ADMIXTURE protocols

View ADMIXTURE computational protocol

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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 in pipelines

 (56)
2018
PMCID: 5783331
PMID: 29364919
DOI: 10.1371/journal.pone.0190555

[…] among populations within the b. tabaci species complex. a principal component analysis (pca), based on allelic data across all 71 whitefly samples was conducted using the snprelate r package []. admixture (v.1.3.0 []) was performed on the whole dataset to estimate the genetic ancestry of each sample. this tool is based on a maximum likelihood approach which provides an estimate of the number […]

2018
PMCID: 5859105
PMID: 29593776
DOI: 10.3389/fgene.2018.00068

[…] et al., ), popgraph (dyer and nason, ); bayescan foll and gaggiotti, , flk (bonhomme et al., ), bayenv2 (günther and coop, ), pcadapt (duforet-frebourg et al., ) faststructure (raj et al., ), admixture (alexander et al., ), tess3 (caye et al., )., indicates methods not yet widely used but show promise–see sections generalized dissimilarity modeling (gdm)–clinal analyses., […]

2018
PMCID: 5863221
PMID: 29608727
DOI: 10.1093/gbe/evy051

[…] (). we compared pairwise fst estimates based on our panel of snps to pairwise estimates based on whole genome sequences ()., semi-supervised and unsupervised clustering analyses were performed using admixture version 1.22 (). analyses were performed in triplicate with different starting seeds and five-fold cross-validation. standard errors were estimated using 200 bootstrap replicates. […]

2018
PMCID: 5877975
PMID: 29463742
DOI: 10.1073/pnas.1716839115

[…] matrix was then used to build a neighbor-joining tree using the ape package in r (). the phylogenetic tree in was rendered using figtree v1.4.2 (tree.bio.ed.ac.uk/software/figtree/)., we ran admixture () both on the masked and unmasked datasets using default parameters for k = 2 to k = 14 and diploid genotype calls for both the ancient genome and the modern reference populations. […]

2018
PMCID: 5910833
PMID: 29610337
DOI: 10.1073/pnas.1717873115

[…] first, we removed individuals that have been labeled as related (), then we used the pipeline reported in gazal et al. () to exclude individuals having up to third-degree relationships. next, we ran admixture () to identify and filter out individuals exhibiting recent population admixture. using the plink software (), we selected only the autosomal biallelic snps with minor allele frequency […]


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ADMIXTURE in publications

 (369)
PMCID: 5946424
PMID: 29747566
DOI: 10.1186/s12864-018-4749-z

[…] and mitochondria [, ], the coyote y-chromosome is divergent from the grey wolf-dog clade. instead, the coyote shares a clade with the red wolf, a group known to contain a high amount of coyote admixture [, ]. the single male great lakes wolf (a sample from minnesota [] carries a strikingly divergent y-chromosome, with 199 derived alleles (16% of the total snvs) unique […]

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

[…] 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, […]

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

[…] 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, […]

PMCID: 5929549
PMID: 29715266
DOI: 10.1371/journal.pone.0196325

[…] a single line of ancestry (uniparental markers) or focusing on the autosomal regions and the x chromosome, which reveal different ancestral components. there is great interest in identifying admixture to show continental ancestry in genetically divergent populations [–]. these methods have been applied to african-american populations [–](zhu et al. 2005, smith et al. 2004, tian et al. […]

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., verifybamid was used to infer whether or not the reads are contaminated across the sample swaps. all the 18 affected cases specifically […]


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

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