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

By Mattias Jakobsson, Noah A. Rosenberg. Bioinform., 2007

6,094 citations recorded by the source corpus.

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.

Subfields: Genetics

View Paper: https://www.semanticscholar.org/paper/a9eb05e4f0dec7b80a7df6b9af73266080b80256

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In Genetics

Citations in the corpus

Acute survivorship of the deep-sea coral Lophelia pertusa from the Gulf of Mexico under acidification, warming, and deoxygenation (2014, methodology): “Once onboard the vessel, small tissue samples were preserved in 95% ETOH and FTA® Technology Classic card (Whatman®).”
STRUCTURE PLOT: a program for drawing elegant STRUCTURE bar plots in user friendly interface (2014, methodology): “STRUCTURE HARVESTER (Earl 2012) program was designed to carry out down-stream processing of STRUCTURE results to calculate Evanno ’ s Δ k value and prepares input file for CLUMPP program (Jakobsson and Rosenberg 2007).”
Characterization of a global germplasm collection and its potential utilization for analysis of complex quantitative traits in maize (2011, methodology): “Results of replicate simulations from both programs were integrated by using the CLUMPP software (Jakobsson and Rosenberg 2007).”
Genetic Diversity, Population Structure, Parentage Analysis, and Construction of Core Collections in the French Apple Germplasm Based on SSR Markers (2016, methodology): “2 (Jakobsson and Rosenberg 2007), was used to compute average individual assignment probabilities (qI) over replicated runs showing a similar mode.”
Continental‐scale assessment of genetic diversity and population structure in quaking aspen (Populus tremuloides) (2013, methodology): “We used clumpp 1.1.2 (Jakobsson & Rosenberg, 2007) to account for problems with multimodality and label-switching between iterations of structure runs.”
Hybridization between a native and introduced predator of Adelgidae: an unintended result of classical biological control. (2012, methodology): “CLUMPP 1.1.2 (Jakobsson and Rosenberg, 2007) was used to combine results from five runs with the resulting optimal value of K. Graphical displays were created using DISTRUCT 1.1 (Rosenberg, 2004).”
Clumpak: a program for identifying clustering modes and packaging population structure inferences across K (2015, methodology): “For each value of K , 40 individual S TRUCTURE runs were conducted and assessed using C LUMPP (Jakobsson & Rosenberg 2007).”
pophelper: an R package and web app to analyse and visualize population structure (2017, methodology): “Two common down-stream approaches are to align assignment clusters across replicate runs using CLUMPP (Jakobsson & Rosenberg 2007) and to visualize the output using DISTRUCT (Rosenberg 2004).”
Discriminant analysis of principal components: a new method for the analysis of genetically structured populations (2010, neutral): “2 [58], which allows to account for the variability in individual membership probabilities across the different runs.”
The challenge of understanding the origin, pathways and extent of fungal invasions: global populations of the Neofusicoccum parvum–N. ribis species complex (2013, positive): “CLUMPP (Jakobsson & Rosenberg, 2007) was used to align multiple runs of Structure at the optimum K value using the Greedy algorithm.”
Host population genetic structure and zooxanthellae diversity of two reef-building coral species along the Florida Reef Tract and wider Caribbean (2010, background): “( Jakobsson and Rosenberg 2007 ) and DISTRUCT (Rosenberg 2004) to visualize the results.”