phyloGenerator2

Overview

A quick way to make very large phylogenies. If you are unfamiliar with phylogenetics, use version 1 of phyloGenerator. pG2 is more powerful, but also more dangerous and less forgiving. Version 1 still builds great phylogenies, is still supported, and (unlike version 2) is suitable for non-specialists. You have been warned! However, if you're interested in building a large phylogeny, please try version 2 out!

Quickstart

If you're on a Mac or Linux computer:

git clone https://github.com/willpearse/phyloGenerator2.git #get pG2
sudo gem install bio #install BioRuby
sudo apt-get install mafft #install MAFFT
git clone https://github.com/stamatak/standard-raxml.git
#...then compile and copy binary to somewhere on $PATH as 'raxml'
./phyloGenerator2/pG_2.rb /full/path/to/param/file #run pG2

...or read the installation instructions!

General advice

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.