PanACEA (Pan-genome Atlas with Chromosome Explorer and Analyzer) is an interactive tool for Pan-Genome visualization. It consists of multi-tiered, hierarchical display pages enabling the navigation of both detailed and high-level views of the data to include both core and variable pan-chromosome regions down to single genes. Regions and genes are functionally annotated to allow for rapid searching and visual identification of regions of interest with the option that user-supplied genomic phylogenies and metadata can be incorporated.

Key Features

  • Exploration on chromosomes and plasmids, including flexible regions.
  • Rapidly find and highlight genes of interest including virulence factors and antimicrobial resistance genes.
  • Display the gain or loss of genes or regions of interest on the genome phylogeny.
  • Allows for easy download of resulting images and tables.

Sample Output

Sample output from PanACEA
The capability of PanACEA as a research tool is demonstrated by highlighting the gat and aga variable regions which are important in differentiating strains of Enterobacter hormaechei. PanACEA displays include pan-chromosome images (A), fGR view (B), and phylogeny (C).


BMC bioinformatics. 2018-06-27; 19.1: 246.
PanACEA: a bioinformatics tool for the exploration and visualization of bacterial pan-chromosomes
Clarke TH, Brinkac LM, Inman JM, Sutton G, Fouts DE
PMID: 29945570


This project has been funded in whole or part with federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services under Award Number U19AI110819.