Key resources table.

Reagent type (species) or resource	Designation	Source or reference	Identifiers	Additional information
Software, algorithm	fineSTRUCTURE	http://paintmychromosomes.com https://doi.org/10.1371/journal.pgen.1002453	SCR_018170
Software, algorithm	MUMmer	http://mummer.sourceforge.net/ https://doi.org/10.1186/gb-2004-5-2-r12	SCR_018171
Software, algorithm	Prokka	https://github.com/tseemann/prokka https://doi.org/10.1093/bioinformatics/btu153	SCR_014732
Software, algorithm	Roary	https://sanger-pathogens.github.io/Roary/ https://doi.org/10.1093/bioinformatics/btv421	SCR_018172
Software, algorithm	TreeBest	http://treesoft.sourceforge.net/treebest.shtml	SCR_018173
Software, algorithm	iTOL	https://itol.embl.de/ https://doi.org/10.1093/nar/gkw290	SCR_018174
Software, algorithm	SuperDCA	https://github.com/santeripuranen/SuperDCA https://doi.org/10.1099/mgen.0.000184	SCR_018175
Software, algorithm	SpydrPick	https://github.com/santeripuranen/SpydrPick https://doi.org/10.1093/nar/gkz656	SCR_018176
Software, algorithm	Circos	http://circos.ca/ https://doi.org/10.1101/gr.092759.109	SCR_011798