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CLUMPP specifications

Information


Unique identifier OMICS_12222
Name CLUMPP
Alternative name CLUster Matching and Permutation Program
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 1.1.2
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Noah A. Rosenberg

Publication for CLUster Matching and Permutation Program

CLUMPP citations

 (686)
library_books

Phylogeography of Aegean green toads (Bufo viridis subgroup): continental hybrid swarm vs. insular diversification with discovery of a new island endemic

2018
BMC Evol Biol
PMCID: 5930823
PMID: 29720079
DOI: 10.1186/s12862-018-1179-0

[…] roups best-explaining the data was assessed by two commonly used statistics, computed by STRUCTURE HARVESTER []: the average log-likelihood Pr(X│K) [] and the ΔK []. Replicate runs were combined with CLUMPP [] and graphs of assignment probabilities were compiled using DISTRUCT []. We also conducted additional STRUCTURE analyses with K = 2 on the continental genotypes only (loc. 20–106), to infer p […]

call_split

Genetic structure of South African Nguni (Zulu) sheep populations reveals admixture with exotic breeds

2018
PLoS One
PMCID: 5919407
PMID: 29698497
DOI: 10.1371/journal.pone.0196276
call_split See protocol

[…] opulations included in each cluster). STRUCTURE HARVESTER [], a web-based program, was used for collating the results generated by the program STRUCTURE. The clustering pattern was implemented in the CLUMPP program and visualised using the software DISTRUCT software version 1.1 [].To further investigate the genetic structure of each population when adopting an approach without assumptions about HW […]

call_split

Genetic diversity in the endangered terrestrial orchid Cypripedium japonicum in East Asia: Insights into population history and implications for conservation

2018
Sci Rep
PMCID: 5915404
PMID: 29691494
DOI: 10.1038/s41598-018-24912-z
call_split See protocol

[…] identify K = 2 as the top level of hierarchical structure, we combined it with the method of selecting the smallest K after the log probability of data [ln Pr(X|K)] values reached a plateau. Programs Clumpp 1.1.2 and Distruct 1.1 were used to combine the results of the 15 replicates of the best K and to visualize the results produced by Clumpp, respectively. […]

library_books

Population structure, genetic diversity and downy mildew resistance among Ocimum species germplasm

2018
BMC Plant Biol
PMCID: 5914031
PMID: 29685108
DOI: 10.1186/s12870-018-1284-7

[…] bability Pr(X|K) and ad hoc ΔK statistic (mean(|L”(K)|) / sd(L(K)) from membership coefficient (qI) matrices. Following selection of the optimal K for all replicated runs, the FULLSEARCH algorithm of CLUMPP software [] was used to identify the optimal permuted order of qI matrices with the greatest pairwise similarity. The average of this permutation provided the best qI matrix representation, whi […]

call_split

Roads to isolation: Similar genomic history patterns in two species of freshwater crabs with contrasting environmental tolerances and range sizes

2018
Ecol Evol
PMCID: 5938456
PMID: 29760905
DOI: 10.1002/ece3.4017
call_split See protocol

[…] for genetic clustering was assessed using STRUCTURE HARVESTER (Earl & vonHoldt, ; Evanno, Regnaut, & Goudet, ), and the ten independent runs for this model were matched using the Greedy algorithm in CLUMPP v. 1.1 (Jakobsson & Rosenberg, ). Resulting barplots were constructed using Distruct v. 1.1 (Rosenberg, ). (2) DAPC (Jombart et al., ), was performed using Adegenet for genetic clustering that […]

library_books

Pharmacogenetic landscape of Metabolic Syndrome components drug response in Tunisia and comparison with worldwide populations

2018
PLoS One
PMCID: 5898725
PMID: 29652911
DOI: 10.1371/journal.pone.0194842

[…] in period of 10000 steps. In order to assess the most likely number of clusters, we calculated delta K as proposed by Evanno et al. []. The similarity of the runs at each K level was evaluated by the CLUMPP software as implemented at the online []. The Distruct software was used to visualize the best alignment of subpopulation inferring population substructure and individual assignment across the […]

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CLUMPP institution(s)
Center for Computational Medicine and Biology, Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
CLUMPP funding source(s)
This work was supported by NIH grant HL084729, by grants from the Burroughs Wellcome Fund and the Alfred P. Sloan Foundation, and by a postdoctoral fellowship from the University of Michigan Center for Genetics in Health and Medicine.

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