header.tex

\usepackage{amsthm,amsmath}
\usepackage{attachfile2} % - [ ] globalise color setting via embedfile & hypgotoe, see https://tex.stackexchange.com/questions/17926/
\usepackage{dnaseq} % ftp://ftp.mpi-sb.mpg.de/pub/tex/mirror/ftp.dante.de/pub/tex/macros/latex/contrib/dnaseq/dnaseq.pdf

\usepackage{fixfoot} % because [^] duplicated footnotes; learned from http://tex.stackexchange.com/a/48254/87927
\DeclareFixedFootnote{\eq}{Authors contributed equally to this work.}
\DeclareFixedFootnote{\corrKL}{Author for correspondence: \href{mailto:katrin.leinweber@uni-konstanz.de}{katrin.leinweber@uni-konstanz.de}}
\DeclareFixedFootnote{\corrMW}{Author for correspondence: \href{mailto:miriam.windler@uni-konstanz.de}{miriam.windler@uni-konstanz.de}}
\DeclareFixedFootnote{\ZuKo}{\href{https://www.zukunftskolleg.uni-konstanz.de/contact/address/}{Zukunftskolleg at the University of Konstanz}}
\DeclareFixedFootnote{\KoRS-CB}{\href{http://www.chembiol.uni-konstanz.de/contact.19.html}{Konstanz Research School Chemical Biology}}
\DeclareFixedFootnote{\SCen}{\href{http://cms.uni-konstanz.de/screening-center/contact/}{Screening Center Konstanz}}
\DeclareFixedFootnote{\BioKN}{\href{http://cms.uni-konstanz.de/en/biology/contact/}{Department of Biology, University of Konstanz}}
\DeclareFixedFootnote{\MMMu}{\href{http://mibi1.uni-muenster.de/Biologie.IMMB.Philipp/index.html}{Institute of Molecular Microbiology and Biotechnology}}

% reduce whitespace above chapter titles; learned from https://tex.stackexchange.com/questions/39988 + \raggedright
\usepackage{titlesec}
\titleformat{\chapter}[display]
    {\normalfont\huge\bfseries\raggedright}{\chaptertitlename\ \thechapter}{20pt}{\Huge}
\titlespacing*{\chapter}{0pt}{0pt}{20pt}

\usepackage[closeFloats]{fltpage} % FPfigure environments leaves large figure their own page & put caption next to it

\usepackage[hang]{footmisc} % learned from http://tex.stackexchange.com/a/126878/87927
\setlength\footnotemargin{10pt}

\usepackage{gensymb}
\usepackage{graphicx}
\usepackage{epstopdf}
\usepackage{subscript} % necessary after June 9th, MikTeX package upgrade
\usepackage{subcaption}

\usepackage{tocloft} % learned from http://www.latex-community.org/forum/viewtopic.php?f=5&t=7701
\setlength{\cftbeforechapskip}{8pt}
\setlength{\cftbeforesecskip}{5pt}
\setlength{\cftbeforesubsecskip}{3pt}

\usepackage{xcolor}
\usepackage{xspace}

% increase thresholds before figures are pushed to own page; learned from Ansgar
\renewcommand{\topfraction}{.85} % default: .7
\renewcommand{\bottomfraction}{.5} % default: .3

% remove some whitespace; learned from http://www.terminally-incoherent.com/blog/2007/09/19/latex-squeezing-the-vertical-white-space/
\usepackage[a4paper,top=3cm,bottom=3cm,inner=3cm,outer=3cm]{geometry}
\setlength{\topskip}{0pt}
\setlength{\topmargin}{0pt}
\setlength{\headsep}{30pt}

% indent 1st line of paragraphs; learned from https://en.wikibooks.org/wiki/LaTeX/Paragraph_Formatting#Paragraph_indent_and_break
\usepackage{indentfirst}
\setlength{\parindent}{15pt} % default

% prevent individual lines on page bottom or top
\clubpenalty=9999
\widowpenalty=9999

% prevent hyphenation; http://tex.stackexchange.com/a/48438
\hyphenation{Achnanthes}
\hyphenation{Achnanthidium}
\hyphenation{ASSIST}
\hyphenation{Bacteroidetes}
\hyphenation{brevistriata}
\hyphenation{Chapter}
\hyphenation{Cymbella}
\hyphenation{Dyadobacter}
\hyphenation{Elstera}
\hyphenation{Fragilaria}
\hyphenation{Konstanz}
\hyphenation{KNIME}
\hyphenation{litoralis}
\hyphenation{longipes}
\hyphenation{microcephala}
\hyphenation{minutissimum}
\hyphenation{multiseries}
\hyphenation{prostrata}
\hyphenation{Pseudonitzschia}
\hyphenation{Table}