In-place differential file compression of non-aligned files with applications to file distribution, backups, and string similarity

We consider in-place differential file compression; that is, compressing a file T of size n with respect to an existing file S of size m, where decompression is in-place by overwriting S with T, using at most MAX(m,n)+O(1) space. In previous work we presented the IPSW algorithm (In-Place Sliding Window). IPSW is fast and the compression achieved compares well with other existing methods, including those that are not in-place. IPSW is most effective when S and T are reasonably well aligned (most large common substrings occur in approximately the same order). Here we present a preprocessing step for string alignment that can be employed when the encoder determines significant gains will be achieved.