Space-Efficient Parallel Construction of Succinct Representations of Suffix Tree Topologies

Abstract

A compressed suffix tree usually consists of three components: a compressed suffix array, a compressed LCP-array, and a succinct representation of the suffix tree topology. There are parallel algorithms that construct the suffix array and the LCP-array, but none for the third component. In this article, we present parallel algorithms on shared memory architectures that construct the balanced parentheses sequence (BPS), an explicit succinct representation of the suffix tree topology, as well as the enhanced balanced parentheses representation (eBPR), an implicit succinct representation of the suffix tree topology. For both representations, this article presents a sequential construction algorithm (a new one for the BPS), a linear work and O (log n ) time parallel construction algorithm, and a heuristic parallel construction algorithm that works very well in practice. The experimental results show that our methods are well suited for real-world applications.