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... Pritchard1
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Our other colleagues in the structure project are Peter Donnelly,
Daniel Falush and Matthew Stephens.
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...12
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The first version of this program was developed while the authors (JP,
MS, PD) were in the Department of Statistics, University of Oxford.
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...23
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Comments and queries can be emailed to us at structure_help@genetics.uchicago.edu.
In view of the considerable volume of email that we receive, please check
this document carefully first.
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... program4
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The software and the manuscript are available from http://pritch.bsd.uchicago.edu.
(Click on ``software''.)
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... chunk.5
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Because of the way that this is parameterized, the map distances in the
input file can be in arbitrary units-e.g., genetic distances, or physical
distances (under the assumption that these are roughly proportional to
genetic distances). Then the estimated value of represents
the rate of switching from one chunks to the next, per unit of whatever
distance was assumed in the input file. E.g., if an admixture event took
place ten generations ago, then
should be estimated as
when the map distances are measured in cM (this is,
where 0.01 is the probability of recombination per centiMorgan), or as
when the map distances are measured in KB (assuming a constant crossing-over
rate of 1cM/MB). The prior for
is log-uniform. The front end tries to make some guesses about sensible
upper and lower bounds for ,
but the user should adjust these to match the biology of the situation.
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... off.6
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If the admixture model is used to estimate
for those individuals without prior population information,
is updated on the basis of those individuals only. If there are very few
such individuals, you may need to fix
at a sensible value.
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... below.7
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The model of correlated allele frequencies implemented now differs slightly
from that in structure Version 1.
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... modes8
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For
here are always multiple symmetric modes that correspond to permuting the
labels; these do not cause serious problems ()
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