-\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})}
-\exstep{Open the Remove Redundancy dialog and adjust the threshold to 90\%. Remove the sequences that are more than 90\% 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 on the dialog 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 context menu. 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 but are only created on loading an
-alignment. If they are deleted then the alignment should be saved and 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 View $\Rightarrow$ 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{Create a new view, and ensure the annotation panel is displayed, and
-enable the display of {\sl Group Consensus} and the display of sequence
-logos to make it easier to see the different residue populations within each group.}
-\exstep{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.
-%
-% The Envision 2 services presented in the webservice menu provides are the first
-% example of one-way services where multiple sequences or sequence IDs can be
-% sent. The {\sl Web service $\Rightarrow$ Envision 2 Services} menu entry
-% provides two sub-menus that enable you to submit the sequences or IDs
-% associated with the alignment or just the currently selected sequences to one
-% of the Envision2 workflows. Selecting any one will open a new browser window on
-% the Envision2 web application. The menu entries and their tooltips provide
-% details of the Envision2 workflow and the dataset set that will be submitted
-% ({\sl i.e.} the database reference type, or associated sequence subset). Please
-% note, due to technical limitations, Jalview can currently only submit small
-% numbers of sequences to the workflows - if no sequence or ID submissions are
-% presented in the submenus, then try to select a smaller number of sequences to
-% submit.
-
-\subsection{Remote Analysis Web Services}
-Remote analysis services enable Jalview to use external computational
-facilities. There are curently three types of service - multiple sequence
-alignment, protein secondary structure prediction, and alignment analysis.
-Many of these are provided by JABA servers, which are described at the end of
-this section. In all cases, Jalview will construct a job based on the alignment
-or currently selected sequences, ask the remote server to run the job, monitor
-status of the job and, finally, retrieve the results of the job and display
-them. The Jalview user is kept informed of the progress of the job through a
-status window.
-
-Currently, web service jobs and their status windows are not stored in Jalview
-Project Files\footnote{This may be rectified in future versions.}, so it is
-important that you do not close Jalview whilst a job is running. It is also
-essential that you have a continuous network connection in order to
-successfully use web services from Jalview, since it periodically checks the
-progress of running jobs.
-
-
-\subsection{JABA Web Services for sequence alignment and analysis}
-\label{jabaservices}
-JABA stands for ``JAva Bioinformatics Analysis'', which is a system developed
-by Peter Troshin and Geoff Barton at the University of Dundee for running
-computationally intensive bioinformatics analysis programs. A JABA installation
-typically provides a range of JABA web services (JABAWS) for use by other
-programs, such as Jalview.
-
-Exercises in the remainder of this section will demonstrate the simplest way of
-installing JABA on your computer, and configuring Jalview so it can access the JABA services. If you
-need any further help or more information about the services, please go to the
-\href{http://www.compbio.dundee.ac.uk/jabaws}{JABAWS home page}.
-%% \subsubsection{Aims}
-%% \begin{list}{$\bullet$}{}
-%% \item Gain experience using the different alignment services provided by
-% JABA
-%%\item Learn about the way that Jalview stores user presets for JABA services
-%%\item Learn how to install JABA services and configure Jalview to access them
-%%\end{list}
-
-\subsection{Changing the Web Services menu layout}
-\label{changewsmenulayout}
-If you are working with a lot of different JABA services, you may wish to change
-the way Jalview lays out the web services menu. You can do this from the Web
-Services tab of the {\sl Preferences} dialog box.
-
-\exercise{Changing the Layout of the Web Services Menu}{
-\label{changewsmenulayoutex}
-\exstep{Make sure you have loaded an alignment into Jalview, and examine the
-current layout of the alignment window's {\sl Web Service} menu.}
-\exstep{Open the preferences dialog box and select the web services tab.}
-\exstep{Ensure the {\sl Enable JABAWS services} checkbox is selected, and unselect
-the {\sl Enable Enfin Services} checkboxes.}
-\exstep{Hit {\sl Refresh Services} to update the web services menu -- once the
-progress bar has completed, open the {\sl Web Service} menu to view the changes.}
-\exstep{Select the {\sl Index by host} checkbox and refresh the services once again.
-
-{\sl Observe the way the layout of the JABAWS Alignment submenu changes.}
-}
-\exstep{Do the same with the {\sl Index by type} checkbox.}
-}
-
-Jalview provides these options for configuring the layout of the {\sl Web Service}
-menu because different Jalview users may have access to a different number of
-JABA services, and each will have their own preference regarding the layout of
-the menu.
-
-\begin{figure}[htbc]
-\begin{center}
-\includegraphics[width=3in]{images/jvjabawsconfig.pdf}
-\caption{{\bf The Jalview Web Services preferences panel.} Options are provided
-for configuring the list of JABA servers that Jalview will use, enabling and
-disabling Enfin services, and configuring the layout of the web services
-menu.}
-\label{jvjabawsconfig}
-\end{center}
-\end{figure}
-
-
-\subsubsection{Testing JABA services}
-The JABAWS configuration dialog shown in Figure \ref{jvjabawsconfig} has colour
-codes to indicate whether the Desktop can access the server, and whether all
-services advertised by the server are functional. The colour codes are:
-
-\begin{list}{$\bullet$}{}
- \item Red - Server cannot be contacted or reports a connection error.
- \item Amber - Jalview can connect, but one or more services are non-functional.
- \item Green - Server is functioning normally.
-\end{list}
- %TODO green and a tick, red and a cros, amber and a value indicating whether its all going
-
-Test results from JABAWS are reported on Jalview's console output (opened from
-the Tools menu). Tests are re-run every time Jalview starts, and when the
-[Refresh Services] button is pressed on the Jalview JABAWS configuration panel.
-
-\subsubsection{Resetting the JABA services setting to their defaults}
-Once you have configured a JABAWS server and selected the OK button of the
-preferences menu, the settings will be stored in your Jalview preferences file,
-along with any preferences regarding the layout of the web services menu. If
-you should ever need to reset the JABAWS server list to its defaults, use the
-`Reset Services' button on the Web Services preferences panel.
-
-\subsection{Running your own JABA server}
-You can download and run JABA on your own machine using the `VMWare' or
-VirtualBox virtual machine environments. If you would like to learn how to do
-this, there are full instructions at the
-\href{http://www.compbio.dundee.ac.uk/jabaws/}{JABA web site}.
-
-\exercise{Installing a JABA Virtual Machine on your computer}{
-\label{jabawsvmex}{\sl This tutorial will demonstrate the simplest way of
-installing JABA on your computer, and configuring Jalview so it can access the JABA services.
-
-{\bf Prerequisites}
-
-You will need a copy of VMWare Player/Workstation/Fusion on your machine.
-}
-
-\exstep{If you do not have VMWare player installed, download it from
-www.vmware.com (this takes a few minutes -- you will need to register and wait
-for an email with a download link).}
-\exstep{Download the JABA virtual appliance archive called `jaba-vm.zip' from
-\textsf{http://www.compbio.dundee.ac.uk/jabaws/archive/jabaws-vm.zip}
-
-WARNING: This is large (about 300MB) and will take some time to download.
-}
-\exstep{Unpack the archive's contents to a place on your machine with at least
-2GB of free space.
-
-(On Windows, right click on the archive, and use the 'Extract archive..' option).
-}
-\exstep{Open the newly extracted directory and double click the VMWare virtual
-machine configuration file (jabaws.vcf). This will launch the VMWare player.
-}
-\exstep{Once VMWare player has started up, it may ask the question ``Did you move or copy
-this virtual appliance?'' -- select `Copy'.}
-\exstep{You may be prompted to download the VMWare linux tools. These are not
-necessary, so close the window or click on `Later'.}
-\exstep{You may also be prompted to install support for one or more devices (USB
-or otherwise). Say `No' to these options.}
-\exstep{Once the machine has loaded, it will display a series of IP addresses
-for the different services provided by the VM. Make a note of the JABAWS URL --
-this will begin with `http:' and end with `/jabaws''.}
-}
-
-\exercise{Configuring Jalview to access your new JABAWS virtual appliance}{
-\label{confnewjabawsappl}
-\exstep{Start Jalview (If you have not done so already).}
-\exstep{Enable the Jalview Java Console by selecting its option from the Tools
-menu.
-
-{\sl Alternately, use the System Java console if you have
-configured it to open when Jalview is launched, {\sl via} your system's Java
-preferences (under the `Advanced' tab on Windows).}}
-\exstep{Open the {\sl Preferences} dialog and locate the Web Services tab.}
-\exstep{Add the URL for the new JABAWS server you started in Exercise
-\ref{jabawsvmex} to the list of JABAWS urls using the `New Service
-URL' button.}
-\exstep{You will be asked if you want to test the service. Hit `Yes' to do this
--- you should then see some output in the console window.
-
-{\sl Take a close look at the output in the console. What do you think is
-happening?}
-}
-\exstep{Hit OK to save your preferences -- you have now added a new JABA
-service to Jalview!}
-\exstep{Try out your new JABA services by loading the ferredoxin sequences from
-http://www.jalview.org/tutorial/alignment.fa}
-\exstep{Launch an alignment using one
-of the JABA methods provided by your server. It will be listed under the JABAWS Alignment submenu of the {\sl Web Service} menu on the alignment window.