Framework for a latex file designed for both arXiv and Systematic Biology submission.

sysbio.tex

%%For arXiv, uncomment this block and comment the next block.
%\documentclass{amsart}
%\usepackage{amsmath,amsfonts,amssymb,amsthm}
%\usepackage[english]{babel}
%\usepackage{graphicx}
%\usepackage{url}
%\usepackage[round]{natbib}
%\newcommand{\forarxiv}[1]{#1}
%\newcommand{\notforarxiv}[1]{}

% For Sys Bio, uncomment this block and comment the previous block.
\documentclass[12pt,letterpaper]{article}
\usepackage{fixltx2e}
\usepackage{textcomp}
\usepackage{fullpage}
\usepackage{amsfonts}
\usepackage{verbatim}
\usepackage[english]{babel}
\usepackage{pifont}
\usepackage{color}
\usepackage{setspace}
\usepackage{lscape}
\usepackage{indentfirst}
\usepackage[normalem]{ulem}
\usepackage{booktabs}
%\usepackage{nag}
\usepackage{natbib}
%\usepackage{bibtex}
\usepackage{float}
\usepackage{latexsym}
%\usepackage{hyperref}
\usepackage{url}
%\usepackage{html}
\usepackage{hyperref}
\usepackage{epsfig}
\usepackage{graphicx}
\usepackage{amssymb}
\usepackage{amsmath}
\usepackage{bm}
\usepackage{array}
%\usepackage{mhchem}
\usepackage{ifthen}
\usepackage{caption}
\usepackage{hyperref}
%\usepackage{xcolor}
\usepackage{amsthm}
\usepackage{amstext}
\linespread{1.66}
\raggedright
\setlength{\parindent}{0.5in}
\setcounter{secnumdepth}{0}
\pagestyle{empty}
\renewcommand{\section}[1]{%
\bigskip
\begin{center}
\begin{Large}
\normalfont\scshape #1
\medskip
\end{Large}
\end{center}}
\renewcommand{\subsection}[1]{%
\bigskip
\begin{center}
\begin{large}
\normalfont\itshape #1
\end{large}
\end{center}}
\renewcommand{\subsubsection}[1]{%
\vspace{2ex}
\noindent
\textit{#1.}---}
\renewcommand{\tableofcontents}{}
\bibpunct{(}{)}{;}{a}{}{,}  % this is a citation format command for natbib
\newcommand{\forarxiv}[1]{}
\newcommand{\notforarxiv}[1]{#1}

% show keys for eqs, etc.
% \usepackage[notref,notcite]{showkeys}

% code
\newcommand{\program}{\textsf{program}}

% theorems, etc
\newtheorem{lem}{Lemma}
\newtheorem{cor}{Corollary}
\newtheorem{prop}{Proposition}
\newtheorem{thm}{Theorem}
\newtheorem{prob}{Problem}
\newtheorem{defn}{Definition}
\newtheorem{obs}{Observation}
\newtheorem{alg}{Algorithm}

\newcommand{\eat}[1]{}



\newcommand{\FIGmassTransport}{
\begin{figure}[ht]
\begin{center}
  \forarxiv{\includegraphics[width=13cm]{mass_transport.pdf}}
\end{center}
\caption{Caption goes here.}
\label{FIGmassTransport}
\end{figure}
}
\newcommand{\refFIGmassTransport}{1}


\begin{document}

\notforarxiv{
\begin{flushright}
Version dated: \today
\end{flushright}
\bigskip
\noindent RH: PHYLOGENETICS AND THE HUMAN MICROBIOME
\bigskip
\medskip
\begin{center}

% Insert your title:
\noindent{\Large \bf Phylogenetics and the human microbiome}
\bigskip

\noindent {\normalsize \sc
Frederick A. Matsen IV$^1$}\\
\noindent {\small \it
$^1$
Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 91802, USA}\\
\end{center}
\medskip
\noindent{\bf Corresponding author:} Frederick A Matsen, Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 91802, USA; E-mail: matsen@fhcrc.org.\\
\vspace{1in}
}

\forarxiv{
\title{Phylogenetics and the human microbiome}
\author{Frederick A. Matsen IV}
\date{\today}
\begin{abstract}
}
\notforarxiv{
\subsubsection{Abstract}
}

Abstract here.

\forarxiv{
\end{abstract}
\maketitle
\section{Introduction}
}

\notforarxiv{
\noindent (Keywords: xxx; yyy; zzz)\\
\vspace{1.5in}
}

Write paper here.

\notforarxiv{
\newpage
\section{Figure Legends}
%\FIGmassTransport
\clearpage

\newpage

%\section{Table}
%\TABlocalMinimum
}

\bibliographystyle{sysbio}
\bibliography{sbreview}
\end{document}