Skip Navigation



Bioinformatics Advance Access published online on May 7, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm233
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
23/14/1801    most recent
btm233v3
btm233v2
btm233v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Jakobsson, M.
Right arrow Articles by Rosenberg, N. A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Jakobsson, M.
Right arrow Articles by Rosenberg, N. A.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

CLUMPP: a cluster matching and permutation program for dealing with label switching d 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. Dr. Mattias Jakobsson, E-mail: mjakob{at}umich.edu


  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 dataset. 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

Associate Editor: Prof. Keith Crandall

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

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 BioinformaticsHome page
G. Guillot
Inference of structure in subdivided populations at low levels of genetic differentiation--the correlated allele frequencies model revisited
Bioinformatics, October 1, 2008; 24(19): 2222 - 2228.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.