One of the applications of PhEVER is the detection of horizontal gene transfer events by comparing a gene family tree with the expected species tree. The discrepancies between the gene family history and the species phylogeny can then be an indication of possible events including a gene duplication, a gene loss or a horizontal gene transfer. The quality of the gene phylogenies is therefore essential and in this perspective, we implemented a procedure based on a rigorous methodology. First, the clustering into families was built with criteria leading to conservative families. Second, maximum likelihood phylogenetic trees were inferred for all families based on conserved aligned blocks. In our databases, for all families containing at least three sequences, pre-computed alignments and phylogenies are therefore already available. This allows for a simple and accurate overview of any family without the need of heavy computations and Number of proteins associated to a family, followed by the proportion of proteins associated to a family in the taxonomic group. can be a useful tool to search for lateral gene transfers in viral genes. For each family containing at least three sequences, 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.