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\@writefile{lot}{\contentsline {table}{\numberline {2}{\ignorespaces {} Format of the data file, in two-row format. Most of these components are optional (see text for details). $M_l$ is an identifier for marker $l$. $r_l$ indicates which allele, if any, is recessive at each marker (dominant genotype data only). $D_{i,i+1}$ is the distance between markers $i$ and $i+1$. $ID^{(i)}$ is the label for individual $i$, $g^{(i)}$ is the geographic origin of individual $i$ (PopData); $f^{(i)}$ is a flag used to incorporate learning samples (PopFlag); $\phi ^{(i)}$ can store a phenotype for individual $i$; $y_1^{(i)},...,y_n^{(i)}$ are for storing extra data (ignored by the program); $(x^{i,1}_l,x^{i,2}_l)$ stores the genotype of individual $i$ at locus $l$. $p_i^{(l)}$ is the phase information for marker $l$ in individual $i$. }}{7}}
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\@writefile{toc}{\contentsline {paragraph}{Estimating admixture proportions when most individuals are admixed.}{12}}
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\@writefile{lof}{\contentsline {figure}{\numberline {1}{\ignorespaces Example showing the components of a project. {\it  Project Data} is the data file; {\it  Project Information} specifies data file format. {\it  Simulation Summary} provides a summary of all MCMC simulations run as part of this project. {\it  Parameter Sets} consists of three groups of MCMC runs that used different parameter settings: ps1, ps2, and ps3; each of these shows the Settings, as well as a list of results for completed MCMC runs with these parameter values. The user can click on any of these to see details.}}{24}}
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\@writefile{lof}{\contentsline {figure}{\numberline {2}{\ignorespaces Importing the data (step 1). The user specifies the directory for the project ({\it  data}, here), the name of the project directory ({\it  sample\_project}; this is a directory within {\it  data}), and the data file to be read by the program {\it  sample\_data}. }}{25}}
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\@writefile{lof}{\contentsline {figure}{\numberline {6}{\ignorespaces The run-time output is shown in the bottom console}}{28}}
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\@writefile{lof}{\contentsline {figure}{\numberline {9}{\ignorespaces Summary plot of estimates of $Q$. Each individual is represented by a single vertical line broken into $K$ colored segments, with lengths proportional to each of the $K$ inferred clusters. The numbers (1..4) correspond to the predefined populations.}}{30}}
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\@writefile{lof}{\contentsline {figure}{\numberline {10}{\ignorespaces {}The triangle plot of $Q$. Each individual is represented by a colored point. The colors correspond to the prior population labels. The estimated ancestry vector for an individual consists of $K$ components which add up to 1. When $K=3$, the ancestry vectors can be plotted onto a triangle, as shown. For a given point, each of the three components is given by the distance to one edge of the triangle. Individuals who are in one of the corners are therefore assigned completely to one population or another. For $K>3$, we represent the data by allowing the user to pick out two of the inferred clusters at a time, and then grouping all the other clusters together.}}{30}}
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\bibcite{BeaumontEtAl01}{{1}{2001}{{Beaumont et~al.}}{{}}}
\bibcite{FalushEtAl03a}{{2}{2003a}{{Falush et~al.}}{{}}}
\bibcite{FalushEtAl07}{{3}{2007}{{Falush et~al.}}{{}}}
\bibcite{FalushEtAl03}{{4}{2003b}{{Falush et~al.}}{{}}}
\bibcite{MurgiaEtAl06}{{5}{2006}{{Murgia et~al.}}{{}}}
\bibcite{PritchardEtAl00}{{6}{2000a}{{Pritchard et~al.}}{{}}}
\bibcite{PritchardEtAl00a}{{7}{2000b}{{Pritchard et~al.}}{{}}}
\bibcite{RosenbergEtAl01Genetics}{{8}{2001}{{Rosenberg et~al.}}{{}}}
\@writefile{toc}{\contentsline {section}{\numberline {11}How to cite this program}{34}}
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