PhEVER is structured under the ACNUC sequence database management system and a large number of tools have been developed around this database management 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 For all figures, only trees with more than four leaves are presented here. Branches with length smaller than 10 À5 were considered unresolved multifurcations and were discarded.