrungen möchte der folgende Aufsatz ins Betriebssystem Linux einführen - mit einem Schwerpunkt auf der Distri- bution LinuxMint. Was ist Linux? „... ein hochstabiles, besonders schnelles und vor allem funktionsfähiges Betriebssystem, das dem Unix-System ähnelt, … . Eine Gemeinschaft Tausender programmierte es und verteilt es nun unter der GNU General Public Li- cense. Somit ist es frei zugänglich für jeden und kos- tenlos! Mehrere Millionen Leute, viele Organisatio- nen und besonders Firmen nutzen es weltweit. Die meisten nutzen es aus folgenden Gründen: • besonders schnell, stabil und leistungs- stark • gratis Support aus vielen Internet- Newsgruppen Tux, der Pinguin, ist das Linux-Maskottchen • übersichtliche Mailing-Listen • massenweise www-Seiten • direkter Mailkontakt mit dem Programmierer sind möglich • Bildung von Gruppen • kommerzieller Support“1 Linux ist heute weit verbreitet im Serverbereich: „Im Oktober 2012 wurden mindes- tens 32% aller Webseiten auf einem Linux-Server gehostet. Da nicht alle Linux-Ser- ver sich auch als solche zu erkennen geben, könnte der tatsächliche Anteil um bis zu 24% höher liegen. Damit wäre ein tatsächlicher Marktanteil von bis zu 55% nicht 1 http://www.linuxnetworx.com/linux-richtig-nutzen magazin-auswege.de – 2.11.2015 Schon mal dran gedacht, Linux auszuprobieren? 1 auszuschliessen. (…) Linux gilt innerhalb von Netzwerken als ausgesprochen sicher und an die jeweiligen Gegebenheiten anpassbar. -
The Next-Gen Apertis Application Framework 1 Contents
The next-gen Apertis application framework 1 Contents 2 Creating a vibrant ecosystem ....................... 2 3 The next-generation Apertis application framework ........... 3 4 Application runtime: Flatpak ....................... 4 5 Compositor: libweston ........................... 6 6 Audio management: PipeWire and WirePlumber ............ 7 7 Session management: systemd ....................... 7 8 Software distribution: hawkBit ...................... 8 9 Evaluation .................................. 8 10 Focus on the development user experience ................ 12 11 Legacy Apertis application framework 13 12 High level implementation plan for the next-generation Apertis 13 application framework 14 14 Flatpak on the Apertis images ...................... 15 15 The Apertis Flatpak application runtime ................. 15 16 Implement a new reference graphical shell/compositor ......... 16 17 Switch to PipeWire for audio management ................ 16 18 AppArmor support ............................. 17 19 The app-store ................................ 17 20 As a platform, Apertis needs a vibrant ecosystem to thrive, and one of the 21 foundations of such ecosystem is being friendly to application developers and 22 product teams. Product teams and application developers are more likely to 23 choose Apertis if it offers flows for building, shipping, and updating applications 24 that are convenient, cheap, and that require low maintenance. 25 To reach that goal, a key guideline is to closely align to upstream solutions 26 that address those needs and integrate them into Apertis, to provide to appli- 27 cation authors a framework that is made of proven, stable, complete, and well 28 documented components. 29 The cornerstone of this new approach is the adoption of Flatpak, the modern 30 application system already officially supported on more than 20 Linux distribu- 1 31 tions , including Ubuntu, Fedora, Red Hat Enterprise, Alpine, Arch, Debian, 32 ChromeOS, and Raspian. -
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. -
Selenium Python Bindings Release 2
Selenium Python Bindings Release 2 Baiju Muthukadan Sep 03, 2021 Contents 1 Installation 3 1.1 Introduction...............................................3 1.2 Installing Python bindings for Selenium.................................3 1.3 Instructions for Windows users.....................................3 1.4 Installing from Git sources........................................4 1.5 Drivers..................................................4 1.6 Downloading Selenium server......................................4 2 Getting Started 7 2.1 Simple Usage...............................................7 2.2 Example Explained............................................7 2.3 Using Selenium to write tests......................................8 2.4 Walkthrough of the example.......................................9 2.5 Using Selenium with remote WebDriver................................. 10 3 Navigating 13 3.1 Interacting with the page......................................... 13 3.2 Filling in forms.............................................. 14 3.3 Drag and drop.............................................. 15 3.4 Moving between windows and frames.................................. 15 3.5 Popup dialogs.............................................. 16 3.6 Navigation: history and location..................................... 16 3.7 Cookies.................................................. 16 4 Locating Elements 17 4.1 Locating by Id.............................................. 18 4.2 Locating by Name............................................ 18 4.3 -
N $NUM GPUS Python Train.Py
Neural Network concurrency Tal Ben-Nun and Torsten Hoefler, Demystifying Parallel and Distributed Deep Learning: An In-Depth Concurrency Analysis, 2018, Data Parallelism vs Model Parallelism Hardware and Libraries ● It is not only a matter of computational power: ○ CPU (MKL-DNN) ○ GPU (cuDNN) ○ FGPA ○ TPU ● Input/Output matter ○ SSD ○ Parallel file system (if you run parallel algorithm) ● Communication and interconnection too, if you are running in distributed mode ○ MPI ○ gRPC +verbs (RDMA) ○ NCCL Install TensorFlow from Source [~]$ wget https://github.com/.../bazel-0.15.2-installer-linux-x86_64.sh [~]$ ./bazel-0.15.2-installer-linux-x86_64.sh --prefix=... [~]$ wget https://github.com/tensorflow/tensorflow/archive/v1.10.0.tar.gz ... [~]$ python3 -m venv $TF_INSTALL_DIR [~]$ source $TF_INSTALL_DIR/bin/activate [~]$ pip3 install numpy wheel [~]$ ./configure ... [~]$ bazel build --config=mkl/cuda \ //tensorflow/tools/pip_package:build_pip_package [~]$ bazel-bin/tensorflow/tools/pip_package/build_pip_package $WHEELREPO [~]$ pip3 install $WHEELREPO/$WHL --ignore-installed [~]$ pip3 install keras horovod ... Input pipeline If using accelerators like GPU, pipeline tha data load exploiting the CPU with the computation on GPU The tf.data API helps to build flexible and efficient input pipelines Optimizing for CPU ● Built from source with all of the instructions supported by the target CPU and the MKL-DNN option for Intel® CPU. ● Adjust thread pools ○ intra_op_parallelism_threads: Nodes that can use multiple threads to parallelize their execution -
Photo Editing
All recommendations are from: http://www.mediabistro.com/10000words/7-essential-multimedia-tools-and-their_b376 Photo Editing Paid Free Photoshop Splashup Photoshop may be the industry leader when it comes to photo editing and graphic design, but Splashup, a free online tool, has many of the same capabilities at a much cheaper price. Splashup has lots of the tools you’d expect to find in Photoshop and has a similar layout, which is a bonus for those looking to get started right away. Requires free registration; Flash-based interface; resize; crop; layers; flip; sharpen; blur; color effects; special effects Fotoflexer/Photobucket Crop; resize; rotate; flip; hue/saturation/lightness; contrast; various Photoshop-like effects Photoshop Express Requires free registration; 2 GB storage; crop; rotate; resize; auto correct; exposure correction; red-eye removal; retouching; saturation; white balance; sharpen; color correction; various other effects Picnik “Auto-fix”; rotate; crop; resize; exposure correction; color correction; sharpen; red-eye correction Pic Resize Resize; crop; rotate; brightness/contrast; conversion; other effects Snipshot Resize; crop; enhancement features; exposure, contrast, saturation, hue and sharpness correction; rotate; grayscale rsizr For quick cropping and resizing EasyCropper For quick cropping and resizing Pixenate Enhancement features; crop; resize; rotate; color effects FlauntR Requires free registration; resize; rotate; crop; various effects LunaPic Similar to Microsoft Paint; many features including crop, scale -
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. -
Install Tani Software
Install Tani Software Windows Under Windows all software comes with an installer which is an executable program. You can start it directly. If You update an installed Tani product it will uninstall the previous version automatically and replaces it with the actual one. All user configuration setting will be preserved. A reboot will be requested in these conditions: The running software can not be stopped. This may be true if an other running program uses the software. Some parts of the software can not be removed because other software holds them open. A program uses the directory holding the software. A hint: If You uninstall the software separately and try installing them again it will request a reboot always. Optionally you can ignore the reboot request. This is always at your own risk. Possibly required files can not be installed. The installed software may not work as expected. Why a reboot is required after uninstall: The uninstall program can not be deleted by itself because it runs. Windows uses random generated file names in this registry key. So the installer cannot check if the reboot will be required or is optional. The installation depending on your Windows patch level may start its internal update. This does not relay on software from Tani GmbH. If Windows will request updates it will do so. During the Windows update an internet connection is required. The installation process will need additional time until the update is finished. More information is available in the Windows Update. For special envoronments it can be necessary running the OPC server or the PLC Engine not as a Windows service. -
How to Create Music with GNU/Linux
How to create music with GNU/Linux Emmanuel Saracco [email protected] How to create music with GNU/Linux by Emmanuel Saracco Copyright © 2005-2009 Emmanuel Saracco How to create music with GNU/Linux Warning WORK IN PROGRESS Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1.2 or any later version published by the Free Software Foundation; with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts. A copy of the license is available on the World Wide Web at http://www.gnu.org/licenses/fdl.html. Revision History Revision 0.0 2009-01-30 Revised by: es Not yet versioned: It is still a work in progress. Dedication This howto is dedicated to all GNU/Linux users that refuse to use proprietary software to work with audio. Many thanks to all Free developers and Free composers that help us day-by-day to make this possible. Table of Contents Forword................................................................................................................................................... vii 1. System settings and tuning....................................................................................................................1 1.1. My Studio....................................................................................................................................1 1.2. File system..................................................................................................................................1 1.3. Linux Kernel...............................................................................................................................2