MultiGPS: software for analyzing collections of multi-condition ChIP-seq datasets
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MultiGPS is a framework for analyzing collections of multi-condition ChIP-seq datasets and characterizing differential binding events between conditions. In analyzing multiple-condition ChIP-seq datasets, MultiGPS encourages consistency in the reported binding event locations across conditions and provides accurate estimation of ChIP enrichment levels at each event.


The following webpage maintains executable JAR files for major versions:


MultiGPS requires Java 8+. To build MultiGPS, you will also need to download and build the seqcode-core library (, and place the build and lib directories on your paths.


An integrated model of multiple-condition ChIP-seq data reveals predeterminants of Cdx2 binding S Mahony, MD Edwards, EO Mazzoni, RI Sherwood, A Kakumanu, CA Morrison, H Wichterle, DK Gifford PLoS Computational Biology (2014) 10(3):e1003501

Major History:

Version 0.74 (2017-04-01): MultiGPS now produces BED files by default (change inherited from update to seqcode-core).

Version 0.73 (2017-02-17): Minor update that includes support for full-genome FASTA files in --seq option and other updates to support Galalxy integration.

Version 0.72 (2016-11-23): First release in this repo. Fixed several bugs for stability.

Version 0.5 (2014-03-01): Initial release with publication. This version predates the current repo, but code is archived here: