phyloGenerator 2 - automated phylogeny generation

Will Pearse

##Quickstart

• Clone this repo (git clone https://github.com/willpearse/phyloGenerator2.git)
• Ensure you have Ruby and BioRuby installed (sudo gem install bio)
• Ensure you have at least RAxML and MAFFT installed (sudo apt-get install mafft; ````````git clone https://github.com/stamatak/standard-raxml.git````), ExAML and ExaBayes if you want to use them
• 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.
• Run the program with ./pG_2.rb /full/path/to/param/file
• ...the parameters are self-explanatory within the demo parameter file. Make sure you set an email addres

##Guidelines and important notes

• Using the output from any program uncritically is a bad idea; using phyloGenerator2 uncritical is exceptionally bad. Do not simply run the program and then use the output off the bat; you must check your DNA alignments.
• phyloGenerator1 was written for a novice user; pG2 is not. I assume, when using this, that you have a basic understanding of how to build a phylogeny. I do not neaten the output from ExaML etc. beyond creating sub-folders
• The parameter file contains a number of settings, not all of them necessary.
• If you set a minimum or maximum length for an alignment that is smaller or greater than your reference data, the program won't find anything.
• The secondary sequence check ('hawkeye') is a very powerful tool. Use it.

##License Is in the file 'LICENSE'. It's essentially MIT but you have to cite the program when you use it :D

The license