create the list of genes and their links
breath first search
boost
minimum spanning trees
tests for gene ordering
Merge pull request #51 from andrewjpage/gene_order

Gene order
Identify low evidence hypothetical proteins overlapped by other proteins
filter out low quality groups
awk syntax fix for extracting genes
remove plots that are no longer needed and rename R raw output files
output embl header files
update plot input files
Merge pull request #52 from andrewjpage/overlapping_proteins

Overlapping proteins
fix r plots
Merge pull request #53 from andrewjpage/overlapping_proteins

fix r plots
increase thresholds for similarity
Conflicts:

	dist.ini
Merge branch 'increase_thresholds' of github.com:andrewjpage/Bio-PanGenome into increase_thresholds