Contents

• Introduction
• Registering.
• What's new in Version 2?
• Overview
• Format for the data file
• Components of the data file:
• Rows
• Columns:
• Missing genotype data
• Formatting errors.
• Modelling decisions for the user
• How long to run the program
• Ancestry Models
• Allele frequency models
• Estimation of $K$ (the number of populations)
• Steps in estimating $K$
• Mild departures from the model can lead to overestimating $K$
• Informal pointers for choosing $K$; is the structure real?
• Isolation by distance data
• Missing data, null alleles... and other such problems
• Dominant loci
• Sequence data and Y chromosome or mtDNA haplotypes
• Multimodality
• Running structure from the command line
• Parameters in file mainparams.
• Parameters in file extraparams.
• Output options
• Priors
• Further miscellaneous options
• Command-line changes to parameter values
• Front End
• Download and installation.
• Overview.
• Building a project.
• Configuring a parameter set.
• Running simulations.
• Batch runs.
• Analyzing the results
• Interpreting the text output
• Output to screen during run
• Printout of $Q$
• Printout of $Q$ when using prior population information
• Printout of estimated allele frequencies ($P$)
• Site by site output for linkage model.
• How to cite this program
• Bibliography
• About this document ...