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

Bioinformatics

Volumn 23, Issue 14, 2007, Pages 1801-1806

  Jakobsson, Mattias ^a   Rosenberg, Noah A ^a  

^a UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; BIOINFORMATICS; CHICKEN; CLUSTER ANALYSIS; CLUSTER MATCHING AND PERMUTATION PROGRAM; COMPUTER PROGRAM; GENE SWITCHING; GENETIC ALGORITHM; GENOTYPE; MATHEMATICAL ANALYSIS; NONHUMAN; POPULATION GENETICS; POPULATION STRUCTURE; PRIORITY JOURNAL; STATISTICAL ANALYSIS;

GALLUS GALLUS;

EID: 34547861256     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btm233     Document Type: Article

References (20)

1. Anderson,E.C. and Thompson,E.A. (2002) A model-based method for identifying species hybrids using multilocus genetic data. Genetics 160, 1217-1229.
2. Chen,C. et al. (2006) FASTRUCT: Model-based clustering made faster. Mol. Ecol. Notes, 6, 980-983.
3. Chen,C. (2007) Bayesian clustering algorithms ascertaining spatial population structure: A new computer program and a comparison study. Mol. Ecol. Notes, doi: 10.1111/j.1471-8286.2007.01769.x.
4. Corander,J. and Marttinen,P. (2006) Bayesian identification of admixture events using multilocus molecular markers. Mol. Ecol., 15, 2833-2843.
5. Corander,J. et al. (2003) Bayesian analysis of genetic differentiation between populations. Genetics, 163, 367-374.
6. Corander,J. et al. (2004) BAPS 2: Enhanced possibilities for the analysis of genetic population structure. Bioinformatics, 20 2363-2369.
7. Dawson,K.J. and Belkhir,K. (2001) A Bayesian approach to the identification of panmictic populations and the assignment of individuals. Genet. Res., 78, 59-77.
8. Evanno,G. et al. (2005) Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Mol. Ecol., 14, 2611-2620.
9. Falush,D. et al. (2003) Inference of population structure using multilocus genotype data: Linked loci and correlated allele frequencies. Genetics, 164, 1567-1587.
10. François,O. et al. (2006) Bayesian clustering using hidden Markov random fields in spatial population genetics. Genetics, 174, 805-816.
11. Golub,G.H. and Van Loan,C.F. (1996) Matrix Computations. 3rd edn. Johns Hopkins University Press, Baltimore.
12. Huelsenbeck,J.P. and Andolfatto,P. (2007) Inference of population structure under a Dirichlet process model. Genetics, 175, 1787-1802.
13. Jasra,A. et al. (2005) Markov chain Monte Carlo methods and the label switching problem in Bayesian mixture modeling, Stat. Sci., 20, 50-67.
14. Nordborg,M. et al (2005) The pattern of polymorphism in Arabidopsis thaliana. PLoS Biol., 3, 1289-1299.
15. Pella,J. and Masuda,M. (2006) The Gibbs and split-merge sampler for population mixture analysis from genetic data with incomplete baselines. Can. J. Fish. Aquat. Sci., 63 576-596.
16. Pritchard,J.K. et al. (2000) Inference of population structure using multilocus genotype data, Genetics, 155, 945-959.
17. Rosenberg,N.A. (2004) DISTRUCT: A program for the graphical display of population structure. Mol. Ecol. Notes, 4, 137-138.
18. Rosenberg,N.A. et al. (2001) Empirical evaluation of genetic clustering methods using multilocus genotypes from 20 chicken breeds. Genetics, 159, 699-713.
19. Rosenberg,N.A. et al. (2002) Genetic structure of human populations. Science, 298, 2381-2385.
20. Stephens,M. (2000) Dealing with label switching in mixture models. J. R. Stat. Soc. B, 62, 795-809.