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!

Known Issues

1) We have had some users who ran into trouble submitting their data to CLUMPAK due to special charterers in file names and in zip names. Please use only alphabetic letters, numbers, and '_' as a spaces.

2) Some users submitted their data in a format which is not recognized or parse correctly by CLUMPAK. CLUMPAK expects file to be archived as a zip (and not rar). For the main pipeline and for Evanno, CLUMPAK expects internal zip files of STRUCTURE runs for single K values. For example, can contain 10 STRUCTURE runs for K=2, K=3 can contain 10 STRUCTURE runs for K=3, etc. These zips zip single runs and NOT A DIRECTORY of runs. Internal zip files are zipped together by an external zip. For example, can contain and described above. Again, the external zip file zips single zip files, and NOT A DIRECTORY of single zip files. If you see the following error message: "loop sysread: Is a directory" it means that you have zipped a directory and not files or zip files