I want to use roary to get a nice phylogeny of my very close related bacteria (indeed they are nearly the same).
I have them annotated and know that they have ~ 90% identical genes in the same arrangement, but still I get the following summary:
Core genes (99% <= strains <= 100%) 0
Soft core genes (95% <= strains < 99%) 0
Shell genes (15% <= strains < 95%) 2
Cloud genes (0% <= strains < 15%) 3814
Total genes (0% <= strains <= 100%) 3816
How is that possible? I know for sure that genes like rpoB or the LSUs and SSUs are present in all 25 geneoms, but I get a 0 for core genes?
nanzhen102
commented
1 year ago
I want to use roary to get a nice phylogeny of my very close related bacteria (indeed they are nearly the same). I have them annotated and know that they have ~ 90% identical genes in the same arrangement, but still I get the following summary: Core genes (99% <= strains <= 100%) 0 Soft core genes (95% <= strains < 99%) 0 Shell genes (15% <= strains < 95%) 2 Cloud genes (0% <= strains < 15%) 3814 Total genes (0% <= strains <= 100%) 3816
How is that possible? I know for sure that genes like rpoB or the LSUs and SSUs are present in all 25 geneoms, but I get a 0 for core genes?