1. A method of characterizing a document in a collection comprising: incrementally updating a suffix tree comprising: for a first batch of documents in a collection, providing an initial suffix tree based on a first sequence of symbols drawn from an alphabet, the suffix tree comprising existing nodes representing respective subsequences occurring in the first sequence of symbols, the existing nodes being associated with information relating to membership of the subsequences in at least one class of repeat subsequences; for a second batch of documents in the collection, receiving a second sequence of symbols drawn from the alphabet; based on the second sequence of symbols, updating the initial suffix tree to form an updated suffix tree, the updating including adding new nodes representing subsequences occurring in the second sequence of symbols that are not represented by the existing nodes; ordering the subsequences represented by the new nodes in a new node data structure, the order of the subsequences in the new node data structure being based on at least one of a length of the respective subsequence and a depth of the respective new node in the updated suffix tree; and processing the ordered new node data structure in an order based on the at least one of subsequence length and subsequence depth, the processing including 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; for at least one of the documents in the collection, outputting information characterizing the at least one document, based on the updated information relating to the at least one class of repeat subsequences associated with the nodes in the updated suffix tree, and wherein at least one of the providing, receiving adding, ordering, and processing is performed with a computer processor.