% Organizing document for the Infernal User's Guide
%


\documentclass[10pt]{article}
%\usepackage{helvetic}
\usepackage{times}
\usepackage{fullpage}
\usepackage{fancybox}  % Must include fancybox *before* fancyvrb;
\usepackage{fancyvrb}  % don't know why.
\usepackage[pdftex]{graphicx}
\usepackage{url}
%\usepackage[backref,colorlinks]{hyperref}
\usepackage[authoryear]{natbib}

\usepackage{verbatim}

\setcounter{secnumdepth}{1}
\renewcommand{\familydefault}{\sfdefault}
\input{macros}

\begin{document}

\bibliographystyle{apalike}

\input{titlepage}
\input{copyright}
\newpage
\tableofcontents

\newpage
\input{introduction}

\newpage
\input{install}

\newpage
\input{tutorial}

\newpage
\input{pipeline}

\newpage
\input{cmbuild}

\newpage
\input{tabular}

% Changes in options between 1.0 and 1.1 are omitted from the 1.1.2+ user guides.
%\newpage
%\input{diffoptions}

\newpage
\input{more}

\newpage
\input{manpages}

\newpage
\input{formats}
\subsection{Dirichlet prior files}
\input{format_prior}

\newpage
\input{ack}

\newpage
\bibliography{master,lab,books,local}
\end{document}
