Big Trees

The Big Tree Working Group focuses on developing and scaling up computational methods for large-scale phylogenetic tree reconstruction, with a specific focus on the broadly-used Maximum Likelihood (ML) method. The group is also working on the Neighbor-Joining method, which is useful when speed is a primary consideration. The goal of this effort is to reconstruct a comprehensive tree of life for the green plants that entails and describes the evolutionary relationships between approximately 500,000 organisms. This tree will then serve as a backbone for the iPToL infrastructure that will successively enrich the bare tree with biological meta-information and provide novel post-tree analysis methods.

To achieve these goals, scalability of the current methods will need to be improved by at least an order of magnitude. In addition, scalable consensus tree reconstruction methods will be required in order to summarize the information contained in potential candidate trees.

The Big Trees Working Group has been collaborating with high performance computing (HPC) specialists in the iPlant core services group to incorporate check-pointing and parallel implementation of RAxML software. Also, the Texas Advanced Computing Center has successfully re-implemented the NINJA neighbor joining program from a standalone java program to an HPC program, written in C++ (WindJammer), that reduces the time required to build a tree of 220,000 species from about 6 days to approximately 4 hours.