\contentsline {section}{\numberline {1}Introduction}{3}
\contentsline {subsection}{\numberline {1.1}Registering.}{3}
\contentsline {subsection}{\numberline {1.2}What's new in Version 2.2?}{3}
\contentsline {section}{\numberline {2}Overview}{3}
\contentsline {section}{\numberline {3}Format for the data file}{4}
\contentsline {subsection}{\numberline {3.1}Components of the data file:}{4}
\contentsline {subsection}{\numberline {3.2}Rows}{5}
\contentsline {subsection}{\numberline {3.3}Individual/genotype data}{6}
\contentsline {subsection}{\numberline {3.4}Missing genotype data}{6}
\contentsline {subsection}{\numberline {3.5}Formatting errors.}{7}
\contentsline {section}{\numberline {4}Modelling decisions for the user}{8}
\contentsline {subsection}{\numberline {4.1}How long to run the program}{8}
\contentsline {subsection}{\numberline {4.2}Ancestry Models}{8}
\contentsline {paragraph}{1. No admixture model.}{8}
\contentsline {paragraph}{2. Admixture model.}{8}
\contentsline {paragraph}{3. Linkage model.}{9}
\contentsline {paragraph}{4. Using prior population information.}{9}
\contentsline {subsection}{\numberline {4.3}Allele frequency models}{10}
\contentsline {paragraph}{Estimating $\lambda $:}{11}
\contentsline {paragraph}{Correlations model:}{11}
\contentsline {paragraph}{Estimating admixture proportions when most individuals are admixed.}{12}
\contentsline {section}{\numberline {5}Estimation of $K$ (the number of populations)}{12}
\contentsline {subsection}{\numberline {5.1}Steps in estimating $K$}{12}
\contentsline {subsection}{\numberline {5.2}Mild departures from the model can lead to overestimating $K$}{13}
\contentsline {subsection}{\numberline {5.3}Informal pointers for choosing $K$; is the structure real?}{13}
\contentsline {subsection}{\numberline {5.4}Isolation by distance data}{14}
\contentsline {section}{\numberline {6}Missing data, null alleles... and other problems}{14}
\contentsline {subsection}{\numberline {6.1}Dominant markers, null alleles, and ambiguous genotypes in polyploids}{15}
\contentsline {subsection}{\numberline {6.2}Sequence data and Y chromosome or mtDNA haplotypes}{16}
\contentsline {subsection}{\numberline {6.3}Multimodality}{16}
\contentsline {section}{\numberline {7}Running {\it structure} from the command line}{16}
\contentsline {subsection}{\numberline {7.1}Command-line changes to parameter values}{17}
\contentsline {section}{\numberline {8}Program parameters}{17}
\contentsline {subsection}{\numberline {8.1}Parameters in file {\it mainparams}.}{18}
\contentsline {subsection}{\numberline {8.2}Parameters in file {\it extraparams}.}{19}
\contentsline {section}{\numberline {9}Front End}{23}
\contentsline {subsection}{\numberline {9.1}Download and installation.}{23}
\contentsline {subsection}{\numberline {9.2}Overview.}{24}
\contentsline {subsection}{\numberline {9.3}Building a project.}{24}
\contentsline {subsection}{\numberline {9.4}Configuring a parameter set.}{25}
\contentsline {subsection}{\numberline {9.5}Running simulations.}{27}
\contentsline {subsection}{\numberline {9.6}Batch runs.}{28}
\contentsline {subsection}{\numberline {9.7}Exporting parameter files from the front end.}{28}
\contentsline {subsection}{\numberline {9.8}Importing results from the command-line program.}{29}
\contentsline {subsection}{\numberline {9.9}Analyzing the results}{29}
\contentsline {paragraph}{Summaries.}{29}
\contentsline {paragraph}{Text results.}{29}
\contentsline {paragraph}{Plots of Ancestry estimates.}{29}
\contentsline {paragraph}{Plots of summary statistics.}{30}
\contentsline {section}{\numberline {10}Interpreting the text output}{31}
\contentsline {subsection}{\numberline {10.1}Output to screen during run}{31}
\contentsline {subsection}{\numberline {10.2}Printout of $Q$}{31}
\contentsline {subsection}{\numberline {10.3}Printout of $Q$ when using prior population information}{32}
\contentsline {subsection}{\numberline {10.4}Printout of estimated allele frequencies ($P$)}{32}
\contentsline {subsection}{\numberline {10.5}Site by site output for linkage model.}{33}
\contentsline {section}{\numberline {11}How to cite this program}{34}
\contentsline {section}{\numberline {12}Bibliography}{34}
