Pangenomics studies analyze the genomic diversity within species by distinguishing between core and accessory parts of the genome potentially exchanged through horizontal transfers. The PPanGGOLiN method employs a pangenome graph framework to explore this genomic diversity. After explaining the relevance of this framework and some developments over it, this seminar will discuss one improvement of PPanGGOLiN to identify gene families that vary under specific conditions, either by tagging genome phenotypes or mapping metagenomics reads against the pangenome.