Given that construction, analysis, and visualization software is still rapidly evolving, determining how to archive and present the data presents a significant challenge to data resource personnel.
Pan-genes
As pan-genes are just sets of gene models grouped by synteny and sequence similarity, these can be represented fairly simply with tables. If addition data is to be attached, for example, classical gene loci, expression data, protein accessions, a relational database may be a good solution.
Databases should provide the ability to download all or a subset of the pan-genes, with or without associated data as a table.
See Visualizing Pan-Genomes for ideas on how to visualize and browse pan-gene data.
See Constructing and analyzing Pan-Genomes for information about pan-gene analyses.
Pan-genomes
[graphs ... difference tables? (e.g. just the insertions, deletions, inversions, translations relative to a reference) ... ?]