Qeseq is an algorithm to detect regions of increased ChIP read density relative to background. Qeseq employs critical novel elements, such as iterative recalibration and neighbor joining of reads to identify enriched regions of any length.
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Mariann Micsinai et al.
Picking ChIP-seq peak detectors for analyzing chromatin modification experiments
Nucl. Acids Res. (2012) 40 (9): e70.