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authorKarl Berry <karl@freefriends.org>2014-02-27 00:01:50 +0000
committerKarl Berry <karl@freefriends.org>2014-02-27 00:01:50 +0000
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+% Copyright 2013 by Sarah Mäusle and Till Tantau
+%
+% This file may be distributed and/or modified
+%
+% 1. under the LaTeX Project Public License and/or
+% 2. under the GNU Free Documentation License.
+%
+% See the file doc/generic/pgf/licenses/LICENSE for more details.
+
+
+\section{Graph Drawing Layouts: Phylogenetic Trees}
+\label{section-library-graphdrawing-phylogenetics}
+
+{\noindent {\emph{by Sarah M\"ausle and Till Tantau}}}
+
+\ifluatex\else This section of the manual can only be typeset using Lua\TeX.\expandafter\endinput\fi
+
+\tikzset{/graph drawing/phylogenetic inner node/.style={
+ /tikz/.cd,
+ draw, circle, inner sep=0pt, minimum size=5pt}
+}
+\tikzset{/graph drawing/phylogenetic edge/.style={
+ /tikz/.cd,
+ thick, rounded corners,edge node={node[auto,font=\tiny, inner sep=2pt]{}}}
+}
+
+
+\includeluadocumentationof{pgf.gd.phylogenetics.library}
+\includeluadocumentationof{pgf.gd.phylogenetics.PhylogeneticTree}
+
+
+\subsection{Generating a Phylogenetic Tree}
+
+...
+
+When a phylogenetic tree is generated, new nodes and edges get
+created. In order to give you a chance at styling them, the following
+styles are executed:
+
+\begin{stylekey}{/graph drawing/phylogenetic inner node}
+ The style is added every newly created inner node. In this manual,
+ this key is set to:
+\begin{codeexample}[code only]
+\pgfgdset{phylogenetic inner node/.style={
+ /tikz/.cd, draw, circle, inner sep=0pt, minimum size=5pt
+ }
+}
+\end{codeexample}
+\end{stylekey}
+
+\begin{stylekey}{/graph drawing/phylogenetic edge=\meta{length}}
+ The style is added every newly created phylogenetic edge. The
+ \meta{length} will be set to the computed evolutionary length of the
+ edge. In this manual, this key is set to:
+\begin{codeexample}[code only]
+\pgfgdset{phylogenetic edge/.style={
+ /tikz/.cd, thick, rounded corners
+ }
+}
+\end{codeexample}
+\end{stylekey}
+
+
+\includeluadocumentationof{pgf.gd.phylogenetics.AuthorDefinedPhylogeny}
+\includeluadocumentationof{pgf.gd.phylogenetics.SokalMichener1958}
+\includeluadocumentationof{pgf.gd.phylogenetics.BalancedMinimumEvolution}
+\includeluadocumentationof{pgf.gd.phylogenetics.BalancedNearestNeighbourInterchange}
+
+
+\subsection{Laying out the Phylogram}
+
+\includeluadocumentationof{pgf.gd.phylogenetics.Maeusle2012}
+
+
+
+\endinput
+
+
+%%% Local Variables:
+%%% mode: latex
+%%% TeX-master: "pgfmanual-pdftex-version"
+%%% End: