Precomputed PPanGGOLiN pangenomes for over 4,600 prokaryotic species (Genome Taxonomy Database clusters), with plasticity regions and modules, downloadable via web, API and command line for projection onto new genomes.

Nucleic Acids Research · Sep 21, 2026Peer-reviewedBioinformatics✦ In-depth digest

Panorama: a robust pangenome-based method for predicting and comparing biological systems across species

Jérôme Arnoux, Jean Mainguy, Laura Bry, Quentin Fernandez De Grado, Yazid Hoblos, David Vallenet, Alexandra Calteau

PANORAMA predicts and compares biological systems across species using pangenome graphs, demonstrating effectiveness on Pseudomonas and Enterobacteriaceae genomes.

PLoS Computational Biology · Jul 10, 2026Peer-reviewedBioinformatics

panModule: detecting conserved modules in the variable regions of a pangenome graph

Adelme Bazin, Claudine Médigue, David Vallenet, Alexandra Calteau

panModule identifies conserved modules in pangenome graphs to understand functional gene organization in microbial genomes.

bioRxiv · Dec 6, 2021 · PreprintBioinformatics

panRGP: a pangenome-based method to predict genomic islands and explore their diversity

Adelme Bazin, Guillaume Gautreau, Claudine Médigue, David Vallenet, Alexandra Calteau

panRGP predicts genomic islands and explores their diversity using pangenome graphs across hundreds of genomes.

Bioinformatics · Sep 9, 2020Peer-reviewedBioinformatics

PPanGGOLiN: Depicting microbial diversity via a Partitioned Pangenome Graph

Guillaume Gautreau, Adelme Bazin, Mathieu Gachet, Rémi Planel, Laura Burlot, Mathieu Dubois, Amandine Perrin, Claudine Médigue, Alexandra Calteau, Stéphane Cruveiller, Catherine Matias, Christophe Ambroise, Eduardo P. C. Rocha, David Vallenet

PPanGGOLiN partitions pangenome graphs to classify gene families into persistent, cloud, and shell partitions, revealing insights into genome dynamics and diversity.

PLoS Computational Biology · Mar 19, 2020Peer-reviewedBioinformatics