GAP is a java-designed software for generalized association plots (Chen, 2002) and exploratory data analysis. It is programmed for the java runtime environment 1.5 (JRE version 1.5.0_04), which is available for most operating systems. 
Last Updated: 2012/05/15


Dr. Han-Ming Wu
Department of Mathematics,
    Tamkang University
    Tamsui, Taiwan, R.O.C.
    E-mail: hmwu AT mail.tku.edu.tw
    Homepage: http://www.hmwu.idv.tw

Dr. Chun-houh Chen
     Institute of Statistical Science,
     Academia Sinica
     Taipei, Taiwan, R. O. C.
    E-mail: cchen AT stat.sinica.edu.tw
    Homepage: http://gap.stat.sinica.edu.tw


Official Website of GAP Software:

Mirror Website

Current Version:
 v0.2.7, Build 20110331




The GAP Main Window [more screenshots...]


  • Clustering Analysis: hierarchical clustering, rank-two ellipse seriation

  • Various Display Conditions

  • Histogram, 2D Scatterplot, 3D Scatterplot (Rotatable)

  • Covariate adjustment MV.

  • Data ordering comparison.



  • MS Windows (XP, 2000, 7) Version
  • MS Windows 7 (64bit) Version: coming soon.
  • Mac Version: coming soon.
  • Linux Version: coming soon.
  • Note:
  • Using larger memory: For example (in the DOS console window):  java -Xms1024m -Xmx2048m GAPSoftware.jar
  • Upgrade: please uninstall the previous version and install the current version.




 Citing GAP

 To cite GAP in your publications, please use some of the following articles:


This package and its contents are Copyright ?2005-2008 Lab for Information Visualization, All Rights Reserved.


 Use of this software you indicates your acceptance of this license agreement and warranty.

 Articles Using/Citing GAP Software

 Articles citing GAP are listed in our web site.

  • Lin, S.H., Liu, C.M., Liu, Y.L., Fann, C. S.J., Hsiao, P.C., Wu, J.Y., Hung, S.I., Chen, C.H., Wu, H.M., Jou, Y.S., Liu, S.K., Hwang, T.J., Hsieh, M.H., Chang, C.C., Yang, W.C., Lin, J.J., Chou, F.H.C., Faraone, S.V., Tsuang, M.T., Hwu, H.G. and Chen, W.J. (2009), Clustering by Neurocognition for Fine Mapping of the Schizophrenia Susceptibility Loci on Chromosome 6p. Genes, Brain and Behavior 8(8):785-794.
  • Tien, Y. J., Lee, Y. S, Wu, H. M. and Chen, C. H.* (2008), Methods for Simultaneously Identifying Coherent Local Clusters with Smooth Global Patterns in Gene Expression Profiles. BMC Bioinformatics 9:155, 1-16.
  • Fielding, A.H., 2007. Cluster and Classification Techniques for the Biosciences, Cambridge University Press; 1 edition.
  • Lee, Y.S., Chen, C.H., Chao, A., Chen, E.S., Wei, M.L., Chen, L.K., Yang, K., Lin, M.C., Wang, Y.H., Liu, J.W., Eng, H.L., Chiang, P.C., Wu, T.S., Tsao, K.C., Huang, C.G., Tien, Y.J., Wang, T.H., Wang, H.S., Lee, Y.S., 2005. Molecular signature of clinical severity in recovering patients with severe acute respiratory syndrome
    coronavirus (SARS-CoV). BMC Genomics 6:132.

Please let us know if we are missing your publications. If you have used GAP in a publication, we would love to learn more about how the software was useful to you. Contact us at: hmwu@mail.tku.edu.tw.  


Frequently asked questions.

Bug Reports/Fixed

Bug reports and fixed. see [GAP Forum]

GAP Forum

Generalized Association Plots (GAP) Forum: Please register in the GAP Forum, so that you can download the software and post questions.


 Some Java Tools and the Numerical/Statistical/Graphics Library I Used in Developing GAP Software:

Send Your Comments to Han-Ming Wu (Hank), hmwu@mail.tku.edu.tw 
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