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Description: MADAP is a flexible clustering tool for the interpretation of one-dimensional genome annotation data. Such data might consist of counts, probabilities, or intensities associated with genome positions. They may be generated by mapping mRNA 5' and 3' sequence tags to genomes, by ChIP-chip or ChIP-Seq assays, or by genome-wide genotype-phenotype association studies. MADAP identifies clusters of data points corresponding to genomic features.