D570 Nucleic Acids Research, 2011, Vol. 39, Database issue We present the ﬁrst public release of PhEVER, a unique database of homologous gene families containing se- quences (i) of all completely sequenced viruses and (ii) from fully sequenced cellular organisms. The protein sequences are clustered—without a priori and according to similarity criteria—into families containing either only viral sequences or both viral and cellular sequences. PhEVER integrates extensive data from up-to-date com- pletely sequenced genomes spanning a wide taxonomic range (2426 non-redundant viral genomes, 1007 non-redundant prokaryotic genomes, 43 eukaryotic genomes ranging from plants to vertebrates). To our knowledge, this is the most complete database of families of homologous viral sequences. Indeed, it not only spans all known viral groups but it also has the unique feature of presenting homologies with eukaryotic and prokaryotic sequences. The database offers a cluster- ing of proteins into homologous families containing at least one viral sequence, as well as pre-computed align- ments and phylogenies for each of these families. Alignments and phylogenies are built according to state-of-the-art phylogeny procedures and we provide tools to edit them and recompute them on the ﬂy (14). We also provide the possibility for users to assign their sequence of interest to a family and to re-build the phyl- ogeny accordingly through the HoSeqI tool (15). PhEVER thus constitutes a comprehensive working tool to detect sequence homologies and possible gene transfer events. Public access and documentation is available through the database webpage and through all dedicated ACNUC retrieval systems (16). FAMILIES OF VIRAL PROTEINS We developed a genome-wide cross-taxa approach to build a database of families of homologous sequences and to provide accurate alignments and phylogenies for the constructed families. The layout of the implementation of the PhEVER database is represented in Figure 1 and the details concerning its sequence content are available in Table 1. In order to avoid redundancy due to the avail- ability of numerous genomes of similar bacterial and viral strains in public databases, we collected all completely sequenced viral and bacterial genomes from RefSeq Viral (17) and Genome Reviews (18), two non-redundant and curated databases of completely sequenced genomes. To this high-quality curated data composed of Archaea, Bacteria and Eukarya, we added nine eukaryotic genomes from Ensembl (Aedes aegypti, Anopheles gambiae, Bos taurus, Caenorhabditis elegans, Danio rerio, Drosophila melanogaster, Gallus gallus, Homo sapiens, Mus musculus) (19) to allow for a large representation of species from the different domains of life. The PhEVER database was structured under the ACNUC system (20) allowing it to be queried using a web interface and a large number of tools speciﬁcally developed for this database management system (14). From the ﬂat ﬁles containing the genomes and their annotations, two databases were built under the ACNUC database management system (20), which is spe- ciﬁcally 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.