website/version2/examples/examples4.html

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   5 <TITLE>JalView - Java alignment editor</TITLE>\r
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  26               <td width="45%"><div align="center"><a href="http://www.compbio.dundee.ac.uk/~andrew/JalviewWebsite/index.html"><img src="../../snap22med.gif" width="291" height="116" border="0"  align="absmiddle"></a></div></td>\r
  27               <td width="55%"><div align="center"><font size="+6"><strong><font face="Geneva, Arial, Helvetica, sans-serif">Jalview \r
  28                   </font></strong></font> </div>\r
  29                 <div align="center"><font size="3" face="Geneva, Arial, Helvetica, sans-serif">a \r
  30                   multiple alignment editor</font> </div></td>\r
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  39       <td width="197" valign="top" nowrap> <p><strong>Downloads</strong></p>\r
  40         <ul>\r
  41           <li><a href="../index.html">Jalview</a></li>\r
  42         </ul>\r
  43         <strong>Examples</strong> <ul>\r
  44           <li><a href="applets.html">Applet</a></li>\r
  45           <li><a href="examples.html">Application</a></li>\r
  46         </ul>\r
  47         <strong>Reference</strong> <ul>\r
  48           <li> <a href="../../jalview.pdf" target="_blank">&quot;The Jalview Java<br>\r
  49             Alignment Editor,&quot;<br>\r
  50             </a></li>\r
  51           <a href="../../jalview.pdf"><em>Bioinformatics</em>, 12, 426-7</a> \r
  52         </ul>\r
  53         <strong>Source Code</strong> <ul>\r
  54           <li>Jalview 2</li>\r
  55         </ul>\r
  56         <p><strong>Feedback</strong></p>\r
  57         <p>&nbsp;&nbsp;&nbsp;<img src="../../help.gif" width="151" height="43"> </p>\r
  58         <p><br>\r
  59           <a href="http://www.bbsrc.ac.uk/"> <img border="0"src="../../bbsrc.jpg"></a> \r
  60         </p></td>\r
  61       <td width="499" valign="top"><!-- InstanceBeginEditable name="Contents" --> \r
  62         Many new features have been added to the Jalview interface, \r
  63           such as the Overview window which aids navigation around the whole alignment.\r
  64         <p align="center"><img src="overview.gif" width="544" height="185"></p>\r
  65         <p align="center"><br>\r
  66           Search using regular expressions.</p>\r
  67         <p align="center"><img src="search.gif" width="429" height="223"></p>\r
  68         The functionality of the original Jalview has been maintained \r
  69           and enhanced in the new interface. Below is an example of an average \r
  70           distance tree, calculated from the input alignment, being used to cluster \r
  71           sequences in the main alignment window.<br>\r
  72           The user has then applied &quot;Conservation Colouring&quot; to the \r
  73           alignment, the result of which shows conservation within the clustered \r
  74           sequences. <img src="tree.gif" width="696" height="360">\r
  75         <p align="center"><font size="3"><strong><a href="examples3.html">&lt; \r
  76           Back</a></strong></font>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<strong><a href="examples5.html"><font size="3">&nbsp;Next \r
  77           &gt;</font></a></strong></p>\r
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