% This is the main LaTeX file which is used to produce the Biopython
% Tutorial documentation.
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% If you just want to read the documentation, you can pick up ready-to-go
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% http://biopython.org/DIST/docs/tutorial/Tutorial.html
% http://biopython.org/DIST/docs/tutorial/Tutorial.pdf
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% If you want to typeset the documentation, you'll need a standard TeX/LaTeX
% distribution (I use teTeX, which works great for me on Unix platforms).
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% http://pauillac.inria.fr/~maranget/hevea/index.html
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% (http://www.lysator.liu.se/~alla/dia/dia.html).
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% format, which you can easily save as .png format using Dia itself.
% They are also checked in as the png files, so if you make
% modifications to the original dia files, the png files should also be
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% Once you're all set, you should be able to generate pdf by running:
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% pdflatex Tutorial.tex  (to get the cross references right)
% pdflatex Tutorial.tex  (to get the table of contents right)
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% Tutorial.aux file generated by LaTeX, then run hevea twice to get
% the references right.
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% If you want to typeset this and have problems, please report them
% at biopython-dev@biopython.org, and we'll try to get things resolved. We
% always love to have people interested in the documentation!

\documentclass{report}
\usepackage{url}
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\usepackage{hevea}
\usepackage{graphicx}

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\begin{document}

\begin{htmlonly}
\title{Biopython Tutorial and Cookbook}
\end{htmlonly}
\begin{latexonly}
\title{
%Hack to get the logo on the PDF front page:
\includegraphics[width=\textwidth]{images/biopython.jpg}\\
%Hack to get some white space using a blank line:
~\\
Biopython Tutorial and Cookbook}
\end{latexonly}

\author{Jeff Chang, Brad Chapman, Iddo Friedberg, Thomas Hamelryck, \\
Michiel de Hoon, Peter Cock, Tiago Antao, Eric Talevich, Bartek Wilczy\'{n}ski}
\date{Last Update -- 21 October 2015 (Biopython 1.66)}

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\begin{rawhtml}
<P ALIGN="center">
<IMG ALIGN="center" SRC="images/biopython.jpg" TITLE="Biopython Logo" ALT="[Biopython Logo]" width="1024" height="288" />
</p>
\end{rawhtml}

\maketitle
\tableofcontents

%\chapter{Introduction}
%\label{chapter:introduction}
\include{Tutorial/chapter_introduction}

%\chapter{Quick Start -- What can you do with Biopython?}
%\label{chapter:quick-start}
\include{Tutorial/chapter_quick_start}

%\chapter{Sequence objects}
%\label{chapter:Bio.Seq}
\include{Tutorial/chapter_seq_objects}

%\chapter{Sequence annotation objects}
%\label{chapter:SeqRecord}
\include{Tutorial/chapter_seq_annot}

%\chapter{Sequence Input/Output}
%\label{chapter:Bio.SeqIO}
\include{Tutorial/chapter_seqio}

%\chapter{Multiple Sequence Alignment objects}
%\label{chapter:Bio.AlignIO}
\include{Tutorial/chapter_align}

%\chapter{BLAST}
%\label{chapter:blast}
\include{Tutorial/chapter_blast}

%\chapter{BLAST and other sequence search tools (\textit{experimental code})}
%\label{chapter:searchio}
\include{Tutorial/chapter_searchio}

%\chapter{Accessing NCBI's Entrez databases}
%\label{chapter:entrez}
\include{Tutorial/chapter_entrez}

%\chapter{Swiss-Prot and ExPASy}
%\label{chapter:swiss_prot}
\include{Tutorial/chapter_uniprot}

%\chapter{Going 3D: The PDB module}
\include{Tutorial/chapter_pdf}

%\chapter{Bio.PopGen: Population genetics}
\include{Tutorial/chapter_popgen}

%\chapter{Phylogenetics with Bio.Phylo}
%\label{sec:Phylo}
\include{Tutorial/chapter_phylo}

%\chapter{Sequence motif analysis using Bio.motifs}
\include{Tutorial/chapter_motifs}

%\chapter{Cluster analysis}
\include{Tutorial/chapter_cluster}

%\chapter{Supervised learning methods}
\include{Tutorial/chapter_learning}

%\chapter{Graphics including GenomeDiagram}
%\label{chapter:graphics}
\include{Tutorial/chapter_graphics}

%\chapter{KEGG}
%\label{chap:kegg}
\include{Tutorial/chapter_kegg}

%\chapter{Cookbook -- Cool things to do with it}
%\label{chapter:cookbook}
\include{Tutorial/chapter_cookbook}

%\chapter{The Biopython testing framework}
%\label{sec:regr_test}
\include{Tutorial/chapter_testing}

%\chapter{Advanced}
%\label{chapter:advanced}
\include{Tutorial/chapter_advanced}

%\chapter{Where to go from here -- contributing to Biopython}
\include{Tutorial/chapter_contributing}

%\chapter{Appendix: Useful stuff about Python}
%\label{sec:appendix}
\include{Tutorial/chapter_appendix}

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\end{thebibliography}
\end{document}

