Prof. Itay Mayrose Lab - Plant Evolution, bioinformatics, & comparative genomics

Clumpak - Cluster Markov Packager Across K

This is a beta version.

We are working on improving CLUMPAK for enhanced flexibility and a better user interface. If you run into problems please email and specify the job ID.
If you haven't received any results within a few hours, please contact us and re-submit. See Known Issues. Thank you!

Estimating the Best K

The method of Evanno enables the user to identify a single k value, out of a range of K values, which captures the uppermost level of structure. This method was purposed by Evonno et al. in 2005 (Molecular Ecology 14, 2005). In addition, we also use ln(Pr(X|K) values in order to identify the k for which Pr(K=k) is highest (as described in STRUCTURE's manual, section 5.1).

Run Best K estimation (click for Instructions):

There are two formats supported for this calculation: one option is to zip full STRUCTURE result files, which were produced for the same data set and for a range of K values. For example, the input might be made of 10 runs for each K value, with K ranging between 2 to 10. A second option, which allows for users of other STURCUTE-like programs to perform this calculation, is to provide CLUMPAK with a text file containing two columns – the first designates K values, and the second designates the perspective log probability of data (or log likelihood) values. Each single run is represented by a line in this file, and multiple rows for each K are expected. See the Help section or the links below for examples.

If you are zipping your files on Windows, we recommend using WinRAR with the 'zip' option. Linux users can use the 'zip' command.

Please indicate the format of the uploaded result files:
STRUCTURE (.zip) ? example
Log Probability table file ? example

Upload your file: ? example