Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
Suffix arrays: a new method for on-line string searches
SODA '90 Proceedings of the first annual ACM-SIAM symposium on Discrete algorithms
A Space-Economical Suffix Tree Construction Algorithm
Journal of the ACM (JACM)
STOC '00 Proceedings of the thirty-second annual ACM symposium on Theory of computing
Reducing the space requirement of suffix trees
Software—Practice & Experience
Succinct representations of lcp information and improvements in the compressed suffix arrays
SODA '02 Proceedings of the thirteenth annual ACM-SIAM symposium on Discrete algorithms
The Enhanced Suffix Array and Its Applications to Genome Analysis
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
Compressed Text Databases with Efficient Query Algorithms Based on the Compressed Suffix Array
ISAAC '00 Proceedings of the 11th International Conference on Algorithms and Computation
Linear-Time Longest-Common-Prefix Computation in Suffix Arrays and Its Applications
CPM '01 Proceedings of the 12th Annual Symposium on Combinatorial Pattern Matching
Optimal suffix tree construction with large alphabets
FOCS '97 Proceedings of the 38th Annual Symposium on Foundations of Computer Science
Opportunistic data structures with applications
FOCS '00 Proceedings of the 41st Annual Symposium on Foundations of Computer Science
Replacing suffix trees with enhanced suffix arrays
Journal of Discrete Algorithms - SPIRE 2002
Journal of the ACM (JACM)
Compressed Suffix Arrays and Suffix Trees with Applications to Text Indexing and String Matching
SIAM Journal on Computing
Succinct suffix arrays based on run-length encoding
Nordic Journal of Computing
A taxonomy of suffix array construction algorithms
ACM Computing Surveys (CSUR)
Compressed Suffix Trees with Full Functionality
Theory of Computing Systems
Compressed indexing and local alignment of DNA
Bioinformatics
An(other) Entropy-Bounded Compressed Suffix Tree
CPM '08 Proceedings of the 19th annual symposium on Combinatorial Pattern Matching
Linear pattern matching algorithms
SWAT '73 Proceedings of the 14th Annual Symposium on Switching and Automata Theory (swat 1973)
Permuted Longest-Common-Prefix Array
CPM '09 Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching
Engineering a compressed suffix tree implementation
Journal of Experimental Algorithmics (JEA)
SPIRE'10 Proceedings of the 17th international conference on String processing and information retrieval
WADS'11 Proceedings of the 12th international conference on Algorithms and data structures
Computing the longest common prefix array based on the burrows-wheeler transform
SPIRE'11 Proceedings of the 18th international conference on String processing and information retrieval
Practical compressed suffix trees
SEA'10 Proceedings of the 9th international conference on Experimental Algorithms
Fast, small, simple rank/select on bitmaps
SEA'12 Proceedings of the 11th international conference on Experimental Algorithms
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Suffix trees (STs) and suffix arrays are well known indices which demand too much space for large inputs. Recently, several works explore a data structure called compressed suffix tree (CST), which offers the same functionality than suffix trees and is based on compressed suffix arrays, compressed longest common prefix information and navigational operations. In this paper, the implementation of a CST based on range-minimum-queries and nearest smaller value queries, which requires roughly more than the space needed to represent the index during the construction, is presented. Experiments show that this index is useful for many applications since, on the one side, one can execute complex traversals such as suffix links and longest common ancestor queries that are essential to deal with several questions about the combinatorial structure of sequences; and, on the other side, the structure results of practical interest for applications using computational environments in which the amount of available memory is restricted, because it fits in main memory of ordinary computers.