Major rewrite to work with GFF files rather than with blast output

blast output can be converted to GFF with Blast2GFF, then input into this script
removed debugging print statement
Added an option to write entire contigs to cluster files rather than cds portions (the latter is default)
Added option to specify if sequences are raw trinity output or consensus seqs and select output dir accordingly

raw contig sequences are written to files in /Users/HeathOBrien/Bioinformatics/Selaginella/ContigClusters
consensus sequences are written to files in /Users/HeathOBrien/Bioinformatics/Selaginella/ConsensusClusters
Added "fast tree option" that does no optimization of topology or branchlengths

specify "RunPhyML.py <filename> fast"
Merge branch 'working'

Conflicts:
	RunPhyml.py
fixed bug in the command parsing and changed option from"contig" to "contigs"
New name for old version of GetOrthologGroup.py that uses blast results rather than GTF file
first commit