Faster Repetition-Aware Compressed Suffix Trees based on Block Trees

Manuel Cáceres and Gonzalo Navarro

The suffix tree is a fundamental data structure in stringology, but its space usage, though linear, is an important problem in applications like Bioinformatics. We design and implement a new compressed suffix tree (CST) targeted to highly repetitive texts, such as large genomic collections of the same species. Our first contribution is to enhance the Block Tree, a data structure that captures the repetitiveness of its input sequence, to represent the topology of trees with large repeated subtrees. Our so-called Block-Tree Compressed Topology (BT-CT) data structure augments the Block Tree nodes with data that speeds up tree navigation. Our Block-Tree CST (BT-CST), in turn, uses the BT-CT to compress the topology of the suffix tree, and also replaces the sampling of the suffix array and its inverse with grammar- and/or Block-Tree-based representations of those arrays.

Our experimental results show that BT-CTs reach navigation speeds comparable to compact tree representations that are insensitive to repetitiveness, while using 2-10 times less space on the topologies of the suffix trees of repetitive collections. Our BT-CST is slightly larger than previous repetition-aware suffix trees based on grammar-compressed topologies, but outperforms them in time, often by orders of magnitude.