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!
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!