doi: 10.1093/bioinformatics/btu568
JAMM (Joint Analysis of NGS replicates via Mixture Model clustering): a peak finder that can integrate information from biological replicates, determine enrichment site widths accurately and resolve neighboring narrow peaks. JAMM is a universal peak finder that is applicable to different types of datasets
The latest release of the stand-alone version can be found here: http://code.google.com/p/jamm-peak-finder/
(You can also use the stand-alone version from this repository, ignoring the Galaxy-specific files. The upstream version might be never, though)
This is a wrapper for JAMM for use in Galaxy (usegalaxy.org)