Faster Compressed Suffix Trees for Repetitive Collections

Gonzalo Navarro and Alberto Ordúñez

Recent compressed suffix trees targeted to highly repetitive sequence collections reach excellent compression performance, but operation times are very high. We design a new suffix tree representation for this scenario that still achieves very low space usage, only slightly larger than the best previous one, but supports the operations orders of magnitude faster. Our suffix tree is still orders of magnitude slower than general-purpose compressed suffix trees, but these use several times more space when the collection is repetitive. Our main novelty is a practical grammar-compressed tree representation with full navigation functionality, which is useful in all applications where large trees with repetitive topology must be represented.