Since the algorithm used in CVTree has been described previously (1, 2, 6) , we only give a brief account here. One collects all protein products in a genome and counts the number of (overlapping) K-tuples to form a raw CV with 20 K or 4 K components, depending on whether protein or coding DNA sequences are used (both options are allowed in CVTree, but protein sequences are recommended). Furthermore, one predicts the number of K-tuples from that of K À 1-mers and K À 2-mers by using a simple Markovian assumption. The differences between the prediction and the actual counts are taken as new components of a 'renormalized' CV. One may consult (1, 2, 6) or the online user's manual (available from the CVTree home page or http://tlife. fudan.edu.cn/cvtree/help/help.pdf) for more detailed description.