Bio-MUST-Apps-FortyTwo

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\useoutertheme{$outertheme$}
$endif$
$endif$
% Use upquote if available, for straight quotes in verbatim environments
\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
\IfFileExists{microtype.sty}{% use microtype if available
  \usepackage[$for(microtypeoptions)$$microtypeoptions$$sep$,$endfor$]{microtype}
  \UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts
}{}
$if(indent)$
$else$
\makeatletter
\@ifundefined{KOMAClassName}{% if non-KOMA class
  \IfFileExists{parskip.sty}{%
    \usepackage{parskip}
  }{% else
    \setlength{\parindent}{0pt}
    \setlength{\parskip}{6pt plus 2pt minus 1pt}}
}{% if KOMA class
  \KOMAoptions{parskip=half}}
\makeatother
$endif$
$if(verbatim-in-note)$
\usepackage{fancyvrb}
$endif$
\usepackage{xcolor}
\IfFileExists{xurl.sty}{\usepackage{xurl}}{} % add URL line breaks if available
\IfFileExists{bookmark.sty}{\usepackage{bookmark}}{\usepackage{hyperref}}
\hypersetup{
$if(title-meta)$
  pdftitle={$title-meta$},
$endif$
$if(author-meta)$
  pdfauthor={$author-meta$},
$endif$
$if(lang)$
  pdflang={$lang$},
$endif$
$if(subject)$
  pdfsubject={$subject$},
$endif$
$if(keywords)$
  pdfkeywords={$for(keywords)$$keywords$$sep$, $endfor$},
$endif$
$if(colorlinks)$
  colorlinks=true,
  linkcolor=$if(linkcolor)$$linkcolor$$else$Maroon$endif$,
  filecolor=$if(filecolor)$$filecolor$$else$Maroon$endif$,
  citecolor=$if(citecolor)$$citecolor$$else$Blue$endif$,
  urlcolor=$if(urlcolor)$$urlcolor$$else$Blue$endif$,
$else$
  hidelinks,
$endif$
  pdfcreator={LaTeX via pandoc}}
%\urlstyle{same} % disable monospaced font for URLs
$if(verbatim-in-note)$
\VerbatimFootnotes % allow verbatim text in footnotes
$endif$
$if(geometry)$
$if(beamer)$
\geometry{$for(geometry)$$geometry$$sep$,$endfor$}
$else$
\usepackage[$for(geometry)$$geometry$$sep$,$endfor$]{geometry}
$endif$
$endif$
$if(beamer)$
\newif\ifbibliography
$endif$
$if(listings)$
\usepackage{listings}
\newcommand{\passthrough}[1]{#1}
\lstset{defaultdialect=[5.3]Lua}
\lstset{defaultdialect=[x86masm]Assembler}
$endif$
$if(lhs)$
\lstnewenvironment{code}{\lstset{language=Haskell,basicstyle=\small\ttfamily}}{}
$endif$
$if(highlighting-macros)$
$highlighting-macros$
$endif$
$if(tables)$
\usepackage{longtable,booktabs}
\usepackage{calc} % for calculating minipage widths
$if(beamer)$
\usepackage{caption}
% Make caption package work with longtable
\makeatletter
\def\fnum@table{\tablename~\thetable}
\makeatother
$else$
% Correct order of tables after \paragraph or \subparagraph
\usepackage{etoolbox}
\makeatletter
\patchcmd\longtable{\par}{\if@noskipsec\mbox{}\fi\par}{}{}
\makeatother
% Allow footnotes in longtable head/foot
\IfFileExists{footnotehyper.sty}{\usepackage{footnotehyper}}{\usepackage{footnote}}
\makesavenoteenv{longtable}
$endif$
$endif$
$if(graphics)$
\usepackage{graphicx}
\makeatletter
\def\maxwidth{\ifdim\Gin@nat@width>\linewidth\linewidth\else\Gin@nat@width\fi}
\def\maxheight{\ifdim\Gin@nat@height>\textheight\textheight\else\Gin@nat@height\fi}
\makeatother
% Scale images if necessary, so that they will not overflow the page
% margins by default, and it is still possible to overwrite the defaults
% using explicit options in \includegraphics[width, height, ...]{}
\setkeys{Gin}{width=\maxwidth,height=\maxheight,keepaspectratio}
% Set default figure placement to htbp
\makeatletter
\def\fps@figure{htbp}
\makeatother
$endif$
$if(links-as-notes)$
% Make links footnotes instead of hotlinks:
\DeclareRobustCommand{\href}[2]{#2\footnote{\url{#1}}}
$endif$
$if(strikeout)$
\usepackage[normalem]{ulem}



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