-The next chapters introduce Jalview's analysis features. Chapter \ref{featannot}
-describes the mechanisms provided by Jalview for interactive creation of sequence and alignment annotation, and how they can be displayed,
-imported and exported and used to reorder the alignment. Chapter
-\ref{featuresfromdb} discusses the retrieval of database references and
-establishment of sequence coordinate systems for the retrieval and display of
-features from databases.
-Chapter \ref{msaservices} describes how to use the range of multiple alignment
-programs provided by JABAWS, and Chapter \ref{aacons} introduces JABAWS AACon
-service for protein multiple alignment conservation analysis.
- In Chapter \ref{alignanalysis}, you will find
-descriptions and exercises on building and displaying trees, PCA analysis,
-alignment redundancy removal, pairwise alignments and alignment conservation
-analysis.
-Chapter \ref{wkwithstructure} introduces the structure visualization
-capabilities of Jalview.
-Chapter \ref{protsspredservices} explains how to perform protein secondary
-structure predictions with JPred, and JABAWS protein disorder prediction
-services are introduced in Chapter \ref{protdisorderpred}.
-Chapter \ref{workingwithnuc} describes functions and visualization techniques relevant
-to working with nucleotide sequences, coding region annotation and nucleotide
-sequence alignments.
-Chapter \ref{jvwebservices} introduces the various web based services
-available to Jalview users, and Chapter \ref{jabaservices} explains how to
-configure the Jalview Desktop for access to new JABAWS servers.
+\newpage
+
+\section{Summary - the rest of the manual}
+
+The first few chapters have covered the basics of Jalview operation: from
+starting the program, importing, exporting, selecting, editing and colouring
+aligments, to the generation of figures for publication, presentation and web
+pages.
+
+The remaining chapters in the manual cover:
+
+\begin{list}{$\circ$}{}
+\item{Chapter \ref{featannot} covers the creation, manipulation and visualisation
+of sequence and alignment annotation, and retrieval of sequence and feature data
+from databases.}
+\item {Chapter \ref{msaservices} explores the range of multiple alignment
+programs offered via Jalview's web services, and introduces the use of
+AACon for protein multiple alignment conservation analysis.}
+\item {Chapter \ref{alignanalysis} introduces Jalview's built in tools for
+multiple sequence alignment analysis, including trees, PCA, and alignment
+conservation analysis. }
+\item {Chapter \ref{3Dstructure} demonstrates the structure visualization
+capabilities of Jalview.}
+\item {Chapter \ref{proteinprediction} introduces protein sequence based
+secondary structure and disorder prediction tools, including JPred.}
+\item {Chapter \ref{dnarna} covers the special functions and
+visualization techniques for working with RNA alignments and protein coding
+sequences.}
+\item {Chapter \ref{jvwebservices} provides instructions on the
+installation of your own Jalview web services.}
+\end{list}