Attack of the Mutant Suffix Trees

This is a thesis for the degree of filosofie licentiat (a Swedish degree between Master of Science and Ph.D.). It comprises three articles, all treating variations and augmentations of suffix trees, and the capability of the suffix tree data structure to efficiently capture similarities between different parts of a string. The presented applications are in the areas of data compression and pattern matching. The first article presents a method of using a suffix tree as an index into a sliding window, in optimal time and space, with applications in probabilistic data compression schemes, such as PPM, as well as in ZivLempel compression. The second article presents a generalized suffix tree which is able to index a select subset of the suffixes of a string, with a construction algorithm which is optimal in time and space. The final article deals with the connection between the explicit context trees of PPM and the implicit mechanism of the Burrows-Wheeler transform for block sorting compression, again utilizing the suffix tree to capture the repetitive characteristics of a string. This document was revised on February 3 1998. The differences from the presented thesis are in corrections of trivial errors only.