Calculating Genome Permulations from RNA Virus sequence

Hi I have been wondering about the ways of getting genome permulations derived from Virus RNA/DNA sequence. Please suggests any tools that I can do that with.

Can you explain what you mean by permulations?

I meant gene order in a genome. Different genome might have different gene order for a set of genes due to the genome rearrangement.

Hope this helps.

Nextstrain tools aren’t the right tools for this question - our entry point is consensus genomes which have been (typically) mapped to a reference.

Thanks James for responding my query.