I would like to perform a whole genome alignment tree and a whole genome SNP calling.
I was thinking to use different tools (e.g. Gegenees, kSNP, Mauve).
My problem is that I have complete genomes and draft genomes. For the complete ones I have sometimes one or more plasmid.
What do you think is the best way of doing it, concatenating Chromosome and Plasmid and analyse them with the drafts or include in the analysis only the Chromosome and the drafts?