Merge pull request #25 from andrewjpage/master

use LSF to do the inital parsing of input files
Merge pull request #26 from andrewjpage/master

Change case of GFF commandline class
Merge pull request #27 from andrewjpage/master

Pass job runner through to extract gffs
Merge pull request #28 from andrewjpage/master

Filter unknowns in LSF jobs
Merge pull request #29 from andrewjpage/master

blocking job
Merge pull request #30 from andrewjpage/master

remove done dependancy job
Merge pull request #31 from andrewjpage/master

Run external applications through lsf
Merge pull request #32 from andrewjpage/master

Output all sequences making up pan genome in multifasta files
Merge pull request #33 from andrewjpage/master

annotate the names of the groups files
Merge pull request #34 from andrewjpage/master

run post analysis as a job
Merge pull request #35 from andrewjpage/master

dont wait in lfs scheduler
Merge pull request #36 from andrewjpage/master

make multifasta files easier to sort
Merge pull request #37 from andrewjpage/master

split big groups based on annotation
Merge pull request #38 from andrewjpage/master

Presence and absence of genes
Merge pull request #39 from andrewjpage/master

Speedup post analysis
read in newick tree and output order of leafs
reorder columns and output new spreadsheet
script to reorder columns in a spreadsheet according to a newick tree
input should guess eol char, output should have rn
Merge pull request #40 from andrewjpage/reorder_spreadsheet

Reorder spreadsheet