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Bioinformatics Advance Access originally published online on May 7, 2007
Bioinformatics 2007 23(14):1801-1806; doi:10.1093/bioinformatics/btm233
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/rcial use, distribution, and reproduction in any medium, provided the original work is properly cited.

CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure

Mattias Jakobsson * and Noah A. Rosenberg

Center for Computational Medicine and Biology, Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: Clustering of individuals into populations on the basis of multilocus genotypes is informative in a variety of settings. In population-genetic clustering algorithms, such as BAPS, STRUCTURE and TESS, individual multilocus genotypes are partitioned over a set of clusters, often using unsupervised approaches that involve stochastic simulation. As a result, replicate cluster analyses of the same data may produce several distinct solutions for estimated cluster membership coefficients, even though the same initial conditions were used. Major differences among clustering solutions have two main sources: (1) ‘label switching’ of clusters across replicates, caused by the arbitrary way in which clusters in an unsupervised analysis are labeled, and (2) ‘genuine multimodality,’ truly distinct solutions across replicates.

Results: To facilitate the interpretation of population-genetic clustering results, we describe three algorithms for aligning multiple replicate analyses of the same data set. We have implemented these algorithms in the computer program CLUMPP (CLUster Matching and Permutation Program). We illustrate the use of CLUMPP by aligning the cluster membership coefficients from 100 replicate cluster analyses of 600 chickens from 20 different breeds.

Availability: CLUMPP is freely available at http://rosenberglab.bioinformatics.med.umich.edu/clumpp.html

Contact: mjakob{at}umich.edu

Associate Editor: Keith Crandall

Received on December 28, 2006; revised on March 14, 2007; accepted on April 25, 2007

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