Abstract Summary: To annotate newly sequenced organisms, cross-species sequence comparison algorithms can be applied to align gene sequences to the genome of a related species. To improve the accuracy of alignment, spaced seeds must be optimized for each comparison. As the number and diversity of genomes increase, an efficient alternative is to cluster pairwise comparisons into groups and identify seeds for groups instead of individual comparisons. Here we investigate a measure of comparison closeness and identify classes of comparisons that show similar seed behavior and therefore can employ the same seed. Availability: Source code is freely available at http://dna.cs.gwu.edu and from Bioinformatics online. Contact: [email protected], [email protected] Supplementary information: Supplementary data are available at http://dna.cs.gwu.edu and Bioinformatics online.