The pangenome is the entire gene set of all strains of a species. It includes genes present in all strains (core genome) and genes present only in some strains of a species (variable or accessory genome).
The core genome represents the genes present in all strains of a species. It typically includes housekeeping genes for cell envelope or regulatory functions.
The variable or accessory genome (also: flexible, dispensable genome) refers to genes not present in all strains of a species. These include genes present in two or more strains or even genes unique to a single strain only, for example, genes for strain specific adaptation such as antibiotic resistance.
What is the advantage of extracting the pangenome?
Open or closed pangenome?
Some bacterial species are considered to have an unlimited large gene repertoire (open pangenome) and other species seem to be limited by a maximum number of genes in their gene pool (closed pangenome).
Open pangenome: number of gene of the pangenome increases with the number of additionally sequenced strains
Closed pangenome: after some sequenced strains, additional strains don't provide new genes to the species pangenome
How to compare the gene content of different strains of a species?
see more tools: http://omictools.com/pangenomics-category