diff --git a/main.tex b/main.tex deleted file mode 100644 index dbee0c9..0000000 --- a/main.tex +++ /dev/null @@ -1,421 +0,0 @@ -% This file was created (at least in part) by the script ParseMdtoLatex by Louis du Plessis -% (Available from https://github.com/taming-the-beast) - -\documentclass[11pt]{article} -\input{preamble} - -% Add your bibtex library here -\addbibresource{master-refs.bib} - - -%%%%%%%%%%%%%%%%%%%% -% Do NOT edit this % -%%%%%%%%%%%%%%%%%%%% -\begin{document} -\renewcommand{\headrulewidth}{0.5pt} -\headsep = 20pt -\lhead{ } -\rhead{\textsc {BEAST v2 Tutorial}} -\thispagestyle{plain} - - -%%%%%%%%%%%%%%%%%% -% Tutorial title % -%%%%%%%%%%%%%%%%%% -\begin{center} - - % Enter the name of your tutorial here - \textbf{\LARGE Tutorial using BEAST v2.4.2}\\\vspace{2mm} - - % Enter a short description of your tutorial here - \textbf{\textcolor{mycol}{\Large Tutorial template}}\\ - - \vspace{4mm} - - % Enter the names of all the authors here - {\Large {\em Author I. Name}} -\end{center} - -Template for an empty tutorial - -%%%%%%%%%%%%%%%%% -% Tutorial body % -%%%%%%%%%%%%%%%%% - -\section{Background}\label{background} - -This is a template tutorial and style guide to help formatting Markdown -tutorials. - -Please start the tutorial by adding some background about the tutorial -in this section, clearly explaining the question/problem and the type of -analysis that the methods in the tutorial should be used for. In the -next section please add a short description of all the programs or -packages used in the tutorial. The tutorial exercise should follow this -part. Please add a short explanation on the dataset used in the tutorial -before starting with the exercise. Please also add a section after the -exercise interpreting the results. End your tutorial with some useful -links. - -Some of the text in this tutorial template is just dummy filler text. -Please do not try to understand it. - -\clearpage - -\section{Programs used in this -Exercise}\label{programs-used-in-this-exercise} - -\subsubsection{BEAST2 - Bayesian Evolutionary Analysis Sampling Trees -2}\label{beast2---bayesian-evolutionary-analysis-sampling-trees-2} - -BEAST2 is a free software package for Bayesian evolutionary analysis of -molecular sequences using MCMC and strictly oriented toward inference -using rooted, time-measured phylogenetic trees \citep{Bouckaert2014}. -This tutorial uses the BEAST2 version 2.4.2. - -\clearpage - -\section{Practical: Exercise title}\label{practical-exercise-title} - -Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce porta -augue id vulputate iaculis. Sed non posuere lectus. Integer at magna -quis nulla tempus cursus. Integer ut nisl elit. Nam pellentesque -pharetra orci eu facilisis. Nullam vitae leo tempus nunc consequat -finibus ut ut nisi. Phasellus vitae faucibus dolor, id venenatis lacus. -Sed eu lacus a nibh luctus semper. Proin non tellus odio. Duis elementum -lorem eget nisl rhoncus feugiat. In hendrerit vehicula purus. Aliquam -ornare libero quis tincidunt efficitur. Nam sapien augue, mattis nec -hendrerit ut, commodo in nisi. - -\subsection{This is a subsection}\label{this-is-a-subsection} - -Quisque a dictum erat. Curabitur congue sapien sit amet pharetra -pretium. Proin posuere euismod velit, eget faucibus ex varius id. Fusce -sodales maximus malesuada. Mauris auctor dui in justo interdum egestas. -Cras dapibus commodo nulla vitae congue. Vestibulum sit amet justo sit -amet ex pretium bibendum. Donec ac mollis lorem, vel semper enim. -Suspendisse sit amet auctor dui. Nullam ac efficitur mauris. Proin -aliquam tincidunt felis nec semper. Vestibulum vestibulum, eros sit amet -consectetur blandit, elit dolor posuere sem, a porta purus odio sit amet -quam. Quisque dapibus erat sem, at vulputate libero dapibus sit amet. -Mauris rhoncus odio nisl, nec interdum lacus consequat nec. Class aptent -taciti sociosqu ad litora torquent per conubia nostra, per inceptos -himenaeos. - -Etiam tincidunt porttitor rutrum. Nulla facilisi. Mauris vehicula, justo -ac ultricies tempus, quam erat hendrerit dui, vel pharetra sapien nibh -vel ex. Sed molestie eu dui in laoreet. Pellentesque ultrices, orci -vitae lacinia suscipit, erat sapien elementum ligula, sit amet viverra -ante lorem eget elit. Cras euismod felis libero, pharetra lobortis arcu -congue vehicula. Nullam posuere dapibus mauris, eget vulputate ligula -auctor eget. Aenean et tempus est. Aliquam vehicula arcu vitae metus -dictum viverra. Aliquam vitae purus mauris. Nullam interdum mauris eget -sagittis consequat. Quisque in orci elementum, eleifend tortor eget, -bibendum orci. Etiam aliquet dolor non neque semper fermentum. Praesent -vitae venenatis mi, ut faucibus ligula. Phasellus vitae lorem neque. -Interdum et malesuada fames ac ante ipsum primis in faucibus. - -\subsubsection{This is a sub-subsection}\label{this-is-a-sub-subsection} - -Etiam posuere urna ut condimentum sagittis. Suspendisse posuere, ex nec -eleifend fringilla, nisl augue posuere augue, elementum mollis justo -felis sed purus. Cum sociis natoque penatibus et magnis dis parturient -montes, nascetur ridiculus mus. Mauris efficitur eros ut turpis -elementum vestibulum. Sed sit amet nisi at nunc luctus laoreet id ac -enim. Aliquam elementum risus id urna dictum fringilla. Aenean lobortis, -risus euismod molestie pulvinar, massa odio pharetra nulla, vitae -facilisis neque magna sed lorem. Praesent ipsum enim, commodo ut -pharetra in, sollicitudin ac massa. Donec et interdum mauris. Ut -molestie, risus quis fermentum placerat, diam risus posuere nisi, eget -viverra tortor neque ac sem. Donec viverra magna non dolor aliquam, in -suscipit massa facilisis. Suspendisse congue arcu sed risus consectetur -commodo. Aenean metus odio, volutpat at tincidunt id, ullamcorper in -dui. Cum sociis natoque penatibus et magnis dis parturient montes, -nascetur ridiculus mus. Cras ut sem in odio sodales iaculis non quis -neque. - -Quisque non mollis massa, nec eleifend dolor. Proin porta elit metus, a -lobortis enim venenatis ac. Nam scelerisque consectetur mi et gravida. -Vestibulum placerat, est vitae euismod finibus, purus nisl viverra quam, -eget condimentum mauris magna vel nisl. Phasellus pretium vitae diam in -volutpat. Cras gravida non quam ut consectetur. Vivamus congue vulputate -lorem. - -\subsection{This is another -subsection}\label{this-is-another-subsection} - -Praesent sodales est in tempor commodo. Suspendisse nulla metus, gravida -eget malesuada vel, viverra eu felis. In vitae leo facilisis, ornare -nunc nec, tempor tortor. Duis pretium mi eros, at consequat neque -tincidunt eget. Mauris vestibulum venenatis arcu, eget lacinia arcu -faucibus ut. Phasellus aliquam dui ipsum, a eleifend lacus fermentum at. -Suspendisse congue orci quis ante consequat ornare. Integer a massa -blandit, vestibulum eros ut, pulvinar augue. Class aptent taciti -sociosqu ad litora torquent per conubia nostra, per inceptos himenaeos. - -Quisque a urna a massa congue rhoncus. Donec bibendum tempus velit. Nam -varius augue sit amet lacinia hendrerit. Proin tincidunt massa ut mi -vestibulum placerat. Phasellus eget dui molestie, aliquet libero -efficitur, vehicula ex. Pellentesque ultricies ante leo, eu lobortis -odio convallis id. Donec vitae risus dui. Nulla orci velit, ultricies -sed finibus quis, blandit quis arcu. Morbi non neque non odio rutrum -condimentum. Vivamus libero metus, vehicula vitae elit ac, tincidunt -pretium dui. Proin condimentum fringilla diam, blandit blandit nisl -dapibus vel. Proin ante felis, accumsan eget ligula et, lobortis dictum -nunc. Mauris a ante dignissim ipsum tincidunt tristique. - -\clearpage - -\section{Tutorial style guide}\label{tutorial-style-guide} - -\subsection{Text styling}\label{text-styling} - -This is how to write \emph{italic text}. - -This is how to write \textbf{bold text}. - -This is how to write \textbf{\emph{bold and italic text}}. - -Do text superscripts like this 7$^{th}$, x$^{2y}$ or x$^{2y + 3z}$. - -\subsection{Lists}\label{lists} - -\subsubsection{Unnumbered lists}\label{unnumbered-lists} - -\begin{itemize} - -\item - Lorem ipsum dolor sit amet, consectetur adipiscing elit. -\item - Integer pharetra arcu ut nisl mollis ultricies. - - \begin{itemize} - - \item - Fusce nec tortor at enim cursus dictum. - \item - Phasellus nec urna quis velit eleifend convallis sodales nec augue. - \end{itemize} -\item - In iaculis turpis in massa facilisis, quis ultricies nibh ultricies. -\item - Nam vitae turpis eu lacus imperdiet mollis id at augue. -\item - Sed sed turpis ac dolor mollis accumsan. -\end{itemize} - -\subsubsection{Numbered lists}\label{numbered-lists} - -\begin{enumerate} -\def\labelenumi{\arabic{enumi}.} - -\item - Lorem ipsum dolor sit amet, consectetur adipiscing elit. -\item - Integer pharetra arcu ut nisl mollis ultricies. - - \begin{enumerate} - \def\labelenumii{\arabic{enumii}.} - - \item - Fusce nec tortor at enim cursus dictum. - \item - Phasellus nec urna quis velit eleifend convallis sodales nec augue. - \end{enumerate} -\item - In iaculis turpis in massa facilisis, quis ultricies nibh ultricies. -\item - Nam vitae turpis eu lacus imperdiet mollis id at augue. -\item - Sed sed turpis ac dolor mollis accumsan. -\end{enumerate} - -\subsubsection{Mixed lists}\label{mixed-lists} - -\begin{enumerate} -\def\labelenumi{\arabic{enumi}.} - -\item - Lorem ipsum dolor sit amet, consectetur adipiscing elit. -\item - Integer pharetra arcu ut nisl mollis ultricies. - - \begin{itemize} - - \item - Fusce nec tortor at enim cursus dictum. - \item - Phasellus nec urna quis velit eleifend convallis sodales nec augue. - \end{itemize} -\item - In iaculis turpis in massa facilisis, quis ultricies nibh ultricies. -\item - Nam vitae turpis eu lacus imperdiet mollis id at augue. -\item - Sed sed turpis ac dolor mollis accumsan. -\end{enumerate} - -\subsection{Figures}\label{figures} - -\begin{figure} - \centering - \includegraphics[width=0.250000\textwidth]{figures/Logo_bw.png} - \caption{This figure is 25\% of the page width.} - \label{fig:example1} -\end{figure} - -\begin{figure} - \centering - \includegraphics[width=0.100000\textwidth]{figures/Logo_bw.png} - \caption{This figure is only 10\% of the page width.} - \label{fig:example2} -\end{figure} - -\section{Code}\label{code} - -A bit of inline monospaced font can be made \lstinline!like this!. -Larger code blocks can be made by using the code environment: - -Java: - -\begin{lstlisting}[language=Java] -public class HelloWorld { - - public static void main(String[] args) { - // Prints "Hello, World" to the terminal window. - System.out.println("Hello, World"); - } - -} -\end{lstlisting} - -XML: - -\begin{lstlisting}[language=XML] - - - - - - - -\end{lstlisting} - -R: - -\begin{lstlisting}[language=R] - > myString <- "Hello, World!" - > print (myString) - [1] "Hello, World!" -\end{lstlisting} - -\section{Equations}\label{equations} - -Inline equations: $ \dot{x} = \sigma(y-x) $ - -Displayed equations: - -\begin{equation} - \left( \sum_{k=1}^n a_k b_k \right)^2 \leq \left( \sum_{k=1}^n a_k^2 \right) \left( \sum_{k=1}^n b_k^2 \right) -\end{equation} - -\subsection{Instruction boxes}\label{instruction-boxes} - -Use block-quotes for step-by-step instruction that the user should -perform (this will produce a framed box on the website): - -\begin{framed} -The data we have is not the data we want, and the data we need is not -the data we have. - -We can input \textbf{any} formatted text in here: - -\begin{itemize} - -\item - Even -\item - Lists -\end{itemize} - -or equations: - -\begin{equation} -(x_1, \ldots, x_n) \left( \begin{array}{ccc} -\phi(e_1, e_1) & \cdots & \phi(e_1, e_n) \\ -\vdots & \ddots & \vdots \\ -\phi(e_n, e_1) & \cdots & \phi(e_n, e_n) -\end{array} \right) -\left( \begin{array}{c} -y_1 \\ -\vdots \\ -y_n -\end{array} \right) -\end{equation} -\end{framed} - -\section{Hyperlinks}\label{hyperlinks} - -Add links to figures like this: - -\begin{itemize} - -\item - Figure \ref{fig:example1} is 25\% of the page width. -\item - Figure \ref{fig:example2} is 10\% of the page width. -\end{itemize} - -Add links to external URLs like \href{http://www.google.com}{this}. - -Links to equations or different sections within the same document are a -little buggy. - -\clearpage - -\section{Useful Links}\label{useful-links} - -\begin{itemize} - -\item - \href{http://www.beast2.org/book.html}{Bayesian Evolutionary Analysis - with BEAST 2} \citep{BEAST2book2014} -\item - BEAST 2 website and documentation: \url{http://www.beast2.org/} -\item - BEAST 1 website and documentation: \url{http://beast.bio.ed.ac.uk} -\item - Join the BEAST user discussion: - \url{http://groups.google.com/group/beast-users} -\end{itemize} - -\clearpage - - - -%%%%%%%%%%%%%%%%%%%%%%% -% Tutorial disclaimer % -%%%%%%%%%%%%%%%%%%%%%%% -% Please do not change the license -% Add the author names and relevant links -% Add any other aknowledgments here -\href{http://creativecommons.org/licenses/by/4.0/}{\includegraphics[scale=0.8]{figures/ccby.pdf}} This tutorial was written by Author I. Name for \href{https://taming-the-beast.github.io}{Taming the BEAST} and is licensed under a \href{http://creativecommons.org/licenses/by/4.0/}{Creative Commons Attribution 4.0 International License}. - - -%%%%%%%%%%%%%%%%%%%% -% Do NOT edit this % -%%%%%%%%%%%%%%%%%%%% -Version dated: \today - - - -\newpage - -%%%%%%%%%%%%%%%% -% REFERENCES % -%%%%%%%%%%%%%%%% - -\printbibliography[heading=relevref] - - -\end{document} \ No newline at end of file