ADMIXTURE protocols

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 Stable
Maintained Yes

Download


Versioning


Add your version

Maintainer


  • person_outline David Alexander <>

Publication for ADMIXTURE

ADMIXTURE IN pipelines

 (69)
2018
PMCID: 5863221
PMID: 29608727
DOI: 10.1093/gbe/evy051

[…] fst estimates based on our panel of snps to pairwise estimates based on whole genome sequences (auton et al. 2015)., semi-supervised and unsupervised clustering analyses were performed using admixture version 1.22 (alexander et al. 2009). analyses were performed in triplicate with different starting seeds and five-fold cross-validation. standard errors were estimated using 200 bootstrap […]

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

[…] was then used to build a neighbor-joining tree using the ape package in r (56). the phylogenetic tree in fig. 1c was rendered using figtree v1.4.2 (tree.bio.ed.ac.uk/software/figtree/)., we ran admixture (25) 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: 5884862
PMID: 29618726
DOI: 10.1038/s41598-018-23727-2

[…] each variant was coded to an additive model based on the minor allele (reference allele). genetic models of association were calculated adjusting for age, sex, bmi, recruitment center, and admixture estimates. admixture estimates were calculated as described previously39 using maximum likelihood estimation of individual ancestries as implemented in admixture40. tests of association […]

2018
PMCID: 5884862
PMID: 29618726
DOI: 10.1038/s41598-018-23727-2

[…] was coded to an additive model based on the minor allele (reference allele). genetic models of association were calculated adjusting for age, sex, bmi, recruitment center, and admixture estimates. admixture estimates were calculated as described previously39 using maximum likelihood estimation of individual ancestries as implemented in admixture40. tests of association between individual […]

2018
PMCID: 5884862
PMID: 29618726
DOI: 10.1038/s41598-018-23727-2

[…] sex, bmi, recruitment center, and admixture estimates. admixture estimates were calculated as described previously39 using maximum likelihood estimation of individual ancestries as implemented in admixture40. tests of association between individual variants and quantitative traits were computed using the wald test from the variance component model implemented in solar. burden tests […]

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

ADMIXTURE reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review ADMIXTURE