parsnp does not recruit all genomes provided

[leogg23]

Hi,

I was trying to align 16 genomes from different pathotypes of the same protist species, but the program only recruited 12. Is there a reason for this? In the bar below the Gingr interface it says that the core is only 87%
Also, is there a way to use the Gingr interface to search only for polymorphic regions. I do not want to scan everything manually, but rather have something that takes me to the next polymorphism. For the little I have scanned I cannot find lots of polymorphisms; for what I can see I can only find polymorphisms of all my sequences to the reference genome but not among them. I know they are very closely related, but there should be differences between pathotypes.

thanks for your help