\newcommand\exampleend{\hfill$\diamond$}
% ##### DCJ stuff #####
\newcommand\dcaj{double cut and join\xspace}
\newcommand\dcjindel{d_{\DCJ}^{id}}
\newcommand\dcj{d_{\DCJ}}
\renewcommand\gg{\mathcal G}
\newcommand\del{\mathcal A}
\newcommand\ins{\mathcal B}
\newcommand\clean{\varnothing}
\newcommand\gdel{\mathcal G_{\!A}}
\newcommand\gins{\mathcal G_{\!B}}
\newcommand\ag{\AG(A,B)}
\renewcommand\r{\lambda} % # runs
\newcommand\R{\Lambda} % # runs after clustering
\newcommand\dr{\Delta\r}
\newcommand\drr{\Delta\r^{\!\rho}}
\newcommand\DR{\Delta\R}
\newcommand\DRR{\Delta\R^{\!\rho}}
%\newcommand\lab[1]{\lambda(#1)}
\newcommand\redu[1]{\left.#1\right|_\mathcal G}
\newcommand\h[1]{#1^h}
\renewcommand\t[1]{#1^t}
\renewcommand\a{$A$\xspace}
\renewcommand\b{$B$\xspace}
\renewcommand\O{\mathcal O}
\renewcommand\AA{$A\!A$\xspace}
\newcommand\AB{$A\!B$\xspace}
\newcommand\BA{$B\!A$\xspace}
\newcommand\BB{$B\!B$\xspace}
\newcommand\ab{\del\ins}
\newcommand\ba{\ins\del}
\def\aa{A\!A}
\def\bb{B\!B}
\def\AAab{A\!A_{\!\del\!\ins}}
\def\AAa{A\!A_{\!\del}}
\def\AAb{A\!A_{\ins}}
\def\BBab{B\!B_{\!\!\del\!\ins}}
\def\BBa{B\!B_{\!\!\del}}
\def\BBb{B\!B_{\ins}}
\def\ABab{A\!B_{\!\!\del\!\ins}}
\def\ABba{A\!B_{\ins\!\del}}
\def\ABa{A\!B_{\!\!\del}}
\def\ABb{A\!B_\ins}
\def\ABm{A\!B_\bullet}
\def\AAo{A\!A_{\!\varnothing}}
\def\ABo{A\!B_{\!\varnothing}}
\def\BBo{B\!B_{\!\varnothing}}
\def\xx{A\!B_\times}
\def\aba{\del\!\gr{\ins\!\del}}
\def\bab{\ins\!\gr{\del\!\ins}}
\newcommand\clusterize{accumulate\xspace}
\newcommand\clustering{accumulating\xspace} %aggregate, unite/unifying
\newcommand\clusterized{accumulated\xspace}
\newcommand\clusterization{accumulation\xspace}
\renewcommand\v[1]{V(#1)}
\newcommand\vset[2]{\v{#1}=\set{#2}}

% ##### math #####
\DeclareMathOperator\AG{AG}
\DeclareMathOperator\DCJ{DCJ}
%\DeclareMathOperator\V{V}
\newcommand\set[1]{\{#1\}}
\newcommand\corresponds{\mathrel{\widehat{=}}}
\newcommand\gleich{=\joinrel=}
\newcommand\subargmax[1]{\lower0.6em\hbox{$\stackrel{\displaystyle\argmax\ }{_{#1}}$}}
\newcommand\subtexting[2]{\lower0.58em\hbox{$\stackrel{\displaystyle#1}{_{#2}}$}}
% \newcommand\Uu{\mathcal U_{{}_{\Box}}}
% \newcommand\Us{\mathcal U_{\triangleleft}}
% \DeclareMathOperator{\isE}{\scalebox{1.5}[1]{\rotatebox[origin=c]{180}{$\exists$}}}
% \DeclareMathOperator{\notE}{\scalebox{1.5}[1]{\rotatebox[origin=c]{180}{$\nexists$}}}
%\DeclareMathOperator{\gc}{\scalebox{-1.5}[1]{$\exists$}}
%\DeclareMathOperator{\ngc}{\scalebox{-1.5}[1]{$\nexists$}}
\newcommand\edge[2]{\{#1,#2\}}
\newcommand\dedge[2]{(#1,#2)}
% \renewcommand{\varnothing}{\{\,\}}
\newcommand{\bo}[1]{#1_{_{\Box}}}
\newcommand{\tri}[1]{#1_\triangleleft}
\newcommand{\pib}{\bo\pi}
\newcommand{\pit}{\tri\pi}
\newcommand\meng{\{1,2,\ldots,N\}}
\newcommand{\abs}[1]{\ensuremath{\lvert #1 \rvert}} % Absolutbetrag. Statt |a| verwenden.
%\newcommand\qed{\qquad\Box}
\newcommand\toinf[1][n]{\toconv{#1}\infty}
\renewcommand\epsilon\varepsilon
\renewcommand\rho\varrho
%proof:
\renewcommand\lq{\text{\textgravedbl}\!\!}\renewcommand\rq{\!\!\text{\textacutedbl}}

% ##### tables #####
% \newcommand\rl[1]{\multicolumn{1}{r|}{#1}}			% item|
% \renewcommand\ll[1]{\multicolumn{1}{|r}{#1}}		% |item
% % \newcommand\cc[1]{\multicolumn{1}{|c|}{#1}} 		% |item|
% \newcommand\lc[2]{\multicolumn{#1}{|c|}{#2}}		%
% \newcommand\cc[1]{\multicolumn{1}{c}{#1}}
% % \renewcommand{\arraystretch}{1.2} % Tabellenzeilen ein bischen h?her machen.
% \newcommand\m[2]{\multirow{#1}{*}{$#2$}}

% ##### Text symbole #####
% \newcommand\subdot[1]{\lower0.5em\hbox{$\stackrel{\displaystyle #1}{.}$}}
% \newcommand\subsubdot[1]{\lower0.5em\hbox{$\stackrel{#1}{.}$}}
\newcommand\stern\circledast

% ##### Textersetzung (Abk?rzungen) #####
% \newcommand\na{\textsl{Naive Algorithm}\xspace}
% \newcommand\sh{\textsl{Simple Heuristic}\xspace}
% \newcommand\ea{\textsl{Exact Algorithm}\xspace}
% \newcommand\rec{\textsl{Reconstruction Algorithm}\xspace}
\newcommand\rfe{\textit{R.~felis}\xspace}
\newcommand\rma{\textit{R.~massiliae}\xspace}
\newcommand\raf{\textit{R.~africae}\xspace}
\newcommand\rco{\textit{R.~conorii}\xspace}
\newcommand\rpr{\textit{R.~prowazekii}\xspace}
\newcommand\rty{\textit{R.~typhi}\xspace}
\newcommand\rbe{\textit{R.~bellii}\xspace}
\newcommand\ric{\textit{Rickettsia}\xspace}
\newcommand\rf{\textit{fel}\xspace}
\newcommand\rms{\textit{mas}\xspace}
\newcommand\ra{\textit{afr}\xspace}
\newcommand\rc{\textit{con}\xspace}
\newcommand\rp{\textit{pro}\xspace}
\newcommand\rt{\textit{typ}\xspace}
\newcommand\rb{\textit{bel}\xspace}
\newcommand\eg{e.\,g.\ }		%\newcommand{\zB}{z.\,B.\ }
\newcommand\resp{resp.\ }	%\newcommand{\bzw}{bzw.\ }%\newcommand{\iAllg}{i.\,Allg.\ }
\newcommand\ie{i.\,e.\ }%\renewcommand{\dh}{d.\,h.\ }
\newcommand\etal{~\textit{et al.\xspace}}
% \newcommand\etalcite[1]{~\textit{et al.} \cite{#1}\xspace}

% Abkuerzung fuer URLs: \hrefn{url}, Vorsicht bei Tilden (~) in den URLs
\newcommand{\hrefn}[1]{\href{#1}{#1}}
\newcommand{\myquote}[1]{\glqq{}#1\grqq{}} % richtige Anfuehrungszeichen: ,, Bla ''
% \newcommand{\str}[1]{{\tt{}#1}} % einheitliche formatierung fuer zeichenketten

% ##### draft #####
\newcommand{\ignore}[1]{}
\newcommand\info[1]{\marginpar{\begin{center}#1\end{center}}}
\newcommand\note{\marginpar{\begin{center}$\longleftarrow$\end{center}}}
\newcommand\picmis[1]{$$\boxed{\mbox{\ttfamily picture #1}}$$}
%Todo am Rand notieren
\begin{comment}
% DONE WITH \usepackage{todo}
\newcommand{\todo}[1]{%
  \ensuremath{\bigstar}%
  \marginpar{%
		\begin{flushleft}%
			\vspace{-1.5\baselineskip}%
			{\small TODO\ \ensuremath{\bigstar}\\#1}%
		\end{flushleft}%
  }%
}%
\end{comment}

\newcommand\opdown[2]{\lower0.75em\hbox{$\stackrel{\displaystyle#1}{\scriptstyle#2}$}}
\newcommand\toconv[2]{\;\lower0.5em\hbox{$\stackrel{\longrightarrow}{\scriptstyle#1\to#2}$}}
\newcommand\wildcard[1]{\fbox{\ttfamily Platzhalter: #1}}

\newcommand{\argmax}{\textrm{argmax}}
\newcommand{\argmin}{\textrm{argmin}}

\newcommand{\matlab}{\lstset{
    language=Matlab,
    basicstyle=\small\sffamily,
    breaklines=true,
    frame=tblr,
    backgroundcolor=\color{yellow!20},
    numbers=none,
    numbersep=4pt,
    numberstyle=\small,
    showstringspaces=false,
    keywordstyle=\color{blue}\bfseries
}}

\newcommand\data[1]{\marginpar{\vspace{-35pt}\begin{center}
                     \includegraphics[width=1cm]{img/cd}
                    \end{center}\vspace{-15pt}\centering\footnotesize\texttt{#1}}}
\renewcommand\vec[1]{\textbf{#1}}
\newcommandx{\unsure}[2][1=]{\todo[linecolor=red,backgroundcolor=red!25,bordercolor=red,#1]{#2}}
\newcommandx{\change}[2][1=]{\todo[linecolor=blue,backgroundcolor=blue!25,bordercolor=blue,#1]{#2}}
\newcommandx{\info}[2][1=]{\todo[linecolor=OliveGreen,backgroundcolor=OliveGreen!25,bordercolor=OliveGreen,#1]{#2}}
\newcommandx{\improvement}[2][1=]{\todo[linecolor=violet,backgroundcolor=violet!25,bordercolor=violet,#1]{#2}}
\newcommandx{\thiswillnotshow}[2][1=]{\todo[disable,#1]{#2}}
