Parallelizing the Phylogeny Problem

Abstract

The problem of determining the evolutionary history of species in the form of phylogenetic trees is known as the phylogeny problem. We present a parallelization of the character compatibility method for solving the phylogeny problem. Abstractly, the algorithm searches through all subsets of characters, which may be traits like opposable thumbs or DNA sequence values, looking for a maximal consistent subset. The notion of consistency in this case is the existence of a particular kind of phylogenetic tree called a perfect phylogeny tree. The two challenges to achieving an efficient implementation are load balancing and efficient sharing of information to enable pruning. In both cases, there is a trade-off between communication overhead and the quality of the solution. For load balancing we use a distributed task queue, which has imperfect load information but avoids centralization bottlenecks. For sharing pruning information, we use a distributed trie, which also avoids centralization but maintains incomplete information. We evaluate several implementations of the trie, the best of which achieves speedups of 50 on a 64-processor CM-5.