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updated docs for release
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doc/PhyG-User-Manual/PhyG-User-Manual.tex

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@@ -128,8 +128,8 @@ \section{Quick Start}
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\subsection{Obtaining and Installing \phyg}
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\phyg source code, precompiled binaries, test data, and documentation in pdf format,
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as well as tutorials, are available from the \phyg \href{https://github.com/amnh/PhyGraph}{GitHub}
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website.
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as well as tutorials, are available from the \phyg \href{https://github.com/amnh/PhyGraph}
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{GitHub} website.
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\subsubsection{Installing from the binaries}
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Download the \phyg binary from the \href{https://github.com/amnh/PhyGraph}{GitHub}
@@ -359,13 +359,13 @@ \section{Output Graph Formats}
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\label{sec:outputgraphs}
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Graph outputs can be in either Newick, eNewick, dot, and pdf formats. Newick
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tree files can be viewed in other programs such as \href{http://tree.bio.ed.ac.uk/software/figtree/}
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{FigTree} or \href{http:/https://uni-tuebingen.de/fakultaeten/mathematisch-naturwissenschaftliche-fakultaet/fachbereiche/informatik/lehrstuehle/algorithms-in-bioinformatics/software/}
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{Dendroscope}. eNewick files can only be viewed in a text editor. \phyg can output a dot
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{FigTree} or \href{https://uni-tuebingen.de/fakultaeten/mathematisch-naturwissenschaftliche-fakultaet/fachbereiche/informatik/lehrstuehle/algorithms-in-bioinformatics/software/dendroscope/}{Dendroscope}.
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eNewick files can only be viewed in a text editor. \phyg can output a dot
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file, along with a pdf file that can be viewed in a vector graphics program. The dot file can
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be viewed (and modified) in \textit{Graphviz}. In order to output pdf files the application
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\textit{dot} must be installed from the \href{https://graphviz.org/download/}{Graphviz} website.
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In macOS systems, the user must also install the \textit{Cairo} renderer. Both \textit{Graphviz}
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and \textit{Cairo} are available in \href{https://brew.sh/}{Homebrew}, the package manager
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and \textit{Cairo} are available in \href{https://brew.sh/}{Homebrew}, a package manager
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for macOS.\\
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\noindent PDFs can also be generated directly from dot files. In a \textit{Terminal},

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