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Clumpak specifications

Information


Unique identifier OMICS_12218
Name Clumpak
Alternative name Clustering Markov Packager Across K
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Beta
Maintained Yes

Publication for Clustering Markov Packager Across K

Clumpak citations

 (124)
call_split

Unraveling the genetic structure of Brazilian commercial sugarcane cultivars through microsatellite markers

2018
PLoS One
PMCID: 5912765
PMID: 29684082
DOI: 10.1371/journal.pone.0195623
call_split See protocol

[…] h 10 iterations at a 100,000 burning period and 200,000 Markov Chain Monte Carlo (MCMC) repeats []. Values of k and ΔK were obtained by Structure Harvester []. Best values for k were confirmed by the CLUMPAK Best k pipeline [].The pair-wise dissimilarity was estimated based on the Jaccard similarity coefficient complement (Dissimilarity = 1 –Similarity) [,]. The phylogenetic tree was constructed a […]

library_books

Spatio temporal genetic structure of Anopheles gambiae in the Northwestern Lake Victoria Basin, Uganda: implications for genetic control trials in malaria endemic regions

2018
PMCID: 5902950
PMID: 29661226
DOI: 10.1186/s13071-018-2826-4

[…] value of K (assumed populations or genetic groups), from 1 to 6. Post-processing of STRUCTURE results, including choosing the optimal K value and producing the graphical output, was implemented using CLUMPAK []. […]

library_books

Detecting hierarchical levels of connectivity in a population of Acacia tortilis at the northern edge of the species’ global distribution: Combining classical population genetics and network analyses

2018
PLoS One
PMCID: 5896914
PMID: 29649222
DOI: 10.1371/journal.pone.0194901

[…] run consisted of a 50,000 burn-in period followed by 50,000 Markov Chain Monte Carlo (MCMC) estimations. The most likely K was estimated using the ΔK method following Evanno et al. [], implemented in CLUMPAK []. […]

call_split

Role of oceanography in shaping the genetic structure in the North Pacific hake Merluccius productus

2018
PLoS One
PMCID: 5868808
PMID: 29579060
DOI: 10.1371/journal.pone.0194646
call_split See protocol

[…] ependent allele frequencies among populations. We used the LOCPRIOR option, with the most likely K determined using Evanno’s ΔK [,]. Graphical representation of STRUCTURE results were performed using CLUMPAK (http://clumpak.tau.ac.il/index.html).Migration rates among populations were estimated using microsatellite data with Migrate-n 3.6.5 []. We conducted searches using one long and four short MC […]

call_split

Genetic homogeneity of the invasive lionfish across the Northwestern Atlantic and the Gulf of Mexico based on Single Nucleotide Polymorphisms

2018
Sci Rep
PMCID: 5864727
PMID: 29567984
DOI: 10.1038/s41598-018-23339-w
call_split See protocol

[…] s, 100,000 MCMC per replicate, and a 10,000 burn-in period. We used an “admixture model” and correlated gene frequencies as implemented in Structure. The five independent runs were averaged using the clumpak server (http://clumpak.tau.ac.il). The K value was determined by comparing the rate of change in the likelihood of K, using the ad hoc statistic ΔK in Structure Harvester 0.6.94.Analyses of Mo […]

call_split

Migratory culture, population structure and stock identity in North Pacific beluga whales (Delphinapterus leucas)

2018
PLoS One
PMCID: 5863979
PMID: 29566001
DOI: 10.1371/journal.pone.0194201
call_split See protocol

[…] defined prior probabilities that each individual was an immigrant (v = 0.01–0.10) and incorporated information on the geographic origin of each sample before running the clustering analysis. We used Clumpak [] to integrate results from multiple runs for different values of K and to implement methods for choosing K.To further explore the origins of individual whales, we assigned individuals to pop […]

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Clumpak institution(s)
Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Ramat Aviv, Israel; Department of Evolutionary Biology and SciLife Lab, Uppsala University, Uppsala, Sweden; Department of Biology, Stanford University, Stanford, CA, USA
Clumpak funding source(s)
A Brown University Undergraduate Teaching and Research Award (UTRA); a Research Experiences for Undergraduates Supplement to a National Science Foundation Faculty Early Career Development Award (DBI-1452622); a Pew Scholar in the Biomedical Sciences supported by The Pew Charitable Trusts; an Alfred P. Sloan Research Fellow

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