Hello everyone! I've been trying to build core genomes of HIV and SIV viruses using Roary. But I keep getting 0 core genes. I've tried changing "minimum percentage identity for blastp" parameter. I used the default value first and here's the result :

Core genes  (99% <= strains <= 100%)    0
Soft core genes (95% <= strains < 99%)  0
Shell genes (15% <= strains < 95%)  0
Cloud genes (0% <= strains < 15%)   511
Total genes (0% <= strains <= 100%) 511

Then I changed it to 70 and here's what I got:

Core genes  (99% <= strains <= 100%)    0
Soft core genes (95% <= strains < 99%)  0
Shell genes (15% <= strains < 95%)  14
Cloud genes (0% <= strains < 15%)   78
Total genes (0% <= strains <= 100%) 92

I don't understand why shell and cloud genes numbers varied!! nor why the core genes number is 0! Is it because these viruses are highly mutable? Should I change the default value of other parameters? if that so , what s are the values of parameters i should use , also , Could anyone recommend me any other tool more specific for core genome viruses analysis to construct core genomes of these viruses? Many thanks