Scaffold Hunter logo

Scaffold Hunter

Scaffold Hunter is a Java-based open source tool for the visual analysis of data sets with a focus on data from the life sciences, aiming at an intuitive access to large and complex data sets. The tool offers a variety of views, e.g. graph, dendrogram, and plot view, as well as analysis methods, e.g. for clustering and classification. Scaffold Hunter has its origin in drug discovery, which is still one of the main application areas, and is evolved into a reusable open source platform for a wider range of applications. The tool offers flexible plugin and data integration mechanisms to allow adaption to new fields and data sets, e.g. from medical image retrieval. Scaffold Hunter is used worldwide in research, both academic and commercial, and for teaching at the Technical University of Dortmund, Germany, and the University of Sydney, Australia.

Please visit our Sourceforge project site for further information or follow one of the direct links to specific subpages:


Close-up view of a scaffold tree Several views showing data and statistical analysis results


Please cite either of the following papers when you use Scaffold Hunter in your publications and refer to the Scaffold Hunter Website at


Scaffold Hunter is currently developed as an open project at Sourceforge and supported by:
Chair of Algorithm Engineering logo
Chair 11: Workgroup Algorithm Engineering
Department of Computer Science
TU Dortmund
Chemistry and Chemical Biology logo
Medicinal Chemistry: Workgroup Koch
Faculty of Chemistry and Chemical Biology
TU Dortmund
MArVL logo
MArVL: Monash Adaptive Visualisation Lab
Faculty of Information Technology
Monash University


The Scaffold Hunter project was initiated by Karsten Klein (Chair 11: Workgroup Algorithm Engineering, TU Dortmund) and Stefan Wetzel (Chemical Biology, MPI for Molecular Physiology Dortmund), a first version of Scaffold Hunter was implemented by the student project group PG504 at TU Dortmund under their supervision. For version 2.x, many parts of it were improved, extended, and rewritten by the student project group PG552 under the supervision of Carsten Gutwenger, Nils Kriege, and Karsten Klein at TU Dortmund.
We would like to thank the members of PG504, Anke Arndt, Vanessa Bembenek, Ambia Ben Ahmed, Philipp Büdenbender, Nils Kriege, Adalbert Gorecki, Sergej Rakov, Michael Rex, Gebhard Schrader, Henning Wagner, André Wiesniewski, and Cengizhan Yücel, and the members of PG552, Bernhard Dick, Thorsten Flügel, Henning Garus, Michael Hesse, Philipp Kopp, Philipp Lewe, Dominic Sacré, Till Schäfer, and Thomas Schmitz, for their contribution and enthusiasm in creating the prototype application. The final reports of PG504 and PG552 can be retrieved here and here, respectively.
Parts of the software have been developed within the programs Google Summer of Code 2013 and 2014 by Jeroen Lappenschaar, Andrey Zhylka and Werner Sturm. The research assistants Nils Kriege, Till Schäfer, Sven Schrinner and Philipp Mewes have contributed to the development of Scaffold Hunter in the last years.