\documentclass{bioinfo}
\copyrightyear{2016} \pubyear{2016}

%% Some pieces required from the pandoc template
\providecommand{\tightlist}{%
  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}

$if(tables)$
\usepackage{longtable}
$endif$

% Pandoc citation processing
$if(csl-refs)$
\newlength{\csllabelwidth}
\setlength{\csllabelwidth}{3em}
\newlength{\cslhangindent}
\setlength{\cslhangindent}{1.5em}
% for Pandoc 2.8 to 2.10.1
\newenvironment{cslreferences}%
  {$if(csl-hanging-indent)$\setlength{\parindent}{0pt}%
  \everypar{\setlength{\hangindent}{\cslhangindent}}\ignorespaces$endif$}%
  {\par}
% For Pandoc 2.11+
\newenvironment{CSLReferences}[3] % #1 hanging-ident, #2 entry spacing
 {% don't indent paragraphs
  \setlength{\parindent}{0pt}
  % turn on hanging indent if param 1 is 1
  \ifodd #1 \everypar{\setlength{\hangindent}{\cslhangindent}}\ignorespaces\fi
  % set entry spacing
  \ifnum #2 > 0
  \setlength{\parskip}{#2\baselineskip}
  \fi
 }%
 {}
\usepackage{calc} % for calculating minipage widths
\newcommand{\CSLBlock}[1]{#1\hfill\break}
\newcommand{\CSLLeftMargin}[1]{\parbox[t]{\csllabelwidth}{#1}}
\newcommand{\CSLRightInline}[1]{\parbox[t]{\linewidth - \csllabelwidth}{#1}}
\newcommand{\CSLIndent}[1]{\hspace{\cslhangindent}#1}
$endif$

$for(header-includes)$
$header-includes$
$endfor$

% hyperref makes the margins screwy.
% https://groups.google.com/forum/#!topic/latexusersgroup/4W_SwGk6zx4
% http://ansuz.sooke.bc.ca/software/latex-tricks.php
% \usepackage[colorlinks=true, allcolors=blue]{hyperref}

\access{Advance Access Publication Date: $access_date.day$ $access_date.month$ $access_date.year$}
\appnotes{Manuscript Category}

\begin{document}
\firstpage{1}

\subtitle{$subject_section$}

\title[$title_short$]{$title_full$}

\author[FirstAuthorLastName \textit{et~al}.]{
$for(author)$
$author.name$\,\textsuperscript{$author.affiliation$},
$endfor$
}

\address{
$for(address)$
\textsuperscript{$address.code$}$address.address$\\
$endfor$
}

\corresp{$corresponding_author_text$}

\history{Received on XXX; revised on XXX; accepted on XXX}

\editor{Associate Editor: XXX}

\abstract{
\textbf{Motivation:} $motivation$\\
\textbf{Results:} $results$\\
\textbf{Availability:} $availability$\\
\textbf{Contact:}$corresponding_author_email$\\
\textbf{Supplementary information:} $supplementary_info$}

\maketitle

$body$

$for(include-after)$
$include-after$
$endfor$

% Bibliography
\bibliographystyle{natbib}
\bibliography{$bibliography$}

\end{document}
