PSMIX: An R package for population structure inference via maximum likelihood method

Baolin Wu, Nianjun Liu, Hongyu Zhao

Research output: Contribution to journalArticlepeer-review

39 Scopus citations

Abstract

Background: Inference of population stratification and individual admixture from genetic markers is an integrative part of a study in diverse situations, such as association mapping and evolutionary studies. Bayesian methods have been proposed for population stratification and admixture inference using multilocus genotypes and widely used in practice. However, these Bayesian methods demand intensive computation resources and may run into convergence problem in Markov Chain Monte Carlo based posterior samplings. Results: We have developed PSMIX, an R package based on maximum likelihood method using expectation-maximization algorithm, for inference of population stratification and individual admixture. Conclusion: Compared with software based on Bayesian methods (e.g., STRUCTURE), PSMIX has similar accuracy, but more efficient computations.

Original languageEnglish (US)
Article number317
JournalBMC bioinformatics
Volume7
DOIs
StatePublished - Jun 22 2006

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