Abstract: A method of updating a suffix tree includes providing an initial suffix tree based on a first sequence of symbols drawn from an alphabet. The suffix tree includes existing nodes representing respective subsequences occurring in the first sequence of symbols. The existing nodes are associated with information relating to membership of the subsequences in at least one class of repeat subsequences. A second sequence of symbols is received and the initial suffix tree is updated to form an updated suffix tree by adding new nodes representing subsequences occurring in the second sequence of symbols that are not represented by the existing nodes. The subsequences represented by the new nodes are ordered in a new node data structure which is processed to updating the information relating to the at least one class of repeat subsequences associated with at least some of the nodes in the updated suffix tree.

Abstract: A method for reconstruction includes providing a directed input graph generated from a set of n-grams and statistics for the n-grams, edges of the graph being joined through nodes of the graph. Each edge has an associated label and a multiplicity of at least one. Each of the n-grams in the set being represented by a respective one of the labels, whereby a Eulerian cycle through the graph traverses each edge the respective multiplicity of times. Reduction rules are applied iteratively to generate a refined graph which is both irreducible and equivalent to the input graph. Information is output based on the labels of the refined graph.

Abstract: A method for reconstruction includes providing a directed input graph generated from a set of n-grams and statistics for the n-grams, edges of the graph being joined through nodes of the graph. Each edge has an associated label and a multiplicity of at least one. Each of the n-grams in the set being represented by a respective one of the labels, whereby a Eulerian cycle through the graph traverses each edge the respective multiplicity of times. Reduction rules are applied iteratively to generate a refined graph which is both irreducible and equivalent to the input graph. Information is output based on the labels of the refined graph.

Abstract: A method of updating a suffix tree includes providing an initial suffix tree based on a first sequence of symbols drawn from an alphabet. The suffix tree includes existing nodes representing respective subsequences occurring in the first sequence of symbols. The existing nodes are associated with information relating to membership of the subsequences in at least one class of repeat subsequences. A second sequence of symbols is received and the initial suffix tree is updated to form an updated suffix tree by adding new nodes representing subsequences occurring in the second sequence of symbols that are not represented by the existing nodes. The subsequences represented by the new nodes are ordered in a new node data structure which is processed to updating the information relating to the at least one class of repeat subsequences associated with at least some of the nodes in the updated suffix tree.