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%
% Tutorials for the command-line utilization of
% the Regulatory Sequence Analysis Tools
%
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%\documentclass{article}
\documentclass[12pt,a4paper, oneside]{scrreprt} % KOMA-class Neukam and Kohm, scrbook alternatively
%\documentclass{book}
%\documentstyle[makeidx]{book}
\makeindex
\include{rsat_latex_commands}

\begin{document}

\RSATtitlePage{Tutorial: command-line utilization of the tools}

\newpage
\tableofcontents
\newpage

\newpage
\input{ug_introduction.tex}

\newpage
\input{ug_configuration.tex}

\newpage
\input{ug_getting_help.tex}

\newpage
\input{ug_sequence_retrieval.tex}

\newpage
\input{ug_pattern_discovery.tex}

\newpage
\input{ug_pattern_discovery_strings.tex}

\newpage
\input{ug_pattern_matching.tex}

\newpage
\input{ug_drawing_graphs.tex}

\newpage
\input{ug_markov_models.tex}

\newpage
\input{ug_pattern_discovery_matrices.tex}

\newpage
\input{ug_pattern_matching_PSSM.tex}

\newpage
\input{ug_matrix_quality.tex}

\newpage
\input{ug_random_sequences.tex}

\newpage
\input{ug_pattern_comparison.tex}

\newpage
\input{ug_compare_classes.tex}

\newpage
\input{ug_comparative_genomics}

\newpage
\input{ug_multiple-family-analysis.tex}

\input{ug_utilities}

\newpage
\input{ig_downloading_genomes}

\newpage
\input{ug_installing_organisms}

\newpage
\input{ug_regulatory_variations}

\newpage
\input{ug_exercises}

\newpage
\input{ug_web_services.tex}

\newpage
\input{ug_graph_analysis.tex}

\newpage
\input{ug_pathway_extraction_tools.tex}

\newpage
\input{ug_bibliography}

\end{document}
