updated docs for release

amnh · Jan 7, 2025 · cad2ba8 · cad2ba8
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diff --git a/doc/PhyG-User-Manual/PhyG-User-Manual.tex b/doc/PhyG-User-Manual/PhyG-User-Manual.tex
@@ -128,8 +128,8 @@ \section{Quick Start}
 
 	\subsection{Obtaining and Installing \phyg}
 		\phyg source code, precompiled binaries, test data, and documentation in pdf format, 
-		as well as tutorials, are available from the \phyg \href{https://github.com/amnh/PhyGraph}{GitHub} 
-		website.
+		as well as tutorials, are available from the \phyg \href{https://github.com/amnh/PhyGraph}
+		{GitHub} website.
 
 	\subsubsection{Installing from the binaries}
 		Download the \phyg binary from the \href{https://github.com/amnh/PhyGraph}{GitHub} 
@@ -359,13 +359,13 @@ \section{Output Graph Formats}
 \label{sec:outputgraphs}
 	Graph outputs can be in either Newick, eNewick, dot, and pdf formats. Newick 
 	tree files can be viewed in other programs such as \href{http://tree.bio.ed.ac.uk/software/figtree/}
-	{FigTree} or \href{http:/https://uni-tuebingen.de/fakultaeten/mathematisch-naturwissenschaftliche-fakultaet/fachbereiche/informatik/lehrstuehle/algorithms-in-bioinformatics/software/}
-	{Dendroscope}. eNewick files can only be viewed in a text editor. \phyg can output a dot 
+	{FigTree} or \href{https://uni-tuebingen.de/fakultaeten/mathematisch-naturwissenschaftliche-fakultaet/fachbereiche/informatik/lehrstuehle/algorithms-in-bioinformatics/software/dendroscope/}{Dendroscope}. 		
+	eNewick files can only be viewed in a text editor. \phyg can output a dot 
 	file, along with a pdf file that can be viewed in a vector graphics program. The dot file can 
 	be viewed (and modified) in \textit{Graphviz}. In order to output pdf files the application 
 	\textit{dot} must be installed from the \href{https://graphviz.org/download/}{Graphviz} website. 
 	In macOS systems, the user must also install the \textit{Cairo} renderer. Both \textit{Graphviz} 
-	and \textit{Cairo} are available in \href{https://brew.sh/}{Homebrew}, the package manager 
+	and \textit{Cairo} are available in \href{https://brew.sh/}{Homebrew}, a package manager 
 	for macOS.\\
 
 	\noindent PDFs can also be generated directly from dot files. In a \textit{Terminal},