PeakAnalyzer is an open-source solution for the automated processing and annotation of genome-wide signal enrichment peaks derived through ChIP-seq, ChIP-chip, DamID and other functional genomic techniques. The software can accurately subdivide multimodal regions of signal enrichment into distinct subpeaks corresponding to binding sites or chromatin modifications, retrieve genomic sequences encompassing the computed subpeak summits, and identify positional features of interest such as intersection with exon/intron gene components, proximity to up- or downstream transcriptional start sites and cis-regulatory elements.