From the flat files containing the genomes and their annotations, two databases were built under the ACNUC database management system (20) , which is specifically aimed at building, storing and querying biological sequence data. One of them contains the nucleic sequences, the other contains the proteins generated by translating all CDS of the complete genomes-using the Figure 1 . Flow chart of the PhEVER building process. Complete genomes and their annotations were retrieved from three external public databases (Ensembl, Genome Reviews and RefSeq Viral) to provide high-quality non-redundant data for Eukarya, Archaea, Bacteria and Viruses. Two databases (nucleic acids, proteins) were constructed from this data to form PhEVER. All annotated CDS and mature peptides were translated and used for the clustering procedure. The homologous families thus produced were annotated in PhEVER, and alignments and phylogenies were built for each family and incorporated in the databases. appropriate genetic codes. For viral genomes presenting polypeptides which further maturate in vivo into mature peptides, the mature peptides were added to the set of translated proteins according to the annotations specified in the given genome ( Figure 1 ). Table 1 lists the global content of the databases as well as their original sources. Annotations were extracted from UniProtKB via the cross-references found in the CDS (21) . Subsequently, sequences in the nucleic and protein PhEVER database were clustered into families and were assigned a family accession number. Alignments and phylogenies were built for each of these families according to state-of-the-art procedures ( Figure 1 ). The classification of all organisms present in the database was retrieved from the taxonomy database at National Centre for Biotechnology Information (11) and is available on the PhEVER web interface.