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

Bioinformatics
Mattias Jakobsson, Noah A Rosenberg

Abstract

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. 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 diffe...Continue Reading

References

Dec 21, 2002·Science·Noah A RosenbergMarcus W Feldman
Apr 10, 2004·Bioinformatics·Jukka CoranderMikko J Sillanpää
Aug 17, 2006·Molecular Ecology·Jukka Corander, Pekka Marttinen
Jan 24, 2007·Genetics·John P Huelsenbeck, Peter Andolfatto

Citations

Mar 16, 2012·Die Naturwissenschaften·C RutzRobert C Fleischer
Mar 30, 2010·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Xiaohong YangJiansheng Li
Jan 19, 2011·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·E L HowardA Koutoulis
Feb 22, 2012·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Tatiana ZerjalMaud I Tenaillon
Jul 27, 2011·Human Genetics·C VelezHarry Ostrer
Oct 19, 2011·Human Genetics·Asif JavedGenographic Consortium
Jun 9, 2012·Journal of Plant Research·Lua Lopez, Rodolfo Barreiro
Mar 11, 2010·Genetica·Mallikarjuna K AradhyaAnne Koehmstedt
Sep 24, 2013·Genetica·José Marcelo Soriano VianaGeísa Pinheiro Paes
Jul 1, 2008·Animal : an International Journal of Animal Bioscience·Antonio ZuccaroD Marletta
Mar 23, 2012·Animal : an International Journal of Animal Bioscience·J M PrystupaYves Plante
Mar 23, 2012·Animal : an International Journal of Animal Bioscience·R BozziF Goyache
Jun 25, 2009·European Journal of Human Genetics : EJHG·Vincenza ColonnaMarina Ciullo
Sep 9, 2010·European Journal of Human Genetics : EJHG·Begoña Martínez-CruzEvelyne Heyer
Jul 19, 2013·Journal of Human Genetics·Jose R SandovalFabricio R Santos
Dec 18, 2013·Nature Communications·Junjie FuGuoying Wang
Aug 30, 2011·Nature Genetics·Jun CaoDetlef Weigel
Aug 12, 2009·Proceedings of the National Academy of Sciences of the United States of America·Adam R BoykoCarlos D Bustamante
Jul 10, 2010·Proceedings of the National Academy of Sciences of the United States of America·Griet CasteleynWim Vyverman
Mar 4, 2011·Proceedings of the National Academy of Sciences of the United States of America·Mary Katherine GonderSarah A Tishkoff
Aug 17, 2011·Proceedings of the National Academy of Sciences of the United States of America·Benjamin K BlackmanLoren H Rieseberg
Mar 21, 2012·Proceedings of the National Academy of Sciences of the United States of America·C SuL David Sibley
Aug 1, 2012·Proceedings of the National Academy of Sciences of the United States of America·Irene StefaniniDuccio Cavalieri
Jul 4, 2009·Bioinformatics·Eric Y DurandOlivier François
Sep 6, 2011·The Journal of Heredity·Justin B LackRonald A Van Den Bussche
Dec 14, 2011·The Journal of Heredity·D Bigi, Giovanna Perrotta
Feb 10, 2012·The Journal of Heredity·Natalie D HalbertJames N Derr
Jul 28, 2012·The Journal of Heredity·Serina FillerGottfried Brem
Oct 23, 2012·The Journal of Heredity·Melody PorlierAnne Charmantier
Jan 18, 2013·The Journal of Heredity·Andres AguilarMatthew O Goldsworthy
May 18, 2013·The Journal of Heredity·David T GauthierJens Carlsson
Jul 31, 2013·The Journal of Heredity·Zhou FangPeter L Morrell
May 23, 2009·Molecular Biology and Evolution·Eric Y DurandOlivier François
Dec 19, 2009·Molecular Biology and Evolution·M W Leino, J Hagenblad
Aug 4, 2012·Phytopathology·Zahi K AtallahKrishna V Subbarao
Apr 15, 2009·Proceedings. Biological Sciences·Karl L EvansBen J Hatchwell
Aug 21, 2009·Proceedings. Biological Sciences·Shiang-Fan ChenStephen J Rossiter
May 20, 2011·Proceedings. Biological Sciences·Silvia CasabiancaCristiano Vernesi
Feb 16, 2012·Annals of Human Genetics·Ugur Hodoglugil, Robert W Mahley
Jan 3, 2013·Annals of Human Genetics·Nuri KodamanScott M Williams
Apr 28, 2012·Science·Pontus SkoglundMattias Jakobsson
Apr 26, 2013·Journal of Clinical Microbiology·Sinisa VidovicDarren R Korber
Mar 17, 2009·Genetics, Selection, Evolution : GSE·Grégoire LeroyXavier Rognon
Oct 13, 2011·BMC Evolutionary Biology·Andreas HapkeOliver Zupke
Oct 30, 2012·BMC Evolutionary Biology·Irene KellerO Seehausen
Dec 12, 2012·BMC Evolutionary Biology·Maria Tereza C ThoméJoão Alexandrino
Oct 29, 2013·BMC Evolutionary Biology·Matthias MarkolfPeter M Kappeler
Sep 18, 2013·BMC Genetics·Xiong-wei LiMaria Jose Aranzana
Feb 15, 2012·BMC Genomics·Agnieszka NiedzielaAndrzej Anioł
Sep 26, 2013·BMC Genomics·Andrew MayMichèle Ramsay
Dec 13, 2012·Malaria Journal·Stella M ChenetAnanias A Escalante
Oct 17, 2012·Environmental Health Perspectives·Carina M SchlebuschKarin Broberg
Dec 3, 2010·PLoS Computational Biology·Marta MeléGenographic Consortium Members
Nov 28, 2007·PLoS Genetics·Sijia WangAndres Ruiz-Linares
May 17, 2008·PLoS Genetics·Olivier FrançoisNoah A Rosenberg
Mar 14, 2009·PLoS Genetics·Matthew V Rockman, Leonid Kruglyak
Aug 23, 2011·PLoS Neglected Tropical Diseases·Naomi A DyerMartin J Donnelly
Feb 20, 2014·PLoS Neglected Tropical Diseases·Mariel A MarlowElisa Cupolillo
Mar 5, 2009·PloS One·Miao HeYali Xue
Aug 13, 2009·PloS One·Laurence FloriMathieu Gautier
Oct 8, 2011·PloS One·Kathrin LangenTimo Thünken
Nov 13, 2012·PloS One·Matthew W BlairAndrés J Cortés
Feb 6, 2013·PloS One·Jessica L PetersenMolly E McCue
Mar 19, 2013·PloS One·Nadia Mhedbi-HajriMarie-Agnès Jacques
Mar 26, 2013·PloS One·Patricia Taboada-EchalarAntonio Salas
Sep 26, 2013·PloS One·Osama AlsmadiThangavel Alphonse Thanaraj
Jan 5, 2014·PloS One·Ross L GoldingayBrendan D Taylor
Dec 19, 2013·PloS One·Maciej K KonopińskiAlena Šediva
Jun 4, 2011·Genetics and Molecular Biology·A M GuastellaS Bordonaro
May 5, 2011·International Journal of Molecular Sciences·Toni SafnerStéphanie Manel
Aug 21, 2013·The American Journal of Tropical Medicine and Hygiene·Linda KotheraHarry M Savage
Jan 15, 2014·Molecular Phylogenetics and Evolution·Luciano CalderónPablo L Tubaro
Oct 3, 2013·Heredity·J A M BertrandC Thébaud
Dec 18, 2013·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Xun WuYu Li
Jun 3, 2014·Nature Communications·Pedro AlmeidaJosé Paulo Sampaio
Jun 3, 2014·Malaria Journal·Aline F AngêllaPaulo Eduardo Martins Ribolla
Jan 30, 2014·Proceedings of the National Academy of Sciences of the United States of America·Nuri KodamanPelayo Correa
May 8, 2014·Molecular Biology and Evolution·Jasmine K JanesFelix A H Sperling
Jun 3, 2014·Genome Génome / Conseil National De Recherches Canada·G Besnard, A El Bakkali
Dec 3, 2013·The Journal of Heredity·Jessica L PetersenMolly E McCue
Mar 29, 2014·BMC Genetics·Supamit MekchaySissades Tongsima
Aug 1, 2014·Human Biology·Doron M BeharNoah A Rosenberg
Aug 26, 2014·SpringerPlus·Ramesh Krishnan RamasamyV Girish Naik
Mar 4, 2014·Molecular Genetics and Genomics : MGG·Padma NimmakayalaUmesh K Reddy
May 30, 2014·Nature·Miguel AlcaideDarren E Irwin
Aug 16, 2014·The Journal of Heredity·Sarah CourbisDeborah Duffield
Feb 11, 2014·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Feng LiXiaoming Wu
Oct 31, 2014·Annals of Botany·Megumi K KimuraYoshihiko Tsumura
Aug 29, 2014·Plant Molecular Biology·Bárbara Salomão de Faria MüllerRosana P Vianello
Nov 2, 2014·Asian-Australasian Journal of Animal Sciences·Sangwon SuhJae-Hwan Kim
Jan 22, 2014·The Journals of Gerontology. Series A, Biological Sciences and Medical Sciences·Nasrine BendjilaliBradley J Willcox
Aug 27, 2013·Molecular Breeding : New Strategies in Plant Improvement·Bin ZhangRuilian Jing
Mar 8, 2016·Applications in Plant Sciences·Charlotte C Germain-AubreyMatthew A Gitzendanner
Feb 18, 2016·Forensic Science International. Genetics·M de la PuenteC Phillips
Dec 17, 2014·International Journal of Molecular Sciences·Carlos Bernard M Cerqueira-SilvaAnete P Souza
Dec 24, 2014·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Zhi-Hui GuoXiao Ma
Feb 13, 2016·Scientific Reports·Christophe DufresnesMatthias Stöck
Feb 20, 2016·BMC Evolutionary Biology·Balaji ChattopadhyayUma Ramakrishnan
Oct 26, 2010·Annals of Human Biology·Stephane MazieresFrancisco Mauro Salzano
Feb 20, 2016·Genetica·Salwa Zehdi-AzouziAmel Salhi Hannachi
Mar 22, 2016·Royal Society Open Science·Cornelya F C KlütschPaul J Wilson
Jan 23, 2016·Frontiers in Plant Science·Xabier SantisoRodolfo Barreiro
Nov 4, 2015·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Marco AndrelloStéphanie Manel
Feb 5, 2016·Ecology and Evolution·Juan CarranzaJ Pérez-González
Feb 5, 2016·Plant Molecular Biology Reporter·M TargońskaM Rakoczy-Trojanowska
Jan 21, 2016·Scientific Reports·Eiji YamamotoHiroyuki Fukuoka
Feb 3, 2016·Evolutionary Applications·Alexandre GouskovChristoph Vorburger
Mar 18, 2015·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·F Z MahammiN Saidi-Mehtar
Aug 21, 2015·International Journal of Legal Medicine·O BulbulP M Schneider
Aug 27, 2014·Ecological Applications : a Publication of the Ecological Society of America·Samuel A CushmanGerard J Allan
Mar 31, 2012·Forensic Science International. Genetics·Y RuizÁ Carracedo
Sep 4, 2015·Molecular Ecology·Rena M SchweizerRobert K Wayne
Feb 2, 2012·Molecular Phylogenetics and Evolution·Yuichi NakajimaKazuhiko Sakai
Jun 20, 2015·American Journal of Human Biology : the Official Journal of the Human Biology Council·Mariela Caputo, Daniel Corach
Mar 5, 2016·Molecular Genetics and Genomics : MGG·Paula Arielle M R ValdisserRosana P Vianello
Oct 27, 2014·BMC Evolutionary Biology·Nora HohmannMarcus A Koch
Oct 17, 2014·BMC Evolutionary Biology·Eddy J DowleS A Trewick
Dec 10, 2015·International Journal of Legal Medicine·Xiangpei ZengBruce Budowle
Aug 4, 2011·International Journal of Evolutionary Biology·Manuella Villar AmadoTomas Hrbek
Sep 17, 2013·Conservation Biology : the Journal of the Society for Conservation Biology·Catherine I Cullingham, Axel Moehrenschlager
Sep 12, 2014·Evolution; International Journal of Organic Evolution·Christophe DufresnesNicolas Perrin
Dec 30, 2014·Evolution; International Journal of Organic Evolution·James M Sobel, Matthew A Streisfeld
Oct 31, 2015·Forensic Science International. Genetics·C SantosM V Lareu
Apr 12, 2016·Ecology and Evolution·Natasha E MckeanM Morgan-Richards
Apr 15, 2015·Molecular Ecology·Maximilian SchweinsbergKathrin P Lampert
Dec 24, 2014·Molecular Ecology·Simit PatelM Pfenninger
Oct 16, 2015·Ecology Letters·Geoffrey M WhileTobias Uller
Oct 21, 2015·Frontiers in Plant Science·Tiegist D AbebeJens Léon
Aug 12, 2014·Scientific Reports·Rui MartinianoDaniel G Bradley
Jun 19, 2013·Scientific Reports·B GandolfiLeslie A Lyons
Aug 22, 2015·Scientific Reports·Hideyuki ItoMiho Inoue-Murayama
May 24, 2014·Scientific Reports·Daniele CanestrelliGiuseppe Nascetti
Oct 21, 2009·Molecular Ecology·J Pérez-González, J Carranza
Jan 14, 2009·American Journal of Physical Anthropology·Rodrigo Rubi-CastellanosHector Rangel-Villalobos
Feb 21, 2009·Evolution; International Journal of Organic Evolution·Daniel BernerAndrew P Hendry
Apr 17, 2009·Molecular Ecology·Jeanne M RobertsonKelly R Zamudio
Nov 20, 2008·Molecular Ecology·Natalie D Halbert, James N Derr
Jul 22, 2008·Evolution; International Journal of Organic Evolution·David B LowryJohn H Willis
Dec 11, 2008·Molecular Ecology·D D ColeT A Crowl
Jan 22, 2009·Evolution; International Journal of Organic Evolution·Catherine E Wagner, Amy R McCune
Sep 5, 2012·Molecular Ecology·Iliana B BaumsMichael E Hellberg
Nov 22, 2012·Ecology and Evolution·Jasmine K JanesRené E Vaillancourt
Oct 10, 2013·Molecular Ecology·Erica A FoleyChagas Disease Working Group in Arequipa
Jan 27, 2012·Evolution; International Journal of Organic Evolution·Robin HopkinsMark D Rausher
Jan 3, 2013·Molecular Ecology·Marie PagèsJ F Cosson
May 5, 2011·American Journal of Physical Anthropology·Noémie S A BeckerEvelyne Heyer
Mar 5, 2013·Molecular Ecology·Daniela KellerMaarten J van Strien
Dec 16, 2011·Molecular Ecology·Stephen J RossiterTigga Kingston
Mar 21, 2012·Molecular Ecology·Rose L AndrewLoren H Rieseberg
Feb 15, 2013·The New Phytologist·Michael C FontaineTatiana Giraud
May 12, 2012·Molecular Ecology·C BurgarellaS C González-Martínez
Sep 16, 2010·Journal of Evolutionary Biology·Y Willi, K Määttänen
Nov 23, 2012·Molecular Ecology·Jason P AndrasCatherine D Harvell
Feb 14, 2013·Molecular Ecology·Fernando Fernández-Mendoza, Christian Printzen
Sep 14, 2011·American Journal of Physical Anthropology·Judith R KiddKenneth K Kidd
Jun 30, 2011·Molecular Ecology·Fusun OzerMary V Ashley
Aug 26, 2010·Molecular Ecology·Juan Ansede-BermejoJaime Martinez-Urtaza
Jun 30, 2010·Evolution; International Journal of Organic Evolution·Ron I Eytan, Michael E Hellberg
May 14, 2011·Molecular Ecology Resources·Olivier François, Eric Y Durand
Mar 21, 2016·Molecular Phylogenetics and Evolution·Raül RamosFumin Lei
Sep 3, 2011·Journal of Fish Biology·Damien BroderickDavid J Welch
Nov 10, 2010·Molecular Ecology·Daniele CanestrelliGiuseppe Nascetti
Jul 24, 2012·Ecology and Evolution·Julia KönigerJosef Greimler
Oct 1, 2010·Molecular Ecology·Shawn R NarumKevin A Meyer
Sep 26, 2013·Evolutionary Applications·Elisabeth FournierTatiana Giraud
Aug 29, 2013·Molecular Ecology·Herman H WirshingA C Baker
Aug 5, 2010·Evolution; International Journal of Organic Evolution·John Paul FoxeBarbara K Mable
Jan 25, 2012·Journal of Evolutionary Biology·Mark SistromM Hutchinson
Apr 5, 2011·Molecular Ecology·Catherine I CullinghamDavid W Coltman
Dec 2, 2011·Molecular Ecology·Anna RunemarkErik I Svensson
Sep 1, 2012·Molecular Ecology·Alyson M AndreasenMatthew L Forister
Mar 20, 2013·Molecular Ecology·Kate L SandersMichael S Y Lee
Nov 16, 2010·Evolution; International Journal of Organic Evolution·Erica Bree Rosenblum, Luke J Harmon
Oct 17, 2013·Molecular Ecology·M Casas-MarceJ A Godoy
Apr 24, 2012·Evolution; International Journal of Organic Evolution·Sonal Singhal, Craig Moritz
Aug 25, 2010·Evolution; International Journal of Organic Evolution·Aaron B A ShaferDavid W Coltman
Jun 8, 2011·Evolution; International Journal of Organic Evolution·Hirokazu TojuTeiji Sota
Sep 6, 2012·Evolution; International Journal of Organic Evolution·Peter J P CroucherRosemary G Gillespie
Oct 3, 2012·Evolution; International Journal of Organic Evolution·Vera S DominguesHopi E Hoekstra
Mar 26, 2011·The Plant Journal : for Cell and Molecular Biology·Yvette Wilson, Andrew Hudson
Sep 20, 2012·Molecular Ecology·Sonal Singhal, Craig Moritz
May 23, 2012·Molecular Ecology·Catherine E WagnerIrby J Lovette
Oct 11, 2011·Molecular Ecology·Isabel S MagalhaesGiorgina Bernasconi
Oct 9, 2013·Ecology and Evolution·Maria Celeste N Banaticla-HilarioKenneth L McNally
Jan 10, 2013·Journal of Evolutionary Biology·L M CaroC D Cadena
Jan 1, 2014·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·L D PhamH N Kadarmideen
Jun 20, 2014·Evolutionary Applications·Fiona R SavoryUma Ramakrishnan
Apr 1, 2014·Ecology and Evolution·Jennafer A P Hamlin, Michael L Arnold
Sep 17, 2014·Molecular Ecology·Ryan C GarrickAdalgisa Caccone
Oct 30, 2013·The Journal of Animal Ecology·Katherine A HarrissonPaul Sunnucks
Apr 12, 2016·Ecology and Evolution· WasimuddinJoëlle Goüy de Bellocq
Oct 24, 2013·Molecular Ecology·J MonzónD E Dykhuizen
Oct 15, 2013·Molecular Ecology·Ke BiCraig Moritz
Aug 8, 2014·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·A SanzP Zaragoza
Nov 3, 2009·Molecular Ecology·Gilles GuillotAlain C Frantz
May 28, 2014·Molecular Ecology·Carlos PradaMary Alice Coffroth
Apr 26, 2014·Molecular Ecology·Nian WangRichard J A Buggs
Jan 23, 2015·Molecular Ecology·Warren BoothCoby Schal
Jan 9, 2014·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·E Ceh, P Dovc