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!


Download software (including manual and examples):

Last update: March 26, 2015

CLUMPAK.zip

Download manual:

CLUMPAK Documentation


Examples for single input file:

CLUMPAK supports three formats for results. Please see the following zip for examples

basic_result_files_examples.zip


Download input examples:

Main pipeline:

The following zip file can be used to test CLUMPAK's "Main pipeline" feature:
Structure_toy_data.zip

If you are using Structure_toy_data.zip for trying our Main pipeline, you can use the following file as a label file:
toy_data_labels.txt

The following zip file can be used to test CLUMPAK's "Main pipeline" feature in ADMIXTURE format:
Admixture_toy_data.zip

If you are using the ADMIXTURE format, you can use the following file as a populations file:toy_data_populations_file.txt


Distruct for many K's:

The following zip file can be used to try our "Distruct for many K's" feature:
Structure_distuct_4_many_Ks_input.zip

If you are using Structure_distuct_4_many_Ks_input.zip for trying our "Distruct for many K's" feature, you can use the following file as a label file:
distruct_labels_data.txt

The following zip file can be used to test CLUMPAK's "Distruct for many K's" feature in ADMIXTURE format:
Admixture_distuct_4_many_Ks_input.zip

If you are using the ADMIXTURE format, you can use the following file as a populations file:
toy_data_populations_file.txt


Compare different programs:

The following two files (along with toy_data_labels.txt) can be used to try our "Compare different programs" feature:
Structure_K6_model1.zip
Structure_K6_model2.zip


Best K by Evanno:

The following zip file can be used to test CLUMPAK's "Best K by Evanno" feature:
Structure_toy_data.zip

The following file can be used to run Evanno with the log probability table file format:
toy_data_log_prob_file.txt


Optional input files:

Populations file: toy_data_populations_file.txt

Labels file: toy_data_labels.txt

Colors file: colors_file.txt

Drawparams file: drawparams.txt


Download data set used for testing CLUMPAK:

A sample of 399 individuals from 16 Jewish and non-Jewish populations at 678 microsatellite markers:

KopelmanEtAl2009.datafile

KopelmanEtAl2009_readme.txt