main.tex

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\title{%
  \begin{minipage}{11cm}
    \centering
    \includegraphics*[width=\textwidth]{img/mgx/logo}
    \Huge
    \textbf{MGX User Guide}
  \end{minipage}
}%

%\title{MGX User Guide}
%\author{Sebastian Jaenicke}
%\vspace{5mm}sebastian.jaenicke@Computational.Bio.Uni-Giessen.DE\vspace{5mm}sjaenick@CeBiTec.Uni-Bielefeld.DE}

\begin{document}
%\frontmatter
\maketitle
\cleardoublepage

\newpage
\thispagestyle{empty}

\tableofcontents

%\mainmatter

\include{installation}
\include{using}
\include{customanalysis}
%\include{extending}

\bibliographystyle{apalike}
%\bibliography{literatur}
%\bibliographystyle{da}
\bibliography{ref}

\listoffigures
\listoftables

% -----------------------------------------------------------
%\backmatter
%\begin{appendix}
%\end{appendix}

\end{document}