The networks are organized according to type and genone. The 172 network files correspond to 4 networks (chromo, phylo, fusion, and composite) for each of 43 genomes. Each network file lists the edges of the network. In the Composite files there is an additional column to specify the nature of the link: 1 fusion 2 chromo 3 phylo 4 chromo + fusion 5 phylo + fusion 6 chromo + phylo 7 fusion + chromo + phylo The abbreviations for genome names are taken from COG (ftp://ftp.ncbi.nlm.nih.gov/pub/COG/): Afu Archaeoglobus fulgidus Hbs Halobacterium sp. NRC-1 Mja Methanococcus jannaschii Mth Methanobacterium thermoautotrophicum Tac Thermoplasma acidophilum Tvo Thermoplasma volcanium Pho Pyrococcus horikoshii Pab Pyrococcus abyssi Ape Aeropyrum pernix Aae Aquifex aeolicus Tma Thermotoga maritima Dra Deinococcus radiodurans Mtu Mycobacterium tuberculosis Mle Mycobacterium leprae Lla Lactococcus lactis Spy Streptococcus pyogenes Bsu Bacillus subtilis Bha Bacillus halodurans Syn Synechocystis Eco Escherichia coli K12 EcZ Escherichia coli O157 Buc Buchnera sp. APS Pae Pseudomonas aeruginosa Vch Vibrio cholerae Hin Haemophilus influenzae Pmu Pasteurella multocida Xfa Xylella fastidiosa Nme Neisseria meningitidis MC58 NmA Neisseria meningitidis Z2491 Hpy Helicobacter pylori 26695 jHp Helicobacter pylori J99 Cje Campylobacter jejuni Mlo Mesorhizobium loti Ccr Caulobacter crescentus Rpr Rickettsia prowazekii Ctr Chlamydia trachomatis Cpn Chlamydia pneumoniae Tpa Treponema pallidum Bbu Borrelia burgdorferi Uur Ureaplasma urealyticum Mpn Mycoplasma pneumoniae Mge Mycoplasma genitalium The nodes of the network are COGs (Clusters of Orthologous Groups). To translate between a COG and a gene(s) we include the COG database as an additional file, which was retrieved from the COG site (http://www.ncbi.nlm.nih.gov/COG/). The networks can be reconstructed from the list of links provided using any graph analysis software. In this work we used Pajek, a freely available program (http://vlado.fmf.uni-lj.si/pub/networks/pajek/).