phyloGenerator2

Overview

pG2 should work on any computer, but my instructions/help is better for Mac/Linux because that's what I'm more familiar with. My inuition is that, if you already do some phylogenetics, you should be able to get pG2 installed within seconds. If you want a one-click download, consider using phyloGenerator 1.

Download here, or clone the GitHub repository

For every operating system, the basic steps are to install:

• Ruby
• BioRuby, a 'Gem' (library) for Ruby
• MAFFT
• At least one of:
  • RAxML (probably the easiest)
  • ExaML
  • ExaBayes
• Make sure each program can be run from the command line by typing mafft, raxml, examl & parse-examl (ExaML), or yyggdrasil (part of ExaBayes). This means changing the names of the RAxML and ExaML binaries, and copying things into wherever you keep programs you can run from the command line.
• Download pG2, or clone using git clone https://github.com/willpearse/phyloGenerator2.git

Once you've installed the program, read through the guide. If you have any questions after that, please check the FAQ. If you then get stuck, please do contact me.

Linux (Ubuntu)

1. sudo apt-get install ruby mafft
2. Only if using ExaML or ExaBayes, install open-mpi
3. Either run (as sudo) or, preferably, step through, everything in install_linux.sh.
4. Download pG2, or clone using git clone https://github.com/willpearse/phyloGenerator2.git

Mac OSX

1. Open Terminal
2. sudo gem install bio
3. Install MAFFT
4. If you wish to use ExaML, install OpenMPI. My advice would be to use somethin like Homebrew to keep track of packages; I can't give any specific advice about this on Mac I'm afraid.
5. Follow the steps in install_linux.sh. You may need to copy somewhere other than the default install directory; run echo $PATH to see where your executable are stored normally.
6. Download pG2, or clone using git clone https://github.com/willpearse/phyloGenerator2.git

Windows (PC)

I can't really give any more precise tips than the overview at the beginning of this page. If you successfully install pG2 on Windows, please do let me know how you did it! There's a beer in it for you!