Mauve stuff

Feature Matrix in Genoplast format

 bbFilter somebugs_bb.backbone 50 27_my_feats.bin gp 1 2 3 4 5 6 7 8 10 11 12 13 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29

27_my_feats.bin.locs has the genomic coordinates of the features

27_my_feats.bin is the binary presence/absence matrix

Extract an XFMA containing only the core genome regions

1) Use projectandStrip to project the 31-way alignment down to a 27-way

 ./projectAndStrip somebugs_bb new_27_somebugs_bb 1 2 3 4 5 6 7 8 10 11 12 13 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29

2) Reconstruct the backbone file with progressiveMauve

 ./progressiveMauve --apply-backbone=new_27_somebugs_bb --output=new_27_somebugs_with_bb

3) Run stripSubsetLCBs to strip out regions present in < 27 organisms

 ./stripSubsetLCBs new_27_somebugs_with_bb new_27_somebugs_with_bb.bbcols my_27_core.xmfa