multiple queries

[romseg]

Dear author,

Thanks for developing and maintaining such useful program.

I am wondering how can I use nucmer with multiple queries? All the information is given for a single multifasta query file, which was useful when I had one query, but now I have 90 multifasta query files (90 different individuals). My goal after alignment with nucmer is to generate a vcf file reporting the small variations for the 90 queries, and to use the vcf file for population structure analysis. I would appreciate your help. Thank you.

Rom