Updated information on how to install Perl modules
Added section on installing DRMAAc in Ubuntu
Renamed perl_bin/ directory to scripts/
Created setup.pl script to check for dependencies and write an example configuration file
Added ability to generate binary files
Added --force option to setup
Re-wrote INSTALL guide to reflect usage of scripts/setup.pl
Updated overview of install steps
Added better comparison of phylip files
Fixed up mapping and ortholog versions of pipeline tests
Added some example scripts for installing to ubuntu
Fixed up to use alternative method of comparing phylip files
Merge branch 'feature/update-install-process' of github.com:apetkau/core-phylogenomics into feature/update-install-process
Updated vcf2pseudalign submodule with new test comparisons
Fixed up snp_matrix and Bio::AlignIO::phylip format to work with latest version of BioPerl (1.006923)
Changed default configuration file to not have so many specific queue names and cpu numbers in it
Added ubuntu installation instructions
Merge pull request #3 from apetkau/feature/update-install-process

Feature/update install process
Changed idlength to longid for alignment formats
Got rid of interleaved() from clustalw alignments