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

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Maintainer


  • person_outline David Alexander <>

ADMIXTURE article

ADMIXTURE citations

 (56)
2018
PMCID: 5884862

[…] 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: 5864727

[…] maximum number of clusters expected. then, a definitive run was performed with k from 1 to 8 with five independent replicates, 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 server67 (http://clumpak.tau.ac.il). the k value was determined […]

2018
PMCID: 5877975

[…] 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: 5849961

[…] individuals from cerro de pasco, peru (4330 m.a.s.l). we performed whole genome sequencing to a mean depth of 34x. we detailed the demographic history of quechua using principal components analysis, admixture and treemix. we performed five tests of selection, (ihs, xp-ehh, δihh, fst and δdaf) on real, and simulated quechua data incorporating details of the demographic history of the population. […]

2018
PMCID: 5838077

[…] without the na native group with k from one to six. for each k value, we ran 10 replicates with 300,000 burn‐in iterations and 1,000,000 mcmc iterations. for both structure analyses, we chose the admixture model and correlated allelic frequencies, and no prior information on individual's origin. we followed the method of evanno, regnaut, and goudet (2005) and used the ad hoc statistic ∆k […]

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

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