- <li><a href="clustalw.html">ClustalW Multiple Alignment and
- re-alignment</a><br>
- The clustal W service remains one of the more popular Jalview
- features.</li>
- <li><a href="muscle.html">Muscle Multiple Alignment</a><br>
- High Quality and High Throughput multiple alignments of proteins. This
- method can sometimes be more accurate than ClustalW when dealing with
- diverse sets of sequences.</li>
- <li><a href="mafft.html">MAFFT</a><br>
- Multiple Alignment with Fast Fourier Transforms - a highly accurate
- and high throughput dna and amino acid alignment method, performing at
- least as well as ClustalW and Muscle.</li>
+ <li>The <a href="../features/seqfetch.html">Sequence Fetcher</a>
+ utilises web services for sequence, alignment and structure retrieval
+ provided by the European Bioinformatics Institute (EBI) and
+ Distributed Annotation System servers that are capable of serving
+ sequences.</li>
+ <li>The <a href="../features/dasfeatures.html">DAS Feature
+ Fetcher</a> enables the retrieval and visualization of features from DAS
+ annotation sources</li>
+ <li>The <a href="dbreffetcher.html">Database Reference
+ Fetcher</a> transfers database references from records available from
+ DAS or the public sequence databases.</li>
+ <li>The <strong>Web Services</strong> menu in each alignment
+ window also provides access to the following:
+ <ul>
+ <li>Programs for <a href="msaclient.html">multiple sequence
+ alignment</a>, made available <em>via</em> <a href="JABAWS.html">Java
+ Bioinformatic Analysis Web Service (JABAWS)</a> servers.</li>
+ <li>Jalview SOAP Web Services for <a href="jnet.html">secondary
+ structure prediction</a> based at the University of Dundee.</li>
+ <li>Services for alignment analysis, such as <a
+ href="shmr.html">Multi-Harmony</a>.
+ <li>Services for submitting IDs and sequences to external
+ bioinformatics services such as Envision2 (see <a href="#envision2">below</a>).</li>
+ </ul>
+ <p>
+ <strong>Web Service Dialog Box</strong>
+ </p> <img src="clwqueued.gif">
+ <p>This dialog box is displayed when a web service job is
+ submitted. It gives the name of the service and any method citation
+ information, and monitors the progress of the calculation. The
+ cancel button will permanently cancel the job, but this is only
+ possible for some services.</p> The <a href="webServicesPrefs.html">Web
+ Services Preference panel</a> controls the display and appearance of the
+ submission and analysis services in the <strong>Web Services</strong>
+ menu.</li>
+ <li>If Jalview encounters problems accessing any services, it may
+ display a <a href="webServicesPrefs.html#wswarnings">warning
+ dialog box</a> (this can be turned off using the web services
+ preferences tab).</li>