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ADMIXTURE specifications

Information


Unique identifier OMICS_02077
Name ADMIXTURE
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Stability No
Maintained No

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Publication for ADMIXTURE

ADMIXTURE citations

 (574)
library_books

Analysis of the canid Y chromosome phylogeny using short read sequencing data reveals the presence of distinct haplogroups among Neolithic European dogs

2018
BMC Genomics
PMCID: 5946424
PMID: 29747566
DOI: 10.1186/s12864-018-4749-z

[…] sents global dog genetic diversity than collections of breed dogs, and the male dogs (n = 104) from our study were subsequently projected onto the resulting components. The proportion of wolf and dog admixture for each dog or wolf sample was estimated using the program ADMIXTURE []. As input, we used autosomal genotypes from the whole genome short-read data called by GATK HaplotypeCaller. Variant […]

library_books

Nonparametric approaches for population structure analysis

2018
Hum Genomics
PMCID: 5944014
PMID: 29743099
DOI: 10.1186/s40246-018-0156-4

[…] imilar to STRUCTURE, PARTITION [], BAPS/BAPS2 [, ], and GENELAND [] take the same modeling approach, which is based on an MCMC algorithm, to sample the posterior distribution. Moreover, FRAPPE [] and ADMIXTURE [, ] adopt the same modeling approach but rely on maximizing the likelihood using an expectation-maximization (EM) algorithm instead of sampling the posterior distribution. In contrast, L-PO […]

library_books

Genome wide scan reveals population stratification and footprints of recent selection in Nelore cattle

2018
PMCID: 5930444
PMID: 29720080
DOI: 10.1186/s12711-018-0381-2

[…] unction from the “stats” package in R software []. The genomic distance between two individuals was estimated as 1 minus the proportion of identical by state (IBS) alleles that they share. Second, an admixture analysis was performed to measure the proportion of individual ancestry from different numbers of hypothetical ancestral populations, using the ADMIXTURE software (version 1.04) []. Thus, an […]

library_books

Mind the gut: genomic insights to population divergence and gut microbial composition of two marine keystone species

2018
Microbiome
PMCID: 5932900
PMID: 29720271
DOI: 10.1186/s40168-018-0467-7

[…] as 1 and 3 were plotted using the Perl script Ploteig (Eigensoft package). In order to infer ancestry among sand lances in various areas, we used the model-based approach implemented in the software Admixture v.1.3.0 []. Admixture estimations were performed for values of K ranging from 2 to 14. Convergence was assumed when the log-likelihood difference among iterations was < 10−4. We employed the […]

call_split

Population structure in Argentina

2018
PLoS One
PMCID: 5929549
PMID: 29715266
DOI: 10.1371/journal.pone.0196325
call_split See protocol

[…] We used block relaxation algorithm as implemented in ADMIXTURE [] to estimate ancestry proportions for each individual given K ancestral populations, where K was incremented from 3 to 10. We used the default setting (folds = 5) to perform ADMIXTURE’s cr […]

library_books

Whole exome sequencing reveals rare variants linked to congenital pouch colon

2018
Sci Rep
PMCID: 5923232
PMID: 29703930
DOI: 10.1038/s41598-018-24967-y

[…] from all the merged samples. The 1000 genomes dataset containing the datasets was considered as a summarized worldwide population. In order to estimate individual ancestries, we used an unsupervised ADMIXTURE (Alexander et al. 2009) to project the samples. […]

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ADMIXTURE institution(s)
Department of Biomathematics, University of California at Los Angeles, Los Angeles, CA, USA

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