High similarity of short regions, however, does not necessarily imply homology (a gene derived from a common ancestral gene) and can lead to false implications of relatedness among sequences that are not homologs. By contrast, global alignments do require that the order and orientation of similar regions is conserved, because similar architecture is often observed in homologous sequences (Bray et al. 2003) . MultiPipMaker and VISTA provide visualization options for alignments that include percent similarity and usersubmitted annotations (e.g., exon locations, repetitive elements). It is important to note that local and global alignment tools are being refined so rapidly that it is becoming difficult to distinguish between them (Frazer et al. 2004) . Readers are referred to two recent reviews of alignment programs for detailed comparisons (Frazer et al. 2003; Pollard et al. 2004) .