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\begin{document}

\title{Supplementary Information for: A random effects branch-site model for detecting episodic diversifying selection.}
\author{Sergei L Kosakovsky Pond$^{1,\ast}$, Ben Murrell$^{2,3}$,Mathieu Fourment$^{4}$, Simon DW Frost$^{5}$, Wayne Delport$^{4}$ and Konrad Scheffler$^{2}$.
\\
\affiliation{
$^1$Department of Medicine, University of California San Diego, San Diego, California;
$^2$Computer Science Division, Department of Mathematical Sciences, University of Stellenbosch, Stellenbosch, South Africa;
$^3$Biomedical Informatics Research Division, eHealth Research and Innovation Platform, Medical Research Council, Tygerberg, South Africa;
$^4$Department of Pathology, University of California San Diego, San Diego, California;
$^5$Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom.
}
}

\shorttitle{Detecting episodic diversifying selection}

\mbeabstract{ }

%[K: changed keywords]
\keywords{episodic selection, random effects model, evolutionary model, branch-site model}
\email{spond@ucsd.edu}

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\begin{figure*}[h]
\begin{centering}
\includegraphics[width=6in]{Figures/SuppFig1}

\caption{P-values of the test for selection along branch 5 for RS1
based on 100 replicates, and estimates of $\omega$ along branch 5
under the alternative ($M_{A}$) model. The horizontal line on p-value
plots shows the expected distribution of p-values if the null model
were true. $\omega$ estimates for the rBS model are plotted on the log scale
to include outliers, but means and variances for the actual values
are given (dashed line corresponds to the correct value \updated{1}{minor 2}{$\omega=1$}).}

\label{4taxa-sim1} 
\end{centering}
\end{figure*}

\newpage

\begin{figure*}
\begin{centering}
\includegraphics[width=6in]{Figures/SuppFig2}

\caption{P-values of the test for selection along branch 5 for RS2
based on 100 replicates, and estimates of $\omega$ along branch 5
under the alternative ($M_{A}$) model. The horizontal line on p-value
plots shows the expected distribution of p-values if the null model
were true. $\omega$ estimates for the rBS model are plotted on the log scale
to include outliers, but means and variances for the actual values
are given (dashed line corresponds to the correct value $\omega=2$).}

\label{4taxa-sim2} 
\end{centering}
\end{figure*}


\begin{figure*}
\begin{centering}
\includegraphics[width=4in]{Figures/SuppFig3}

\caption{The 16-taxon tree used for simulations, each branch is 0.1 substitutions long, except for the middle branch which is 0.2 substitutions long).
Branches in box (A) had an evolutionary configuration depicted in the colored bar (A) and the rest of the branches had configuration (B).
}

\label{suppfig1} 
\end{centering}
\end{figure*}

\end{document}