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CLUMPP

Description

clumpp website

CLUMPP is a program that deals with label switching and multimodality problems in population-genetic cluster analyses. CLUMPP permutes the clusters output by independent runs of clustering programs such as structure, so that they match up as closely as possible. The user has the option of choosing one of three algorithms for aligning replicates, with a tradeoff of speed and similarity to the optimal alignment.

Environment Modules

Run module spider clumpp to find out what environment modules are available for this application.

Environment Variables

  • HPC_CLUMPP_DIR - installation directory
  • HPC_CLUMPP_BIN - executable directory
  • HPC_CLUMPP_DOC - documentation directory
  • HPC_CLUMPP_EXE - examples directory
  • HPC_CLUMPP_CONF - paramfile directory

Additional Usage Information

You must have configuration files to be able to run this software. The example configuration file can be copied using the following command: 

cp $HPC_CLUMPP_CONF/* .

Citation

If you publish research that uses clumpp you have to cite it as follows:

Mattias Jakobsson, Noah A. Rosenberg, CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure, Bioinformatics, Volume 23, Issue 14, July 2007, Pages 1801–1806, https://doi.org/10.1093/bioinformatics/btm233

Categories

biology