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Phylogenetic footprinting is an increasingly popular comparative genomics method for detecting regulatory elements in DNA sequences. With the profusion of possible methods to use for phylogenetic footprinting, the biologist needs some guidance to choose the most appropriate tool. We present methods for comparing tools on phylogenetic footprinting data. More specifically, we discuss two different classes of comparative experiments: those on simulated data and those on real orthologous promoter regions. We then report the results of a series of such empirical comparisons. The tools compared are the alignment-based methods using ClustalW and Dialign, and the motif-finding programs MEME and FootPrinter. Our results show that methods taking the species' phylogenetic relationships into consideration obtain better accuracy.