D572 Nucleic Acids Research, 2011, Vol. 39, Database issue Figure 2. Global information on PhEVER content. (A) Number of species, proteins, families in each viral group [groups correspond to the NCBI Taxonomy following the ICTV nomenclature (36); groups corresponding to the Baltimore classiﬁcation are additionally indicated in Roman notation (24)]. (B) Venn diagram of the number of families, non-orphan families and families containing Bacteria and Eukarya. aOrphan families are families containing only one viral sequence and no other sequence. This sequence presents no sufﬁcient similarity with any sequence of the database, bNon-orphan families are all families containing at least two sequences, cFamilies containing at least one viral sequence and one eukaryotic (E) sequence, dFamilies containing at least one viral sequence and one bacterial (B) sequence and eFamilies containing at least one viral sequence, one eukaryotic sequence and one bacterial sequence (E+B). can be a useful tool to search for lateral gene transfers in viral genes. For each family containing at least three se- quences, alignments were estimated using MUSCLE with default parameters (25). All alignments were treated with Gblocks (26) to select conserved blocks. Phylogenetic trees were inferred by maximum likelihood using PhyML (27) with a JTT evolutionary model (28). Branch support was inferred using the Shimodaira–Hasegawa-like non-parametric procedure implemented in PhyML (27,29). To accommodate for weak phylogenetic signal, a thorough exploration of the tree space was made through topological rearrangements using the Nearest Neighbor Interchange topology search method. Finally, for visualization purposes, the trees were then rooted using midpoint rooting. This procedure allowed us to build accurate phylogenies sustained by branches of high support values. Indeed, Figure 3 shows that 80% of all branch supports have a value higher than 75 and one-third are above 95. Global statistics are biased by the presence of low branch supports. These are mostly due to few small families of less than 10 leaves, indicating that most families present robust phylogenies (Figure 3B). Finally, Figure 3C indicates that the low branch support values are attributable to very similar sequences with small branch lengths and might be linked to unresolved topologies. By contrast, all branch lengths longer than 0.15 subst/site display a high branch support which reveals the accuracy of our phylogenetic inference procedure. QUERY THE DATABASE PhEVER is structured under the ACNUC sequence database management system and a large number of tools have been developed around this database manage- ment system [see (16) for an overview]. PhEVER can therefore be queried using (i) web applications, (ii) standalone software (iii) or embedded within Python, R or C code. The PhEVER web interface is available at http://pbil.univ-lyon1.fr/databases/phever and allows to search for sequences or families by combining several criteria (including species, gene names, annotation terms) as well as by crossing taxa. The graphical user interface QUERY_WIN and the terminal-based interface Raa_query (16) implement more features than the web interface and allow for remote ACNUC access and query as well as for the automatization of querying processes through standalone software. Finally the C language API, Python language API (16) and the seqinR package for R (30) implement tools for integrating queries in user designed code. Note that the PhEVER database can also be installed on a local machine or server for fastest data access. All ﬁles necessary for the PhEVER