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 evolseq@post.tau.ac.il 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!


Compare Different Programs


The compare feature of CLUMPAK allows the user to compare the results obtained for the same K value from different programs OR using the same program with a different model OR examining the same individuals using a different subset of the data. For example, for K=2 the user might have 10 runs obtained using STRUCTURE and 10 additional runs obtained using ADMIXTURE. As part of the compare feature, results are first examined separately (similarly to how runs are analyzed and summed in CLUMPAK's main pipeline). Cluster labels are aligned across K values, as well as across the two sets of results. In addition, CLUMPAK will analyze the two sets of results together in order to determine whether the two sets reach at different solutions.


Run Compare Different Programs (click for Instructions):


The required inputs are two zip files, each containing the results obtained from one model/program. The two sets of results will be compared, as explained above.

A second input file, which is optional and affects only the graphical display of the results, is a text file which contains two columns: the first column contains the population code (an integer) for each population, and the second column contains the population name. The format of this file is identical to the format of INFILE_LABEL_BELOW in DISTRUCT. If the file is found, the input order of populations on the rows of the file will be used for the left-right order of graphing of populations. If this file is not provided, the default is to print the population codes as labels.

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


Upload first zip file containing STRUCTURE/ADMIXTURE runs: ?

Please indicate the format of the uploaded result files:
STRUCTURE ? example
ADMIXTURE ?

Upload second zip file containing STRUCTURE/ADMIXTURE runs: ?

Please indicate the format of the uploaded result files:
STRUCTURE ? example
ADMIXTURE ?

Upload populations file (optional): ? example

Upload labels file for DISTRUCT (optional): ? example


Computational:

CLUMPP: default parameters are the LargeKGreedy algorithm, random input order, and 2000 repeats

Search method:
Full search
Greedy
LargeKGreedy

Please choose the number of random input orders repeats:

MCL: threshold for similarity scores:

Default (dynamic)
User Defined: (0≤X<1)

DISTRUCT: threshold for minimal cluster size:

Default
User Defined: (0≤X<1)

Graphical:

Upload a drawparams file (optional): ?

Upload a colors file (optional): ?