title: CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  CLUMPP is freely available at http://rosenberglab.bioinformatics.med.umich.edu/clumpp.html.
authors.affiliation: Center for Computational Medicine and Biology, Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA. mjakob@umich.edu
authors.forename: Mattias
authors.initials: M
authors.lastname: Jakobsson
authors.forename: Noah A
authors.initials: NA
authors.lastname: Rosenberg
mesh_terms: D000465:Algorithms; D000818:Animals; D002645:Chickens; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D003627:Data Interpretation, Statistical; D005828:Genetics, Population; D005838:Genotype; D008957:Models, Genetic; D015233:Models, Statistical; D011157:Population Dynamics; D012984:Software