Changed path to python install for update from 2.6 to 2.7
Added a list of clusters corresponding to chloroplast-encoded genes to excluded from analyses

These are being excluded because many chloroplast genes overlap resulting in chimeric
transcripts. These transcripts can be extremely long, causing the analysis to really bog down
changed os.path to simply path since that is what was imported
Removed comments that were preventing the first part of pipeline from running

These were in place so that I could trouble-shoot later steps without rerunning the
early ones

The entire pipeline seems to be working now and I have run it for 3/4 species, with the
fourth running now
Added the --preservecase option to the mafft command
remove the comment from one of the lines writing commands to log file
modified to include S_willdenowii reference sequences when making monophyletic clusters

--but not when making consensus sequences
modified to allow specification of which step the analysis should be started at
major rewrite to include "blast_hit" feature and CDS feature based on ORF that contians blast hit

multiple non-overlapping hits are also included
added get_orf and get_orf_coords functions to identify ORF that contains specified blastx coordinates
Added info about a number of recently added scripts
first commit