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), oryyggdrasil(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