Large Scale Phylogenetic Computation

Coronaviruses provide a challenge to phylogenetic analysis because they have large genomes that lack of proof reading thus leading to a high mutation frequency. Furthermore, Coronaviruses evolve not only via mutation but also via recombination and locus insertion and deletion (e.g., as seen in SARS-CoV).

Influenza is similarly challenging as it has a complex genome organization comprised of eight segments. The genome organization of influenza permits evolution via mutations and segmental reassortment. Complex mixtures of these events can be associated with host shifts that lead to pandemics.

The tree of life project is computationally challenging because the search space is vast and the organisms have very old 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 and self-built computing clusters comprised of commodity PC components.

Project Researchers

Daniel Janies, Ph.D. (Principal Investigator)

Project Funding Participation

Assembling the Tree of Life: An Integrative Approach to Investigating Cnidarian Phylogeny

Project Publications