Abstract Summary: Identifying and masking repetitive elements is usually the first step when analyzing vertebrate genomic sequence. Current repeat identification software is sensitive but slow, creating a costly bottleneck in large-scale analyses. We have developed MaskerAid , a software enhancement to RepeatMasker that increased the speed of masking more than 30-fold at the most sensitive setting. Availability: On request from the authors (see http://sapiens.wustl.edu/MaskerAid). Contact: [email protected] These authors contributed equally to this work. * To whom correspondence should be addressed. ** Current address: Incyte Genomics, 4633 World Parkway Cir., St. Louis, MO 63134 USA, [email protected]