Department of Bioinformatics and Computational Biology


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Description A bioinformatics web app for detecting positive selection in proteins using a sliding window substitution rate analysis. Click the link below to use SWAKK.
Development Information
Language Perl CGI
Current Version 2.1.0
License Not required
Status active
Last Updated 2016-01-15
Citations Liang H, Zhou W, Landweber L. (2006).
SWAKK: a web server for detecting positive selection in proteins using a sliding window substitution rate analysis.
Nucleic Acids Research 34:Suppl2 W382-384.
News Updated codebase from Princeton migration.
Help and Support
Contact Han Liang[1]

SWAKK is a valuable bioinformatic tool for detecting amino acid sites or regions of a protein under positive selection. It estimates the ratio of non-synonymous to synonymous substitution rates (Ka/Ks) between a pair of protein-coding DNA sequences, by sliding a 3D window, or sphere, across one reference structure. The program displays the results on the 3D protein structure. In addition, for comparison or when a reference structure is unavailable, the web app can also perform a sliding window analysis on the primary sequence.


Browser Requirements

SWAKK is compatible with all major browsers, including Internet Explorer, Firefox, Safari, and Chrome. Javascript must be enabled by the browser.


Login is not required — it is free for anyone to use.

Release History

  • Version 2.1.0 was released on 2016-01-15 [externally accessible].
  • Version 2.0.0 was released on 2015-08-04.
  • Ported/updated to more modern standards during 2015 (MDACC).
  • Version 1.0.0 was released on 2006-02-14 (Princeton).


For questions or support related to the use of SWAKK, please visit on the project's forum page.
For other inquiries, please contact Dr. Han Liang.


This website is for educational and research purposes only.