PhyloJava is a client/server tool dedicated to phylogenetic tree reconstruction. This program allows phylogenetic tree inferences according to most usual methods (distance methods, maximum parsimony, maximum likelihood).

Phylogenetic trees are computed on a remote server, and are sent via internet to a graphical interface (the client) that allows the user to handle alignments and phylogenetic trees. The user therefore only has to install the graphical interface on his computer, and can submit tree reconstruction jobs on a remote server. Default phylojava server is the one installed at the Pôle Bionformatique Lyonnais (PBIL).