EvoBio2

Instructions for setting up your computer for Evolutionary Biology 2 course of UL

Disclaimer

Please note that while the software and provided links in this instruction have been tested and shown to work as intended, we cannot accept any responsibility for any issues that may arise during installation or any potential damage to your system. Use at your own risk. None of the software used in this course is available through official channels like the Microsoft Store or Mac App Store. Consequently you will encounter security warnings along the lines of 'the downloaded software is from an unidentified developer', or the operating system 'prevented an unrecognized app from starting'. To continue installation:

• Windows --> select "More info" --> Run anyway
• Mac --> System Preferences -> Privacy & Security -> Open anyway.

Text editor

Text editors and word processors are two distinct types of software. Word processors (like MS Word on Windows or Textedit on Mac) are used for creating and editing formatted text documents. Text editors however, can only create and edit plain text-files and are therefore ideal for coding. Basically scripts and configuration files are plain text-files. Often text-editors also have features like syntax highlighting, line number and indentation assistance. Anytime you need to create or modify input files for analyses during this course, do not use a word processor, but please use a text editor!

• Windows users are recommended to use Notepad++
• Mac users are recommended to use Textmate

File compression

Software packages or file archives are often distributed in a compressed format. Reasons for compression can be to reduce file size (less disk space, faster transfers), bundling mutliple files while preserving structure, or to warrant data intergrity. A commonly used format is .zip (Windows, Mac), whereas other formats tend to be OS specific: .rar, .7z (Windows) and .dmg, .tar.gz (Mac). In particular for (de)compressing .zip files dedicated software is useful.

• Windows users are recommended to use 7Zip
• Mac users can use the built-in Archive Utility

Java

Some of the programs we use (Mesquite in particular) require Java. To check if Java (JDK only) is installed on your system: open a command prompt on Windows, or a terminal session on Mac, and type: java -version. When installed, you should see something like 'java version x' or 'OpenJDK version y'. In case you see 'unable to locate' or 'no java runtime present' then Java is missing and should be installed:

• Windows users can download java from java.com

• For Mac users, which version of java to download depends on your OS version and sytem architecture (x64 or ARM):

  users on 10.14 or older (tested on 10.13.6) can download a standalone java installer
  users on 10.15 or later with x64 (tested on 12.7.1) can download java jdk-22_macos-x64_bin.dmg
  users on ARM systems a.k.a. M1/M2/M3 (tested on 14.6.1) can dowload java jdk-22_macos-aarch64_bin.dmg

  Open the disk image (double-click the .dmg file). Allow installation as described under disclaimer

For archival purposes and troubleshooting, the above links are obtained from the Oracle download pages: https://www.oracle.com/java/technologies/downloads/#jdk22-windows
https://www.oracle.com/java/technologies/downloads/#jdk22-mac

Paup

The acronym stands for 'Phylogenetic Analysis Using Parsimony', but nowadays this program does a lot more than just parsimony (i.e. distance, likelihood, model-testing). Paup was written nearly 4 decades ago by David Swofford, but infrequent updates are still released. The latest release information and download instructions are on phylosulotions. Please install the latest version (4.0a168 as of this writing) for your OS:

• Windows users can download the Paup executable

• Mac users can download the paup4a168_osx.gz
  Open the zip archive (double-click the .gz file). Move paup4a168_osx to your /Applications folder.
  Open a terminal and make Paup executable:

  chmod a+x /Applications/paup4a168_osx

  For easy access you might add Paup to your path:

  sudo ln -s /Applications/paup4a168_osx /usr/local/bin

  Note: There is no graphical interface (GUI) for current Mac operating systems (i.e. any system more recent than 10.14, roughly the end of 2019). But don't worry, the command line is always faster than the GUI!

Mesquite

Mesquite is a free and open-source program for manipulating datasets and trees (not for phylogeny reconstruction!). The latest release information and download instructions are on MesquiteProject. For this course we will be using version 3.81. Please install or add the Mesquite-folder to a proper location (i.e. Program Files on Windows or Applications folder on Mac).

• Windows users can download Mesquite.3.81-Windows.zip
• Mac users can download Mesquite.3.81_macOS_10.15_and_later.dmg
  Open the disk image (double-click te .dmg file).
  Move the Mesquite_Folder to your /Applications folder (do not run the starter app from the mounted disk image).
  Allow installation as described under disclaimer

MrBayes

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters. The datasets analysed during this practical are small, so there is no need to install an MPI version of MrBayes (which takes longer to install/configure); please install a serial version. The releases below are obtained from the MrBayes repository.

• Windows users can download MrBayes version 3.2.7.
  The 32 and 64 bit executables are in bin (e.g. C:\Program Files\MrBayes-3.2.7-WIN\bin\).
• Mac users can download MrBayes version 3.2.7.
  Open the zip archive (double-click the .gz file).
  Move mrbayes-3.2.7 to your /Applications folder.
  Open a terminal window and run:

  cd /Applications/mrbayes-3.2.7
  ./configure
  make && sudo make install
  

Geneious

Geneious is a commercial program to visually inspect chromatograms and manipulate sequence-data. For this course, dowload a fully functional free trial-version (Geneious Prime 2024 as of this writing). This version expires in 30 days. Therefore, do not install too far in advance of the course! Sign up with your email address, download a version compatible with your OS, install and optionally add plug-ins (e.g. Clustal, NCBI, Paup).