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 (the number of populations)
  • Steps in estimating
  • Mild departures from the model can lead to overestimating
  • Informal pointers for choosing ; 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.
  • Exporting parameter files from the front end.
  • Importing results from the command-line program.
  • Analyzing the results
  
  
• Interpreting the text output
  • Output to screen during run
  • Printout of
  • Printout of when using prior population information
  • Printout of estimated allele frequencies ()
  • Site by site output for linkage model.
  
  
• How to cite this program
• Bibliography
• Bibliography
• About this document ...