skip rows missing data
dont split groups
Merge pull request #69 from andrewjpage/core_alignment_missing_file

Core alignment missing file
run core alignment job after gene alignments
test the help message is displayed
sort fasta file
make sure the order of the core alignment is always sorted correctly
query pan genome help text works
multiple empty files
Merge pull request #70 from andrewjpage/core_alignment_missing_file

Core alignment missing file
construct job ids in a sub
cd hit defaults off by 100
job ids
remove splitting of groups based on annotation
Merge pull request #71 from andrewjpage/job_runner_ids_lsf

Job runner ids lsf