Bipartite gene-sharing network of double-stranded DNA viruses

Bipartite gene-sharing network of double-stranded DNA viruses. The network was built by connecting each virus genome to all the gene families present in that genome, and each gene family to all the virus genomes in which it is present. By construction, the network has two classes of nodes, corresponding to virus genomes and orthologous gene families. Two networks are provided: the complete gene-sharing network (*_fullnet_*), which includes all gene families, and a core network (*_corenet_*), which only includes gene families with low turnover rates (equivalently, high within-lineage retention). Details on the network construction and a comprehensive analysis of its structure can be found in Iranzo J, Krupovic M, Koonin EV. 2016. The Double-Stranded DNA Virosphere as a Modular Hierarchical Network of Gene Sharing. mBio 7:10.1128/mbio.00978-16. File contents dsDNAvirus_*_viruses.tsv: Tab-delimited list of virus genomes, with the following columns: (1) virus node ID; (2) virus name; (3) corresponding entry in Iranzo et al (mBio 2016) Supplemental Table S2 ("0" implies that the virus is not present in the core network); (4) taxonomic group at the time of publication. dsDNAvirus_*_genes.tsv: Tab-delimited list of gene families, with the following columns: (1) gene node ID; (2) representative sequence ID; (3) corresponding entry in Iranzo et al (mBio 2016) Supplemental Table S1 ("0" implies that the gene family is not present in the core network); (4) annotation. The representative sequence ID can be an NCBI GI, a RefSeq/GenBank ID, or exceptionally, a local identifier referring to an open reading frame (ORF) within an NCBI nucleotide or genome ID. dsDNAvirus_*_links.tsv: Tab-delimited list of links in the network. Each row correspond to a link, with the virus node ID in the first column and the gene family node ID in the second column.