Representative Genomes
- HRGMv2_Rep_Genome/     : Genome sequences (FASTA format) for 4,824 HRGMv2 representative genomes (one per species) - HRGMv2_Rep_Genome.tar.gz     : Compressed archive of the HRGMv2_Rep_Genome/ folder Pangenomes
- HRGMv2_Pangenomes/
    : Pangenome data for all 4,824 species, structured as follows:
    For Multi-genome species (2,639 species): Species with more than one non-redundant genome. Each folder contains the full output of Panaroo v1.3.0. (Refer to the Panaroo GitHub for detailed file descriptions.)
        - combined_DNA_CDS.fasta.gz         - combined_protein_CDS.fasta.gz         - combined_protein_cdhit_out.txt         - combined_protein_cdhit_out.txt.clstr         - final_graph.gml         - gene_data.csv.gz         - gene_presence_absence.csv         - gene_presence_absence.Rtab         - gene_presence_absence_roary.csv         - pan_genome_reference.fa – nucleotide sequences         - pan_genome_reference.faa – amino acid sequences         - pre_filt_graph.gml         - struct_presence_absence.Rtab         - summary_statistics.txt         - emapper_results/ – eggNOG-mapper results for pan_genome_reference.fa         - rgi_results/ - RGI results for pan_genome_reference.fa     For Single-genome species (2,185 species): Species with only one non-redundant genome. Pangenomes were generated directly from the representative genome, including:
        - pan_genome_reference.fa – nucleotide sequences         - pan_genome_reference.faa – amino acid sequences         - emapper_results/ – eggNOG-mapper results for pan_genome_reference.fa         - rgi_results/ – RGI results results for pan_genome_reference.fa - For bulk download:
    1. HRGMv2_Pangenomes.tar.gz – Archive of the entire HRGMv2_Pangenomes/ folder     2. Pangenome_download_link_info.tsv – Table with full download URLs for each species