Building large phylogenetic trees on coarse-grained parallel machines

Phylogenetic analysis is an area of computational biology concerned with the reconstruction of evolutionary relationships between organisms, genes, and gene families. Maximum likelihood evaluation has proven to be one of the most reliable methods for constructing phylogenetic trees. The huge computa- tional requirements associated with maximum likelihood analysis means that it is not feasible to produce large phylogenetic trees using a single processor. We have completed a fully cross platform coarse grained distributed application, DPRml, which overcomes many of the limitations imposed by the current set of parallel phylogenetic programs. We have completed a set of efï¬ciency tests that show how to maximise efï¬ciency while using the program to build large phylogenetic trees. The software is publicly available under the terms of the GNU general public li- cence from the system webpage at http://www.cs.nuim.ie/distribute