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Documentation for structure software: Version 2.

Jonathan K. Pritchard ¹²³
William Wen

Department of Human Genetics
University of Chicago
920 E 58th St, CLSC 507
Chicago IL 60637, USA

Software from
http://pritch.bsd.uchicago.edu
click on ``software''

Differences between $2.0\beta$ and .

Modelling decisions for the user

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

Running structure from the command line

Front End

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.

Jonathan Pritchard 2003-07-10