+\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.
+
+{\sl Note: You can watch the JABA VM appliance's process working by opening the
+process monitor on your system. (On Windows XP, this involves right-clicking the
+system clock and opening the task manager -- then selecting the 'Processes' tab
+and sort by CPU).}
+}
+}
+
+\section{Multiple Sequence Alignment}
+\label{msaservices}
+Sequences can be aligned using a range of algorithms provided by JABA web
+services. These include ClustalW\footnote{{\sl ``CLUSTAL W: improving the
+sensitivity of progressive multiple sequence alignment through sequence
+weighting, position specific gap penalties and weight matrix choice."} Thompson
+JD, Higgins DG, Gibson TJ (1994) {\sl Nucleic Acids Research} {\bf 22},
+4673-80}, Muscle\footnote{{\sl ``MUSCLE: a multiple sequence alignment method
+with reduced time and space complexity"} Edgar, R.C.
+(2004) {\sl BMC Bioinformatics} {\bf 5}, 113}, MAFFT\footnote{{\sl ``MAFFT: a
+novel method for rapid multiple sequence alignment based on fast Fourier
+transform"} Katoh, K., Misawa, K., Kuma, K. and Miyata, T. (2002) {\sl Nucleic
+Acids Research} {\bf 30}, 3059-3066. and {\sl ``MAFFT version 5:
+improvement in accuracy of multiple sequence alignment"} Katoh, K., Kuma, K.,
+Toh, H. and Miyata, T. (2005) {\sl Nucleic Acids Research} {\bf 33}, 511-518.},
+ProbCons,\footnote{PROBCONS: Probabilistic Consistency-based Multiple Sequence
+Alignment.
+Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S.
+(2005) {\sl Genome Research} {\bf 15} 330-340.} T-COFFEE\footnote{T-Coffee:
+A novel method for multiple sequence alignments. (2000) Notredame, Higgins and
+Heringa {\sl JMB} {\bf 302} 205-217} and Clustal Omega.\footnote{Fast, scalable
+generation of high-quality protein multiple sequence alignments using Clustal
+Omega. Sievers F, Wilm A, Dineen DG, Gibson TJ, Karplus K, Li W, Lopez R,
+McWilliam H, Remmert M, Soding J, Thompson JD, Higgins DG (2011) {\sl Molecular
+Systems Biology} {\bf 7} 539
+\href{http://dx.doi.org/10.1038/msb.2011.75}{doi:10.1038/msb.2011.75}} Of these,
+T-COFFEE is the slowest, but also the most accurate. ClustalW is historically
+the most widely used. Muscle is faster than ClustalW and probably the most
+accurate for smaller alignments and MAFFT is probably the best for large
+alignments, however Clustal Omega, which was released in 2011, is arguably the
+fastest and most accurate tool for protein multiple alignment.
+
+
+To run an alignment web service, select the appropriate method from the {\sl
+Web Service $\Rightarrow$ Alignment $\Rightarrow$ \ldots} submenu (Figure
+\ref{webservices}). For each service you may either perform an alignment with
+default settings, use one of the available presets, or customise the parameters
+with the `{\sl Edit and Run ..}' dialog box. Once the job is submitted, a
+progress window will appear giving information about the job and any errors that
+occur. After successful completion of the job, a new window is opened with the
+results, in this case an alignment. By default, the new alignment will be
+ordered in the same way as the input sequences; however, many alignment programs
+re-order the input to place homologous sequences close together. This ordering
+can be recovered using the `Original ordering' entry within the {\sl Calculate
+$\Rightarrow$ Sort } sub menu.