The tree of life project is computationally challenging because the search space is is vast and the organisms have deep as well as recent divergence times. Thus phylogenetic analyses will require heuristic estimates and exploration of various optimality criteria, alignments, and parameters for transformation costs. We will address the computational costs through parallelization, the synergistic implementation of heuristic tree search strategies. Analyses will be of multiple genes and methods to safeguard against accepting a result specific to one approach. Finally, no one gene can be expected to provide resolution of ancient and recent phylogenetic groups. Via simultaneous analysis of many genes we seek an additive phylogenetic signal that overcomes noise that is expected to be random to that signal.