ADMIXTURE

Description

ADMIXTURE website  

ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm.

Specifically, ADMIXTURE uses a block relaxation approach to alternately update allele frequency and ancestry fraction parameters. Each block update is handled by solving a large number of independent convex optimization problems, which are tackled using a fast sequential quadratic programming algorithm. Convergence of the algorithm is accelerated using a novel quasi-Newton acceleration method. The algorithm outperforms EM algorithms and MCMC sampling methods by a wide margin.

Required Modules

Serial

• ADMIXTURE

Parallel (OpenMP)

• intel
• ADMIXTURE

Parallel (MPI)

• intel
• openmpi
• ADMIXTURE

System Variables

• HPC_{{#uppercase:ADMIXTURE}}_DIR - installation directory

Citation

If you publish research that uses ADMIXTURE you have to cite it as follows:

H. Zhou, D. H. Alexander, and K. Lange. A quasi-Newton method for accelerating the convergence of iterative optimization algorithms. Statistics and Computing, 2009.