PeakAnalyzer requires a peak file and a feature annotation file in BED or GTF format. Complete annotation files for the current builds of the human (HG19) and mouse (MM9) genomes are provided with the software distribution.

The input files required by PeakSplitter are those commonly generated by peak-finding programs: a file containing chromosome start and end locations of peak enrichment loci, and a .wig signal file describing the size and shape of each peak.