AUTHOR=Porras-Hurtado Liliana , Ruiz Yarimar , Santos Carla , Phillips Christopher , Carracedo Ángel , Lareu Maviky 

TITLE=An overview of STRUCTURE: applications, parameter settings, and supporting software

JOURNAL=Frontiers in Genetics

VOLUME=4

YEAR=2013

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2013.00098

DOI=10.3389/fgene.2013.00098

ISSN=1664-8021

ABSTRACT=<p><bold>Objectives:</bold> We present an up-to-date review of <italic>STRUCTURE</italic> software: one of the most widely used population analysis tools that allows researchers to assess patterns of genetic structure in a set of samples. <italic>STRUCTURE</italic> can identify subsets of the whole sample by detecting allele frequency differences within the data and can assign individuals to those sub-populations based on analysis of likelihoods. The review covers <italic>STRUCTURE's</italic> most commonly used ancestry and frequency models, plus an overview of the main applications of the software in human genetics including case-control association studies (CCAS), population genetics, and forensic analysis. The review is accompanied by supplementary material providing a step-by-step guide to running <italic>STRUCTURE</italic>.</p><p><bold>Methods:</bold> With reference to a worked example, we explore the effects of changing the principal analysis parameters on <italic>STRUCTURE</italic> results when analyzing a uniform set of human genetic data. Use of the supporting software: <italic>CLUMPP</italic> and <italic>distruct</italic> is detailed and we provide an overview and worked example of <italic>STRAT</italic> software, applicable to CCAS.</p><p><bold>Conclusion:</bold> The guide offers a simplified view of how <italic>STRUCTURE</italic>, <italic>CLUMPP</italic>, <italic>distruct</italic>, and <italic>STRAT</italic> can be applied to provide researchers with an informed choice of parameter settings and supporting software when analyzing their own genetic data.</p>