An application of an OR-Parallel Prolog system to phylogenetic analysis

Abstract

In this paper we discuss an application of our OR-Parallel Prolog system to a search problem of importance in practice: the construction of phylogenetic trees. The use of a maximum likelihood method to construct such trees is based on concrete models of evolutional processes and is well-motivated statistically. However, the use of maximum likelihood methods has been hindered by the computational cost to calculate the likelihood of possible alternative trees (i.e. their confidence scores) at each search step for the optimal tree. To cope with this problem, we used OR-parallel Prolog as a “coordination language” to orchestrate the search for the optimal tree. A numerical computation written in C computed the likelihood of each alternative tree and a symbolic computation written in Prolog performed a parallel A* tree search. For constructing phylogenetic trees of bacterial organisms, our parallel algorithm allowed us to increase the size of the search space, allowing us to include nearly optimal as well as optimal intermediate trees in the search. Our priority mechanism reduced the generation of useless tasks and resulted in superlinear speedups in some cases.