This is a big improvement over the old MakeUSeq.java application. Tim Mosbruger's also added build targets for deploying to remote servers.
Afraid of the command line? No problem! Give the GUI_ClickMe.jar a try. It wraps a point, click, and drag style GUI around the USeq (and TiMAT2) command line applications. Allows job queuing, saves results, and parameters.
A community challenge was recently held to benchmark the state of the art in chIP-seq detection packages. USeq took 1st in the False Discovery Rate estimation and 2nd the False vs. True positive discrimination categories! See http://seqanswers.com/forums/showthread.php?t=1039 for details.
A description of the statistics and comparison of methods used in USeq is now published, see Nix DA, Courdy SJ, Boucher KM: Empirical methods for controlling false positives and estimating confidence in chIP-seq peaks. BMC Bioinformatics. 2008 Dec 5;9(1):523.
USeq is now launched. First supported application, chIP-seq with a robust empirical FDR estimation.