-\begin{figure}
-\begin{center}
-\includegraphics[width=2.5in]{images/trees1.pdf}
-\includegraphics[width=2.5in]{images/trees2.pdf}
-\includegraphics[width=1.25in]{images/trees4.pdf}
-\caption{{\bf Calculating Trees} Jalview provides four built in models for calculating trees.
-Jalview can also load precalculated trees in Newick format (right).}
-\label{trees1}
-\end{center}
-\end{figure}
-
-
-Clicking on the tree brings up a cursor across the height of the tree. The
-sequences are automatically partitioned and coloured (Figure \ref{trees2}). To
-group them together, select the {\sl Calculate $\Rightarrow$ Sort $\Rightarrow$
-By Tree Order $\Rightarrow$ \ldots} alignment window menu option and choose the
-correct tree. The sequences will then be sorted according to the leaf order
-currently shown in the tree view. The coloured background to the sequence IDs
-can be removed with {\sl Select $\Rightarrow$ Undefine Groups} from the
-alignment window menu. Note that tree partitioning will also remove any groups
-and colourschemes on a view, so create a new view ([CTRL-T]) if you wish to
-preserve these.
-
-\begin{figure}
-\begin{center}
-\includegraphics[width=5in]{images/trees3.pdf}
-\caption{{\bf Interactive Trees} The tree level cutoff can be used to designate
-groups in Jalview.}
-\label{trees2}
-\end{center}
-\end{figure}
-
-%\subsubsection{Multiple Views and Input Data recovery from PCA and Tree Viewers}
-% move to ch. 3 ?
-%Both PCA and Tree viewers are linked analysis windows. This means that their selection and display are linked to a particular alignment, and control and reflect the selection state for a particular view.
-
-\subsubsection{Recovering input Data for a Tree or PCA Plot Calculation}
-\parbox[c]{5in}{
-The {\sl File $\Rightarrow$ Input Data } option will open a new alignment window containing the original data used to calculate the tree or PCA plot (if available). This function is useful when a tree has been created and then the alignment subsequently changed.
-}
-\parbox[c]{1.25in}{\centerline{\includegraphics[width=1.25in]{images/pca_fmenu.pdf}
-}}
-
-\subsubsection{Changing the associated View for a Tree or PCA Viewer}
-\parbox[c]{4in}{
-The {\sl View $\Rightarrow$ Associated Nodes With $\Rightarrow$ .. } submenu is shown when the viewer is associated with an alignment that is involved in multiple views. Selecting a different view does not affect the tree or PCA data, but will change the colouring and display of selected sequences in the display according to the colouring and selection state of the newly associated view.
-} \parbox[c]{3in}{\centerline{
-\includegraphics[width=2.5in]{images/pca_vmenu.pdf} }}
-
-
-\exercise{Trees}{
-\exstep{Ensure that you have at least 1G memory available in Jalview
-(Either start with this link:
-\href{http://www.jalview.org/services/launchApp?jvm-max-heap=1G}{http://www.jalview.org/services/launchApp?jvm-max-heap=1G},
-or in the Development section of the Jalview web site
-(\href{http://www.jalview.org/development/development-builds}{http://www.jalview.org/development/development-builds})
-in the ``latest official build'' row in the table, go to the
-``Webstart'' column, click on ``G2''.)}
-\exstep{Open the alignment at \textsf{http://www.jalview.org/tutorial/alignment.fa}. Select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$ Neighbour Joining Using BLOSUM62}. A new tree window will appear.}
-\exstep{Click on the tree window. A cursor will appear. Note that placing this cursor divides the tree into a number of groups by colour. Place the cursor to give about 4 groups, then select {\sl Calculate $\Rightarrow$ Sort $\Rightarrow$ By Tree Order $\Rightarrow$ Neighbour Joining Tree using BLOSUM62 from ... }. The sequences are reordered to match the order in the tree and groups are formed implicitly.}
-\exstep{Select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$
-Neighbour Joining Using \% Identity}. A new tree window will appear. The group colouring
-makes it easy to see the differences between the two trees, calculated using
- different methods.} \exstep{Select from sequence 2 column 60 to sequence 12 column 123. Select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$ Neighbour Joining Using BLOSUM62}. A new tree window will appear. It can be seen that the tree contains 11 sequences. It has been coloured according to the already selected groups from the first tree and is calculated purely from the residues in the selection.
-Comparing the location of individual sequences between the three trees illustrates the importance of selecting appropriate regions of the alignment for the calculation of trees.
-}
-\exstep{Recover the {\sl Input Data} for the tree you just calculated from the {\sl File} menu. Check the {\sl Edit $\Rightarrow$ Pad Gaps } option is {\sl not} ticked, and insert one gap anywhere in the alignment. Now select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$ Neighbour Joining Using BLOSUM62}.
-
-A warning dialog box {\bf ``Sequences not aligned'' } appears because the sequences input to the tree calculation are of different lengths. }
-
-\exstep{Now select {\sl Edit $\Rightarrow$ Pad Gaps } and try to perform the tree calculation again - this time a new tree should appear.
-
-This demonstrates the use of the {\sl Pad Gaps } editing preference, which ensures that all sequences are the same length after editing. }
-
-}
-
-\subsection{Tree Based Conservation Analysis}
-\label{treeconsanaly}
-
-Trees reflect the pattern of global sequence similarity exhibited by the
-alignment, or region within the alignment, that was used for their calculation.
-The Jalview tree viewer enables sequences to be partitioned into groups based
-on the tree. This is done by clicking within the tree viewer window. Once subdivided, the
-conservation between and within groups can be visually compared in order to
-better understand the pattern of similarity revealed by the tree and the
-variation within the clades partitioned by the grouping. The conservation based
-colourschemes and the group associated conservation and consensus annotation
-(enabled using the alignment window's {\sl View $\Rightarrow$ Autocalculated
-Annotation $\Rightarrow$ Group Conservation} and {\sl Group Consensus} options)
-can help when working with larger alignments.
-
-\exercise{Tree Based Conservation Analysis}{
-\label{consanalyexerc}
-\exstep{Load the PF03460 PFAM seed alignment using the sequence fetcher. Colour it with the {\sl Taylor colourscheme}, and apply {\sl Conservation } shading. }
-\exstep{Build a Neighbour joining tree using BLOSUM62 and use the {\sl Sort
-Alignment By Tree} option in the tree viewer submenu to order alignment using the calculated tree.} \exstep{Select a point on the tree to partition the alignment, and examine the variation in colouring between different groups.
-
-You may find it easier to browse the alignment if you first uncheck the {\sl
-Annotations $\Rightarrow$ Show Annotations} option, and open the Overview Window
-within the View menu to aid navigation.}
-\exstep{Try changing the colourscheme to BLOSUM62 (whilst ensuring that {\sl Apply Colour to All Groups} is selected)}
-{\sl Note: You may want to save the alignment and tree as a project file, since
-it is used in the next few exercises. } }
-
-\subsection{Redundancy Removal}
-
-The redundancy removal dialog box is opened using the {\sl Edit $\Rightarrow$ Remove Redundancy\ldots} option in the alignment menu. As its menu option placement suggests, this is actually an alignment editing function, but it is convenient to describe it here. The redundancy removal dialog box presents a percentage identity slider which sets the redundancy threshold. Aligned sequences which exhibit a percentage identity greater than the current threshold are highlighted in black. The [Remove] button can then be used to delete these sequences from the alignment as an edit operation\footnote{Which can usually be undone. A future version of Jalview may allow redundant sequences to be hidden, or represented by a chosen sequence, rather than deleted.}.
-\begin{figure}
-\begin{center}
-\includegraphics[width=5.5in]{images/redundancy.pdf}
-\end{center}
-\label{removeredundancydialog}
-\caption{The Redundancy Removal dialog box opened from the edit menu. Sequences that exceed the current percentage identity threshold and are to be removed are highlighted in black.}
-\end{figure}
-
-\exercise{Remove Redundant Sequences}{
-
-\exstep{Re-use or recreate the alignment and tree which you worked with in the
-tree based conservation analysis exercise (exercise \ref{consanalyexerc}). In
-the alignment window, you may need to deselect groups using Esc key.}
-\exstep{In the Edit menu select Remove Redundancy to open the Redundancy
-threshold selection dialog. Adjust the redundancy threshold value, start
-at 50 and increase the value to 65. Sequences selected will change colour in the Sequence ID panel. Select ``Remove'' to
-remove the sequences that are more than 65\% similar under this alignment.}
-\exstep{Select the Tree viewer's {\sl View $\Rightarrow$ Mark Unlinked Leaves} option, and note that the removed sequences are now prefixed with a * in the tree view.}
-\exstep{Use the [Undo] button in the Redundancy threshold selection dialog box
-to recover the sequences. Note that the * symbols disappear from the tree display.}
-\exstep{Experiment with the redundancy removal and observe the relationship between the percentage identity threshold and the pattern of unlinked nodes in the tree display.}
-}
-
-\subsection{Subdividing the Alignment According to Specific Mutations}
-
-It is often necessary to explore variations in an alignment that may correlate
-with mutations observed in a particular region; for example, sites exhibiting
-single nucleotide polymorphism, or residues involved in substrate recognition in
-an enzyme. One way to do this would be to calculate a tree using the specific
-region, and subdivide it in order to partition the alignment.
-However, calculating a tree can be slow for large alignments, and the tree may
-be difficult to partition when complex mutation patterns are being analysed. The
-{\sl Select $\Rightarrow$ Make groups for selection } function was introduced to
-make this kind of analysis easier. When selected, it will use the characters in
-the currently selected region to subdivide the alignment. For example, if a
-single column is selected, then the alignment (or each group defined on the
-alignment) will be divided into groups based on the residue or nucleotide found
-at that position. These new groups are annotated with the characters in the
-selected region, and Jalview's group based conservation analysis annotation and
-colourschemes can then be used to reveal any associated pattern of sequence
-variation across the whole alignment.
-
-\subsection{Automated Annotation of Alignments and Groups}
-
-On loading a sequence alignment, Jalview will normally\footnote{Automatic
-annotation can be turned off in the {\sl Visual } tab in the {\sl Tools
-$\Rightarrow$ Preferences } dialog box.} calculate a set of automatic annotation
-rows which are shown below the alignment. For nucleotide sequence alignments,
-only an alignment consensus row will be shown, but for amino acid sequences,
-alignment quality (based on BLOSUM 62) and physicochemical conservation will
-also be shown. Conservation is calculated according to Livingstone and
-Barton\footnote{{\sl ``Protein Sequence Alignments: A Strategy for the
-Hierarchical Analysis of Residue Conservation." } Livingstone C.D. and Barton
-G.J. (1993) {\sl CABIOS } {\bf 9}, 745-756}.
-Consensus is the modal residue (or {\tt +} where there is an equal top residue).
-The inclusion of gaps in the consensus calculation can be toggled by
-right-clicking on the the Consensus label and selecting {\sl Ignore Gaps in
-Consensus} from the pop-up context menu located with consensus annotation row.
-Quality is a measure of the inverse likelihood of unfavourable mutations in the alignment. Further details on these
-calculations can be found in the on-line documentation.
-
-These annotations can be hidden and deleted via the context menu linked to the
-annotation row; but they are only created on loading an alignment. If they are
-deleted then the alignment should be saved and then reloaded to restore them.
-Jalview provides a toggle to autocalculate a consensus sequence upon editing. This is normally selected by default, but can be turned off for
-large alignments {\sl via} the {\sl Calculate $\Rightarrow$ Autocalculate
-Consensus} menu option if the interface is too slow.
-
-\subsubsection{Group Associated Annotation}
-\label{groupassocannotation}
-Group associated consensus and conservation annotation rows reflect the
-sequence variation within a particular group. Their calculation is enabled
-by selecting the {\sl Group Conservation} or {\sl Group Consensus} options in
-the {\sl Annotation $\Rightarrow$ Autocalculated Annotation } submenu of the
-alignment window.
-
-\subsubsection{Alignment and Group Sequence Logos}
-\label{seqlogos}
-
-The consensus annotation row that is shown below the alignment can be overlaid
-with a sequence logo that reflects the symbol distribution at each column of
-the alignment. Right click on the Consensus annotation row and select the {\sl Show
-Logo} option to display the Consensus profile for the group or alignment.
-Sequence logos can be enabled by default for all new alignments {\sl via} the
-Visual tab in the Jalview desktop's preferences dialog box.
-
-\exercise{Group Conservation Analysis}{
-\exstep{Re-use or recreate the alignment and tree which you worked with in the
-tree based conservation analysis exercise (exercise \ref{consanalyexerc})}
-\exstep{In the View menu, create a new view. Ensure the annotation panel
-is displayed (Show annotation in Annotations menu). Enable the display
-of {\sl Group Consensus} option by checking {\sl Group Consensus} in the {\sl Annotation $\Rightarrow$
-Autocalculated Annotation } submenu in the sequence alignment window. Then display of sequence
-logos to make it easier to see the different residue populations within each
-group. Activate logo by right clicking on the Consensus annotation row to open
-the pop-up menu and select the {\sl Show Logo} option.}
-\exstep{In the column alignment ruler, select a column exhibiting about 50\%
-conservation that lies within the central conserved region of the alignment. Subdivide the alignment according to
-this selection using {\sl Select $\Rightarrow$ Make groups for selection}.}
-\exstep{Re-order the alignment according to the new groups that have been
-defined. Click on the group annotation row IDs to select groups exhibiting a
-specific mutation.}
-\exstep{Select another column exhibiting about 50\% conservation
-overall, and subdivide the alignment further. Note that the new groups
-inherit the names of the original groups, allowing you to identify the
-combination of mutations that resulted in the subdivision.
-}
-\exstep{Clear the groups, and try to subdivide the alignment using two
-non-adjacent columns.
-
-{\sl Hint: You may need to hide the intervening columns before you can select
-both of the columns that you wish to use to subdivide the alignment.}}
-\exstep{Switch back to the original view, and experiment with subdividing
-the tree groups made in the previous exercise.}
-}
-
-\subsection{Other Calculations}
-
-
-\subsubsection{Pairwise Alignments}
-
-Jalview can calculate optimal pairwise alignments between arbitrary sequences {\sl via} the {\sl Calculate $\Rightarrow$ Pairwise Alignments\ldots} menu option. Global alignments of all pairwise combinations of the selected sequences are performed and the results returned in a text box.
-
-\begin{figure}[]
-\begin{center}
-\includegraphics[width=4in]{images/pairwise.pdf}
-\caption{{\bf Pairwise alignment of sequences.} Pairwise alignments of three selected sequences are shown in a textbox.}
-\label{pairwise}
-\end{center}
-\end{figure}
-
-\pagebreak[2]
-
-\section{Webservices}
-\label{jvwebservices}
-The term ``Webservices'' refers to a variety of data exchange
-mechanisms based on HTTP.\footnote{HTTP: Hyper-Text Transfer Protocol.}
-
-\parbox[c]{4.5in}{Jalview can exploit public webservices to access databases
-remotely, and also submit data to public services by opening pages with your web browser. These types of
-services are `one-way', {\sl i.e.} data is either sent to the webservice or
-retrieved from it by Jalview. The desktop application can also interact
-with `two-way' remote analysis services in order to offload computationally
-intensive tasks to High Performance Computing facilities. Most of these two-way
-services are provided by {\bf Ja}va {\bf B}ioinformatics {\bf A}nalysis {\bf
-W}eb {\bf S}ervice (JABAWS) servers\footnote{See
-http://www.compbio.dundee.ac.uk/jabaws for more information and to download
-your own server.}, which provides an easily installable system for performing
-a range of bioinformatics analysis tasks. }
-\parbox[c]{1.75in}{\includegraphics[width=1.65in]{images/wsmenu.pdf}}
-
-\subsection{One-Way Web Services}
-
-There are two types of one way service in Jalview. Database services,
-which were introduced in in Section \ref{fetchseq}, provide sequence and
-alignment data. They can also be used to add sequence IDs to an alignment
-imported from a local file, prior to further annotation retrieval, as described
-in Section \ref{featuresfromdb}. A second type of one way service is provided
-by Jalview's DAS sequence feature retrieval system, which is described
-in Section \ref{dasfretrieval}.
-% The final type of one way service are sequence
-% and ID submission services.
-% exemplified by the `Envision2 Services' provided
-% by the ENFIN Consortium\footnote{ENFIN is the European Network for Functional
-% INtegration. Please see http://www.enfin.org for more information. }.
-
-% \subsubsection{One-way submission services}
-% Jalview can use the system's web browser to submit sets of sequences and
-% sequence IDs to web based applications. Single sequence IDs can be passed to
-% a web site using the user definable URL links listed under the {\sl
-% Links} submenu of the sequence ID popup menu. These are configured
-% in the {\sl Connections} tab of the {\sl Preferences} dialog box.