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moved to new repository
authoramwaterhouse <Andrew Waterhouse>
Thu, 16 Jun 2005 15:54:10 +0000 (15:54 +0000)
committeramwaterhouse <Andrew Waterhouse>
Thu, 16 Jun 2005 15:54:10 +0000 (15:54 +0000)
42 files changed:
website/Templates/jtemplate.dwt [deleted file] patch | blob | history
website/version2/examples/applets.html [deleted file] patch | blob | history
website/version2/examples/exampleFile.jar [deleted file] patch | blob | history
website/version2/examples/examples.html [deleted file] patch | blob | history
website/version2/examples/examples2.html [deleted file] patch | blob | history
website/version2/examples/examples3.html [deleted file] patch | blob | history
website/version2/examples/examples4.html [deleted file] patch | blob | history
website/version2/examples/examples5.html [deleted file] patch | blob | history
website/version2/examples/globins.jar [deleted file] patch | blob | history
website/version2/examples/glut.msf [deleted file] patch | blob | history
website/version2/examples/glut.newick [deleted file] patch | blob | history
website/version2/examples/jalviewlite.jar [deleted file] patch | blob | history
website/version2/examples/jpred.jpg [deleted file] patch | blob | history
website/version2/examples/jpredQ.jpg [deleted file] patch | blob | history
website/version2/examples/lipase.msf [deleted file] patch | blob | history
website/version2/examples/muscle.jpg [deleted file] patch | blob | history
website/version2/examples/overview.gif [deleted file] patch | blob | history
website/version2/examples/pca.gif [deleted file] patch | blob | history
website/version2/examples/pdb.gif [deleted file] patch | blob | history
website/version2/examples/search.gif [deleted file] patch | blob | history
website/version2/examples/serprot.msf [deleted file] patch | blob | history
website/version2/examples/tree.gif [deleted file] patch | blob | history
website/version2/examples/uniprot.gif [deleted file] patch | blob | history
website/version2/examples/wrap.gif [deleted file] patch | blob | history
website/version2/index.html [deleted file] patch | blob | history
website/version2/webstart/JalviewX.jar [deleted file] patch | blob | history
website/version2/webstart/JalviewX.jnlp [deleted file] patch | blob | history
website/version2/webstart/activation.jar [deleted file] patch | blob | history
website/version2/webstart/axis.jar [deleted file] patch | blob | history
website/version2/webstart/castor.zip [deleted file] patch | blob | history
website/version2/webstart/commons-discovery.jar [deleted file] patch | blob | history
website/version2/webstart/commons-logging.jar [deleted file] patch | blob | history
website/version2/webstart/jaxrpc.jar [deleted file] patch | blob | history
website/version2/webstart/jhall.jar [deleted file] patch | blob | history
website/version2/webstart/log4j-1.2.8.jar [deleted file] patch | blob | history
website/version2/webstart/logo_big.gif [deleted file] patch | blob | history
website/version2/webstart/mail.jar [deleted file] patch | blob | history
website/version2/webstart/regex.jar [deleted file] patch | blob | history
website/version2/webstart/saaj.jar [deleted file] patch | blob | history
website/version2/webstart/wsdl4j.jar [deleted file] patch | blob | history
website/version2/webstart/xercesImpl.jar [deleted file] patch | blob | history
website/version2/webstart/xml-apis.jar [deleted file] patch | blob | history

diff --git a/website/Templates/jtemplate.dwt b/website/Templates/jtemplate.dwt
deleted file mode 100755 (executable)
index 69b84d6..0000000
--- a/website/Templates/jtemplate.dwt
+++ /dev/null
@@ -1,67 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">\r
-<html>\r
-<head>\r
-<!-- TemplateBeginEditable name="doctitle" --> \r
-<TITLE>JalView - Java alignment editor</TITLE>\r
-<!-- TemplateEndEditable --> \r
-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">\r
-<!-- TemplateBeginEditable name="head" --><!-- TemplateEndEditable --> \r
-<style type="text/css">\r
-<!--\r
-td {\r
-       font-family: Geneva, Arial, Helvetica, sans-serif;\r
-       font-size: 12px;\r
-}\r
--->\r
-</style>\r
-</head>\r
-\r
-<body>\r
-<div align="left">\r
-  <table border="0">\r
-    <tr> \r
-      <td width="700" ><center>\r
-          <table width="550" border="0">\r
-            <tr>\r
-              <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
-              <td width="55%"><div align="center"><font size="+6"><strong><font face="Geneva, Arial, Helvetica, sans-serif">Jalview \r
-                  </font></strong></font> </div>\r
-                <div align="center"><font size="3" face="Geneva, Arial, Helvetica, sans-serif">a \r
-                  multiple alignment editor</font> </div></td>\r
-            </tr>\r
-          </table>\r
-          </center></td>\r
-    </tr>\r
-  </table>\r
- <br>\r
-  <table border="0">\r
-    <tr> \r
-      <td width="197" valign="top" nowrap> <p><strong>Downloads</strong></p>\r
-        <ul>\r
-          <li><a href="../version2/index.html">Jalview</a></li>\r
-        </ul>\r
-        <strong>Examples</strong> <ul>\r
-          <li><a href="../version2/examples/applets.html">Applet</a></li>\r
-          <li><a href="../version2/examples/examples.html">Application</a></li>\r
-        </ul>\r
-        <strong>Reference</strong> <ul>\r
-          <li> <a href="../jalview.pdf" target="_blank">&quot;The Jalview Java<br>\r
-            Alignment Editor,&quot;<br>\r
-            </a></li>\r
-          <a href="../jalview.pdf"><em>Bioinformatics</em>, 12, 426-7</a> \r
-        </ul>\r
-        <strong>Source Code</strong> <ul>\r
-          <li>Jalview 2</li>\r
-        </ul>\r
-        <p><strong>Feedback</strong></p>\r
-        <p>&nbsp;&nbsp;&nbsp;<img src="../help.gif" width="151" height="43"> </p>\r
-        <p><br>\r
-          <a href="http://www.bbsrc.ac.uk/"> <img border="0"src="../bbsrc.jpg"></a> \r
-        </p></td>\r
-      <td width="499" valign="top"><!-- TemplateBeginEditable name="Contents" -->Contents<!-- TemplateEndEditable --> \r
-      </td>\r
-    </tr>\r
-  </table>\r
-</div>\r
-</body>\r
-</html>\r
diff --git a/website/version2/examples/applets.html b/website/version2/examples/applets.html
deleted file mode 100755 (executable)
index b811a99..0000000
--- a/website/version2/examples/applets.html
+++ /dev/null
@@ -1,145 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">\r
-<html><!-- InstanceBegin template="/Templates/jtemplate.dwt" codeOutsideHTMLIsLocked="false" -->\r
-<head>\r
-<!-- InstanceBeginEditable name="doctitle" -->\r
-<TITLE>JalView - Java alignment editor</TITLE>\r
-<!-- InstanceEndEditable --> \r
-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">\r
-<!-- InstanceBeginEditable name="head" --><!-- InstanceEndEditable --> \r
-<style type="text/css">\r
-<!--\r
-td {\r
-       font-family: Geneva, Arial, Helvetica, sans-serif;\r
-       font-size: 12px;\r
-}\r
--->\r
-</style>\r
-</head>\r
-\r
-<body>\r
-<div align="left">\r
-  <table border="0">\r
-    <tr> \r
-      <td width="700" ><center>\r
-          <table width="550" border="0">\r
-            <tr>\r
-              <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
-              <td width="55%"><div align="center"><font size="+6"><strong><font face="Geneva, Arial, Helvetica, sans-serif">Jalview \r
-                  </font></strong></font> </div>\r
-                <div align="center"><font size="3" face="Geneva, Arial, Helvetica, sans-serif">a \r
-                  multiple alignment editor</font> </div></td>\r
-            </tr>\r
-          </table>\r
-          </center></td>\r
-    </tr>\r
-  </table>\r
- <br>\r
-  <table border="0">\r
-    <tr> \r
-      <td width="197" valign="top" nowrap> <p><strong>Downloads</strong></p>\r
-        <ul>\r
-          <li><a href="../index.html">Jalview</a></li>\r
-        </ul>\r
-        <strong>Examples</strong> <ul>\r
-          <li><a href="applets.html">Applet</a></li>\r
-          <li><a href="examples.html">Application</a></li>\r
-        </ul>\r
-        <strong>Reference</strong> <ul>\r
-          <li> <a href="../../jalview.pdf" target="_blank">&quot;The Jalview Java<br>\r
-            Alignment Editor,&quot;<br>\r
-            </a></li>\r
-          <a href="../../jalview.pdf"><em>Bioinformatics</em>, 12, 426-7</a> \r
-        </ul>\r
-        <strong>Source Code</strong> <ul>\r
-          <li>Jalview 2</li>\r
-        </ul>\r
-        <p><strong>Feedback</strong></p>\r
-        <p>&nbsp;&nbsp;&nbsp;<img src="../../help.gif" width="151" height="43"> </p>\r
-        <p><br>\r
-          <a href="http://www.bbsrc.ac.uk/"> <img border="0"src="../../bbsrc.jpg"></a> \r
-        </p></td>\r
-      <td width="499" valign="top"><!-- InstanceBeginEditable name="Contents" -->\r
-        <p>Jalview2 comes in two distinct flavours.<br>\r
-          <br>\r
-          The main application allows connection to multiple web services provided\r
-          at the University of Dundee as well as a host of additional useful features\r
-          such as printing, making images from your alignment and annotating your\r
-          alignment. <br>\r
-          You need to download and install this software.</p>\r
-        <p> Pressing one of the buttons below will load up a cut down version\r
-          of Jalview2 multiple alignment editor, which runs within your web browser.</p>\r
-        <H4>Alignment 1 - Serine proteases (6 sequences x 279 residues)</H4>\r
-        <center>\r
-\r
-               <applet code="jalview.bin.JalviewLite"\r
-                               archive="jalviewlite.jar"\r
-                               width="200" height="40">\r
-          <param name="file" value="serprot.msf">\r
-        </applet>\r
-\r
-               </center>\r
-        <H4>Alignment 2 - Lipases (16 sequences x 487 residues)</H4>\r
-        <center>\r
-               <applet code="jalview.bin.JalviewLite"\r
-                               archive="jalviewlite.jar"\r
-                               width="200" height="40">\r
-          <param name="file" value="lipase.msf">\r
-                 <param name="defaultColour" value="Clustal">\r
-                 <param name="showFullId" value="false">\r
-        </applet></center>\r
-        <H4>Alignment 3 - Glutathione S-transferases (61 sequences x 290 residues) With associated tree</H4>\r
-               <center>\r
-          <applet code="jalview.bin.JalviewLite"\r
-                               archive="jalviewlite.jar"\r
-                               width="200" height="40">\r
-            <param name="file" value="glut.msf">\r
-                       <param name="defaultColour" value="Strand Propensity">\r
-                       <param name="showConsensus" value="false">\r
-                       <param name="showConservation" value="false">\r
-                       <param name="treeFile" value="glut.newick">\r
-          </applet>\r
-                 </center>\r
-        <p>The applet takes the following Parameters:</p>\r
-        <table width="325" border="1" align="center" >\r
-          <tr>\r
-            <td width="103"><strong>name</strong></td>\r
-            <td width="190"><strong>value</strong></td>\r
-          </tr>\r
-          <tr>\r
-            <td>file</td>\r
-            <td><em>fileName</em></td>\r
-          </tr>\r
-          <tr>\r
-            <td>showFullId</td>\r
-            <td>true false</td>\r
-          </tr>\r
-          <tr>\r
-            <td>showAnnotation</td>\r
-            <td>true false</td>\r
-          </tr>\r
-          <tr>\r
-            <td>showConservation</td>\r
-            <td>true false</td>\r
-          </tr>\r
-          <tr>\r
-            <td>showQuality</td>\r
-            <td>true false</td>\r
-          </tr>\r
-          <tr>\r
-            <td>showConsensus</td>\r
-            <td>true false</td>\r
-          </tr>\r
-          <tr>\r
-            <td>defaultColour</td>\r
-            <td>Clustal, Blosum62, % Identity, Zappo, Hydrophobic, Helix Propensity,\r
-              Strand Propensity, Turn Propensity, Buried Index, Nucleotide</td>\r
-          </tr>\r
-        </table>\r
-        <p align="center">&nbsp;</p>\r
-        <!-- InstanceEndEditable --> \r
-      </td>\r
-    </tr>\r
-  </table>\r
-</div>\r
-</body>\r
-<!-- InstanceEnd --></html>\r
diff --git a/website/version2/examples/exampleFile.jar b/website/version2/examples/exampleFile.jar
deleted file mode 100755 (executable)
index 334887b..0000000
Binary files a/website/version2/examples/exampleFile.jar and /dev/null differ
diff --git a/website/version2/examples/examples.html b/website/version2/examples/examples.html
deleted file mode 100755 (executable)
index 59194f5..0000000
--- a/website/version2/examples/examples.html
+++ /dev/null
@@ -1,83 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">\r
-<html><!-- InstanceBegin template="/Templates/jtemplate.dwt" codeOutsideHTMLIsLocked="false" -->\r
-<head>\r
-<!-- InstanceBeginEditable name="doctitle" -->\r
-<TITLE>JalView - Java alignment editor</TITLE>\r
-<!-- InstanceEndEditable --> \r
-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">\r
-<!-- InstanceBeginEditable name="head" --><!-- InstanceEndEditable --> \r
-<style type="text/css">\r
-<!--\r
-td {\r
-       font-family: Geneva, Arial, Helvetica, sans-serif;\r
-       font-size: 12px;\r
-}\r
--->\r
-</style>\r
-</head>\r
-\r
-<body>\r
-<div align="left">\r
-  <table border="0">\r
-    <tr> \r
-      <td width="700" ><center>\r
-          <table width="550" border="0">\r
-            <tr>\r
-              <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
-              <td width="55%"><div align="center"><font size="+6"><strong><font face="Geneva, Arial, Helvetica, sans-serif">Jalview \r
-                  </font></strong></font> </div>\r
-                <div align="center"><font size="3" face="Geneva, Arial, Helvetica, sans-serif">a \r
-                  multiple alignment editor</font> </div></td>\r
-            </tr>\r
-          </table>\r
-          </center></td>\r
-    </tr>\r
-  </table>\r
- <br>\r
-  <table border="0">\r
-    <tr> \r
-      <td width="197" valign="top" nowrap> <p><strong>Downloads</strong></p>\r
-        <ul>\r
-          <li><a href="../index.html">Jalview</a></li>\r
-        </ul>\r
-        <strong>Examples</strong> <ul>\r
-          <li><a href="applets.html">Applet</a></li>\r
-          <li><a href="examples.html">Application</a></li>\r
-        </ul>\r
-        <strong>Reference</strong> <ul>\r
-          <li> <a href="../../jalview.pdf" target="_blank">&quot;The Jalview Java<br>\r
-            Alignment Editor,&quot;<br>\r
-            </a></li>\r
-          <a href="../../jalview.pdf"><em>Bioinformatics</em>, 12, 426-7</a> \r
-        </ul>\r
-        <strong>Source Code</strong> <ul>\r
-          <li>Jalview 2</li>\r
-        </ul>\r
-        <p><strong>Feedback</strong></p>\r
-        <p>&nbsp;&nbsp;&nbsp;<img src="../../help.gif" width="151" height="43"> </p>\r
-        <p><br>\r
-          <a href="http://www.bbsrc.ac.uk/"> <img border="0"src="../../bbsrc.jpg"></a> \r
-        </p></td>\r
-      <td width="499" valign="top"><!-- InstanceBeginEditable name="Contents" --> \r
-        <p>Many alignment tools which require time consuming and/or large proccessing \r
-          power are currently being developed as Web Services within the Barton \r
-          Group, Dundee, and added to the Jalview interface.</p>\r
-        <p>&nbsp;</p>\r
-        <center><img src="jpredQ.jpg" width="519" height="252">\r
-        <table width="100" border="1" cellspacing="5" cellpadding="5">\r
-          <tr>\r
-            <td><img src="jpred.jpg" width="451" height="257"></td>\r
-          </tr>\r
-        </table>\r
-               </center>\r
-        <p align="center">&nbsp; </p>\r
-        <p align="center">&nbsp;</p>\r
-        <p align="center"><a href="examples2.html"><strong><font size="3">Next \r
-          &gt;</font></strong></a></p>\r
-        <!-- InstanceEndEditable --> \r
-      </td>\r
-    </tr>\r
-  </table>\r
-</div>\r
-</body>\r
-<!-- InstanceEnd --></html>\r
diff --git a/website/version2/examples/examples2.html b/website/version2/examples/examples2.html
deleted file mode 100755 (executable)
index f453b83..0000000
--- a/website/version2/examples/examples2.html
+++ /dev/null
@@ -1,78 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">\r
-<html><!-- InstanceBegin template="/Templates/jtemplate.dwt" codeOutsideHTMLIsLocked="false" -->\r
-<head>\r
-<!-- InstanceBeginEditable name="doctitle" -->\r
-<TITLE>JalView - Java alignment editor</TITLE>\r
-<!-- InstanceEndEditable --> \r
-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">\r
-<!-- InstanceBeginEditable name="head" --><!-- InstanceEndEditable --> \r
-<style type="text/css">\r
-<!--\r
-td {\r
-       font-family: Geneva, Arial, Helvetica, sans-serif;\r
-       font-size: 12px;\r
-}\r
--->\r
-</style>\r
-</head>\r
-\r
-<body>\r
-<div align="left">\r
-  <table border="0">\r
-    <tr> \r
-      <td width="700" ><center>\r
-          <table width="550" border="0">\r
-            <tr>\r
-              <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
-              <td width="55%"><div align="center"><font size="+6"><strong><font face="Geneva, Arial, Helvetica, sans-serif">Jalview \r
-                  </font></strong></font> </div>\r
-                <div align="center"><font size="3" face="Geneva, Arial, Helvetica, sans-serif">a \r
-                  multiple alignment editor</font> </div></td>\r
-            </tr>\r
-          </table>\r
-          </center></td>\r
-    </tr>\r
-  </table>\r
- <br>\r
-  <table border="0">\r
-    <tr> \r
-      <td width="197" valign="top" nowrap> <p><strong>Downloads</strong></p>\r
-        <ul>\r
-          <li><a href="../index.html">Jalview</a></li>\r
-        </ul>\r
-        <strong>Examples</strong> <ul>\r
-          <li><a href="applets.html">Applet</a></li>\r
-          <li><a href="examples.html">Application</a></li>\r
-        </ul>\r
-        <strong>Reference</strong> <ul>\r
-          <li> <a href="../../jalview.pdf" target="_blank">&quot;The Jalview Java<br>\r
-            Alignment Editor,&quot;<br>\r
-            </a></li>\r
-          <a href="../../jalview.pdf"><em>Bioinformatics</em>, 12, 426-7</a> \r
-        </ul>\r
-        <strong>Source Code</strong> <ul>\r
-          <li>Jalview 2</li>\r
-        </ul>\r
-        <p><strong>Feedback</strong></p>\r
-        <p>&nbsp;&nbsp;&nbsp;<img src="../../help.gif" width="151" height="43"> </p>\r
-        <p><br>\r
-          <a href="http://www.bbsrc.ac.uk/"> <img border="0"src="../../bbsrc.jpg"></a> \r
-        </p></td>\r
-      <td width="499" valign="top"><!-- InstanceBeginEditable name="Contents" -->\r
-        <p>Several of the most popular sequence alignment algorithms and / or \r
-          programs have been implemented as web services which Jalview has access \r
-          to.</p>\r
-        <p>The figure below shows the web service status window indicating that \r
-          a Muscle Alignment job as run to completion. The window shows important \r
-          feedback regarding the alignement. </p>\r
-        <p><img src="muscle.jpg" width="518" height="377"> </p>\r
-        <p align="center">&nbsp;</p>\r
-        <p align="center"><strong><font size="3"><a href="examples.html">&lt; \r
-          Back</a>&nbsp;&nbsp;&nbsp;&nbsp;<a href="examples3.html">Next &gt;</a></font></strong></p>\r
-        <!-- InstanceEndEditable --> \r
-      </td>\r
-    </tr>\r
-  </table>\r
-</div>\r
-</body>\r
-<!-- InstanceEnd --></html>\r
diff --git a/website/version2/examples/examples3.html b/website/version2/examples/examples3.html
deleted file mode 100755 (executable)
index b64aac3..0000000
--- a/website/version2/examples/examples3.html
+++ /dev/null
@@ -1,78 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">\r
-<html><!-- InstanceBegin template="/Templates/jtemplate.dwt" codeOutsideHTMLIsLocked="false" -->\r
-<head>\r
-<!-- InstanceBeginEditable name="doctitle" -->\r
-<TITLE>JalView - Java alignment editor</TITLE>\r
-<!-- InstanceEndEditable --> \r
-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">\r
-<!-- InstanceBeginEditable name="head" --><!-- InstanceEndEditable --> \r
-<style type="text/css">\r
-<!--\r
-td {\r
-       font-family: Geneva, Arial, Helvetica, sans-serif;\r
-       font-size: 12px;\r
-}\r
--->\r
-</style>\r
-</head>\r
-\r
-<body>\r
-<div align="left">\r
-  <table border="0">\r
-    <tr> \r
-      <td width="700" ><center>\r
-          <table width="550" border="0">\r
-            <tr>\r
-              <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
-              <td width="55%"><div align="center"><font size="+6"><strong><font face="Geneva, Arial, Helvetica, sans-serif">Jalview \r
-                  </font></strong></font> </div>\r
-                <div align="center"><font size="3" face="Geneva, Arial, Helvetica, sans-serif">a \r
-                  multiple alignment editor</font> </div></td>\r
-            </tr>\r
-          </table>\r
-          </center></td>\r
-    </tr>\r
-  </table>\r
- <br>\r
-  <table border="0">\r
-    <tr> \r
-      <td width="197" valign="top" nowrap> <p><strong>Downloads</strong></p>\r
-        <ul>\r
-          <li><a href="../index.html">Jalview</a></li>\r
-        </ul>\r
-        <strong>Examples</strong> <ul>\r
-          <li><a href="applets.html">Applet</a></li>\r
-          <li><a href="examples.html">Application</a></li>\r
-        </ul>\r
-        <strong>Reference</strong> <ul>\r
-          <li> <a href="../../jalview.pdf" target="_blank">&quot;The Jalview Java<br>\r
-            Alignment Editor,&quot;<br>\r
-            </a></li>\r
-          <a href="../../jalview.pdf"><em>Bioinformatics</em>, 12, 426-7</a> \r
-        </ul>\r
-        <strong>Source Code</strong> <ul>\r
-          <li>Jalview 2</li>\r
-        </ul>\r
-        <p><strong>Feedback</strong></p>\r
-        <p>&nbsp;&nbsp;&nbsp;<img src="../../help.gif" width="151" height="43"> </p>\r
-        <p><br>\r
-          <a href="http://www.bbsrc.ac.uk/"> <img border="0"src="../../bbsrc.jpg"></a> \r
-        </p></td>\r
-      <td width="499" valign="top"><!-- InstanceBeginEditable name="Contents" --> \r
-        <p align="center">Jalview will search Uniprot to find the exact protein \r
-          sequence match from any input alignment file. This can be used to display \r
-          sequence features, moving the mouse over the displayed feature will \r
-          reveal more information. </p>\r
-        <p align="center"><img src="uniprot.gif" width="516" height="252"></p>\r
-        <p align="center"><br>\r
-          Jalview allows the alignment to be &quot;wrapped&quot;</p>\r
-        <p align="center"><img src="wrap.gif" width="494" height="386"></p>\r
-        <p align="center"><strong><font size="3"><a href="examples2.html">&lt; \r
-          Back</a>&nbsp;&nbsp;&nbsp;&nbsp;<a href="examples4.html">Next &gt;</a></font></strong></p>\r
-        <!-- InstanceEndEditable --> \r
-      </td>\r
-    </tr>\r
-  </table>\r
-</div>\r
-</body>\r
-<!-- InstanceEnd --></html>\r
diff --git a/website/version2/examples/examples4.html b/website/version2/examples/examples4.html
deleted file mode 100755 (executable)
index 043bb8a..0000000
--- a/website/version2/examples/examples4.html
+++ /dev/null
@@ -1,84 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">\r
-<html><!-- InstanceBegin template="/Templates/jtemplate.dwt" codeOutsideHTMLIsLocked="false" -->\r
-<head>\r
-<!-- InstanceBeginEditable name="doctitle" -->\r
-<TITLE>JalView - Java alignment editor</TITLE>\r
-<!-- InstanceEndEditable --> \r
-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">\r
-<!-- InstanceBeginEditable name="head" --><!-- InstanceEndEditable --> \r
-<style type="text/css">\r
-<!--\r
-td {\r
-       font-family: Geneva, Arial, Helvetica, sans-serif;\r
-       font-size: 12px;\r
-}\r
--->\r
-</style>\r
-</head>\r
-\r
-<body>\r
-<div align="left">\r
-  <table border="0">\r
-    <tr> \r
-      <td width="700" ><center>\r
-          <table width="550" border="0">\r
-            <tr>\r
-              <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
-              <td width="55%"><div align="center"><font size="+6"><strong><font face="Geneva, Arial, Helvetica, sans-serif">Jalview \r
-                  </font></strong></font> </div>\r
-                <div align="center"><font size="3" face="Geneva, Arial, Helvetica, sans-serif">a \r
-                  multiple alignment editor</font> </div></td>\r
-            </tr>\r
-          </table>\r
-          </center></td>\r
-    </tr>\r
-  </table>\r
- <br>\r
-  <table border="0">\r
-    <tr> \r
-      <td width="197" valign="top" nowrap> <p><strong>Downloads</strong></p>\r
-        <ul>\r
-          <li><a href="../index.html">Jalview</a></li>\r
-        </ul>\r
-        <strong>Examples</strong> <ul>\r
-          <li><a href="applets.html">Applet</a></li>\r
-          <li><a href="examples.html">Application</a></li>\r
-        </ul>\r
-        <strong>Reference</strong> <ul>\r
-          <li> <a href="../../jalview.pdf" target="_blank">&quot;The Jalview Java<br>\r
-            Alignment Editor,&quot;<br>\r
-            </a></li>\r
-          <a href="../../jalview.pdf"><em>Bioinformatics</em>, 12, 426-7</a> \r
-        </ul>\r
-        <strong>Source Code</strong> <ul>\r
-          <li>Jalview 2</li>\r
-        </ul>\r
-        <p><strong>Feedback</strong></p>\r
-        <p>&nbsp;&nbsp;&nbsp;<img src="../../help.gif" width="151" height="43"> </p>\r
-        <p><br>\r
-          <a href="http://www.bbsrc.ac.uk/"> <img border="0"src="../../bbsrc.jpg"></a> \r
-        </p></td>\r
-      <td width="499" valign="top"><!-- InstanceBeginEditable name="Contents" --> \r
-        Many new features have been added to the Jalview interface, \r
-          such as the Overview window which aids navigation around the whole alignment.\r
-        <p align="center"><img src="overview.gif" width="544" height="185"></p>\r
-        <p align="center"><br>\r
-          Search using regular expressions.</p>\r
-        <p align="center"><img src="search.gif" width="429" height="223"></p>\r
-        The functionality of the original Jalview has been maintained \r
-          and enhanced in the new interface. Below is an example of an average \r
-          distance tree, calculated from the input alignment, being used to cluster \r
-          sequences in the main alignment window.<br>\r
-          The user has then applied &quot;Conservation Colouring&quot; to the \r
-          alignment, the result of which shows conservation within the clustered \r
-          sequences. <img src="tree.gif" width="696" height="360">\r
-        <p align="center"><font size="3"><strong><a href="examples3.html">&lt; \r
-          Back</a></strong></font>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<strong><a href="examples5.html"><font size="3">&nbsp;Next \r
-          &gt;</font></a></strong></p>\r
-        <!-- InstanceEndEditable --> \r
-      </td>\r
-    </tr>\r
-  </table>\r
-</div>\r
-</body>\r
-<!-- InstanceEnd --></html>\r
diff --git a/website/version2/examples/examples5.html b/website/version2/examples/examples5.html
deleted file mode 100755 (executable)
index acc8a35..0000000
--- a/website/version2/examples/examples5.html
+++ /dev/null
@@ -1,78 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">\r
-<html><!-- InstanceBegin template="/Templates/jtemplate.dwt" codeOutsideHTMLIsLocked="false" -->\r
-<head>\r
-<!-- InstanceBeginEditable name="doctitle" --> \r
-<TITLE>JalView - Java alignment editor</TITLE>\r
-<!-- InstanceEndEditable --> \r
-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">\r
-<!-- InstanceBeginEditable name="head" --><!-- InstanceEndEditable --> \r
-<style type="text/css">\r
-<!--\r
-td {\r
-       font-family: Geneva, Arial, Helvetica, sans-serif;\r
-       font-size: 12px;\r
-}\r
--->\r
-</style>\r
-</head>\r
-\r
-<body>\r
-<div align="left">\r
-  <table border="0">\r
-    <tr> \r
-      <td width="700" ><center>\r
-          <table width="550" border="0">\r
-            <tr>\r
-              <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
-              <td width="55%"><div align="center"><font size="+6"><strong><font face="Geneva, Arial, Helvetica, sans-serif">Jalview \r
-                  </font></strong></font> </div>\r
-                <div align="center"><font size="3" face="Geneva, Arial, Helvetica, sans-serif">a \r
-                  multiple alignment editor</font> </div></td>\r
-            </tr>\r
-          </table>\r
-          </center></td>\r
-    </tr>\r
-  </table>\r
- <br>\r
-  <table border="0">\r
-    <tr> \r
-      <td width="197" valign="top" nowrap> <p><strong>Downloads</strong></p>\r
-        <ul>\r
-          <li><a href="../index.html">Jalview</a></li>\r
-        </ul>\r
-        <strong>Examples</strong> <ul>\r
-          <li><a href="applets.html">Applet</a></li>\r
-          <li><a href="examples.html">Application</a></li>\r
-        </ul>\r
-        <strong>Reference</strong> <ul>\r
-          <li> <a href="../../jalview.pdf" target="_blank">&quot;The Jalview Java<br>\r
-            Alignment Editor,&quot;<br>\r
-            </a></li>\r
-          <a href="../../jalview.pdf"><em>Bioinformatics</em>, 12, 426-7</a> \r
-        </ul>\r
-        <strong>Source Code</strong> <ul>\r
-          <li>Jalview 2</li>\r
-        </ul>\r
-        <p><strong>Feedback</strong></p>\r
-        <p>&nbsp;&nbsp;&nbsp;<img src="../../help.gif" width="151" height="43"> </p>\r
-        <p><br>\r
-          <a href="http://www.bbsrc.ac.uk/"> <img border="0"src="../../bbsrc.jpg"></a> \r
-        </p></td>\r
-      <td width="499" valign="top"><!-- InstanceBeginEditable name="Contents" --> \r
-        <p align="center">Jalview maintains the ability to perform Principal Component \r
-          Analysis on an alignment. The method is used to cluster similar sequences, \r
-          the user may then select sequences from this 3D visual display.</p>\r
-        <p align="center"><img src="pca.gif" width="394" height="396"></p>\r
-        <p align="center"><br>\r
-          PDB structures may be displayed if Jalview can find a match of the input \r
-          sequence and Uniprot. </p>\r
-        <p align="center"><img src="pdb.gif" width="395" height="397"></p>\r
-        <p align="center"><strong><a href="examples4.html"><font size="3">&lt; \r
-          Back</font></a></strong></p>\r
-        <!-- InstanceEndEditable --> \r
-      </td>\r
-    </tr>\r
-  </table>\r
-</div>\r
-</body>\r
-<!-- InstanceEnd --></html>\r
diff --git a/website/version2/examples/globins.jar b/website/version2/examples/globins.jar
deleted file mode 100755 (executable)
index a0d70eb..0000000
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diff --git a/website/version2/examples/glut.msf b/website/version2/examples/glut.msf
deleted file mode 100755 (executable)
index 0c9c83c..0000000
--- a/website/version2/examples/glut.msf
+++ /dev/null
@@ -1,299 +0,0 @@
-PileUp\r
-\r
-\r
-\r
-   MSF:  439  Type: P    Check:  2277   .. \r
-\r
- Name: AJPMQA oo  Len:  439  Check:  4128  Weight:  1.00\r
- Name: AJFBQA oo  Len:  439  Check:  6903  Weight:  1.00\r
- Name: AJAAQ oo  Len:  439  Check:  4168  Weight:  1.00\r
- Name: AJFBQB oo  Len:  439  Check:  5921  Weight:  1.00\r
- Name: AJPMQ1 oo  Len:  439  Check:  4951  Weight:  1.00\r
- Name: AJFBQ oo  Len:  439  Check:  7754  Weight:  1.00\r
- Name: AJYLNB oo  Len:  439  Check:  1096  Weight:  1.00\r
- Name: AJRZQG oo  Len:  439  Check:  7565  Weight:  1.00\r
- Name: AJLCQB oo  Len:  439  Check:  5610  Weight:  1.00\r
- Name: AJRZQB oo  Len:  439  Check:  5547  Weight:  1.00\r
- Name: AJFBQD oo  Len:  439  Check:  2775  Weight:  1.00\r
- Name: AJPMQ2 oo  Len:  439  Check:  3516  Weight:  1.00\r
- Name: AJRZQD oo  Len:  439  Check:  1469  Weight:  1.00\r
- Name: AJBHQ oo  Len:  439  Check:  2409  Weight:  1.00\r
- Name: AJDHQ oo  Len:  439  Check:  5591  Weight:  1.00\r
- Name: AJMSQ oo  Len:  439  Check:  9358  Weight:  1.00\r
- Name: AJMSQ3 oo  Len:  439  Check:   166  Weight:  1.00\r
- Name: AJHYQ oo  Len:  439  Check:   415  Weight:  1.00\r
- Name: AJRTQ oo  Len:  439  Check:  9855  Weight:  1.00\r
- Name: AJHUQ oo  Len:  439  Check:  1969  Weight:  1.00\r
- Name: AJCHQ oo  Len:  439  Check:  7657  Weight:  1.00\r
- Name: AJFF2C oo  Len:  439  Check:  4626  Weight:  1.00\r
- Name: AJFF1M oo  Len:  439  Check:  6582  Weight:  1.00\r
- Name: AJSM2V oo  Len:  439  Check:  8742  Weight:  1.00\r
- Name: AJSM2H oo  Len:  439  Check:  4241  Weight:  1.00\r
- Name: AJKXQ oo  Len:  439  Check:  5092  Weight:  1.00\r
- Name: AJZJQ2 oo  Len:  439  Check:  4171  Weight:  1.00\r
-\r
-//\r
-\r
-\r
-\r
-AJPMQA          .......... .......... .......... .......... .......... \r
-AJFBQA          .......... .......... .......... .......... .......... \r
-AJAAQ           .......... .......... .......... .......... .......... \r
-AJFBQB          .......... .......... .......... .......... .......... \r
-AJPMQ1          .......... .......... .......... .......... .......... \r
-AJFBQ           .......... .......... .......... .......... .......... \r
-AJYLNB          .......... .......... .......... .......... .......... \r
-AJRZQG          .......... .......... .......... .......... .......... \r
-AJLCQB          .......... .......... .......... .......... .......... \r
-AJRZQB          .......... .......... .......... .......... .......... \r
-AJFBQD          ........MA QILAPSTQWQ MRFTKSSRHA SPITSNTWSS LLMKQNKK.T \r
-AJPMQ2          ........MA QILAPSTQWQ MRITKTSPCA TPITSKMWSS LVMKQTKKVA \r
-AJRZQD          ......MAQA VVPAMQCQVG AVR....ARP AAAAAAAGGR VWGVRRTGRG \r
-AJBHQ           ....MQVRRD DDGAGGCAGD AVPGGGEGQD GVPARQPAGR VWGVSRAARA \r
-AJDHQ           .......... .......... .......... .......... .......... \r
-AJMSQ           .......... .......... .......... .......... .......... \r
-AJMSQ3          .......... .......... .......... .......... .......... \r
-AJHYQ           .......... .......... .......... .......... .......... \r
-AJRTQ           .......... .......... .......... .......... .......... \r
-AJHUQ           .......... .......... .......... .......... .......... \r
-AJCHQ           .......... .......... .......... .......... .......... \r
-AJFF2C          .......... .......... .......... .......... .......... \r
-AJFF1M          .......... .......... ...MALRVAG LFLKKELVAP ATQQLRLLRT \r
-AJSM2V          .......... .......... .......... .......... .......... \r
-AJSM2H          .......... .......... .......... .......... .......... \r
-AJKXQ           .......... .......... .......... .......... .......... \r
-AJZJQ2          .......... .......... .......... .......... .......... \r
-\r
-\r
-AJPMQA          .......... ....MSSLSD LINFNLSDST EKIIAEYIWV GGS..GIDIR \r
-AJFBQA          .......... ....MSLLSD LINLNLSEST EKIIAEYIWV GGS..GMDLR \r
-AJAAQ           .......... ....MSLLSD LINLDLSETT EKIIAEYIWI GGS..GLDLR \r
-AJFBQB          .......... ....MSLLSD LINLNLSDTT EKVIAEYIWI GGS..GLDLR \r
-AJPMQ1          .......... .....MSLSD LINLDLSGTT EKIIAEYIWI GGS..GLDLR \r
-AJFBQ           .......... ....MSSISD LVNLNLSDST ERVIAEYIWV GGS..GMDMR \r
-AJYLNB          .......... ....MSLLSD LINLNLSDTT EKIIAEYIWV GGS..GVDLR \r
-AJRZQG          .......... ....MASLTD LVNLNLSDTT EKIIAEYIWI GGS..GMDLR \r
-AJLCQB          .......... ....MALLSD LVNLDLSSIN DKIIAEYIWI GGS..GMDLR \r
-AJRZQB          .......... ....MANLTD LVNLNLSDCS DKIIAEYIWV GGS..GIDLR \r
-AJFBQD          SSFRVLAVKS DGSTINRLEG LLNLDITPFT DKIIAEYIWI GGT..GIDVR \r
-AJPMQ2          HSFRVMAVNS ENGTINRVED LLNLDITPFT DSIIAEYIWI GGT..GIDVR \r
-AJRZQD          TSRVMAVSTE TTGVVTRMEQ LLNMDTTPFT DKIIAEYIWV GGT..GIDLR \r
-AJBHQ           TSKVLALGPE TTGVIQRMQQ LLDMDTTPFT DKIIAEYIWV GGS..GIDLR \r
-AJDHQ           .......... .......... .......... .......... .......... \r
-AJMSQ           ......MATS ASSHLNKGIK QMYMSLPQGE .KVQAMYIWV DGT..GEGLR \r
-AJMSQ3          ......MATS ASSHVNKGIK QMYMSLPQGE .KIQAMYIWV NGT..GEPLR \r
-AJHYQ           ......MATS ASSHLNKNIK QMYLCLPQGE .KVQAMYIWV DGT..GEGLR \r
-AJRTQ           ......MATS ASSHLNKGIK QMYMNLPQGE .KIQLMYIWV DGT..GEGLR \r
-AJHUQ           ......MTTS ASSHLNKGIK QVYMSLPQGE .KVQAMYIWI DGT..GEGLR \r
-AJCHQ           ......MATS ASSHLSKAIK HMYMKLPQGE .KVQAMYIWI DGT..GEHLR \r
-AJFF2C          ..SARILEDS PNARINKTIL DRYLSLPLQE NIVQATYVWI DGT..GEDLR \r
-AJFF1M          GNRSQFLANS PNTALDKSIL QRYRNLETPA NRVQATYLWI DGT..GENIR \r
-AJSM2V          .......... .......... .......... MTFKAEYIWI DGTEPTAKLR \r
-AJSM2H          .......... .......... .......... MSIKAEYIWI DGTQPTAKLR \r
-AJKXQ           .......... .......... .......... MSYQAEYIWI DGTEPEPLMR \r
-AJZJQ2          .......... .......... .........M TKYKLEYIWL DGYTPTPNLR \r
-\r
-\r
-AJPMQA          AR.TLPGPVS DPAKLPKWNY DGSSTNQAPG KDSEVILYPQ AIFKDPFR.N \r
-AJFBQA          AR.TLPGPVD DPAKLPKWNY DGSSTDQAPG DDSEVILYPQ AIFKDPFR.N \r
-AJAAQ           AR.TLPGPVT DPSQLPKWNY DGSSTGQAPG EDSEVIIYPQ AIFKDPFR.N \r
-AJFBQB          AR.TLPGPVK NPSELPKWNY DGSSTGQAPG QDSEVIIYPQ AIFKDPFR.N \r
-AJPMQ1          AR.TLPGPVT DPSELPKWNY DGSSTGQAPG QDSEVILYPQ AIFKDPFR.N \r
-AJFBQ           AR.TLSGPVK DPSKLPKWNY DGSSTGQAPG QDSEVILYPQ TIFRDPFR.N \r
-AJYLNB          AR.TLSGPVN DPSKLPKWNY DGSSTGQAPG KDSEVILWPQ AIFKDPFR.N \r
-AJRZQG          AR.TLSGPVT DPSKLPKWNY DGQAPGQAPG EDSEVILYPQ AIFKDPFR.N \r
-AJLCQB          AR.TISRPVS .DPSELPKWN YDGSSTGQAP GEDSEVIIYP QAIFKDPFKN \r
-AJRZQB          AR.TVKGPIT DVSQLPKWNY DGSSTGQAPG EDSEVILYPQ AIFKDPFR.D \r
-AJFBQD          SR.TISKPVE HPSELPKWNY DGSSTGQAPG EDSEVILYPQ AIFKDPFR.N \r
-AJPMQ2          SR.TISKPVS HPSEVPKWNY DGSSTGQAPG EDSEVILYPQ AIFKDPFR.N \r
-AJRZQD          SR.TISKPVE DPSELPKWNY DGSSTGQAPG EDSEVILYPQ AIFKDPFR.N \r
-AJBHQ           SR.TISKPVE DPSELPKWNY DGSSTGQAPG EDSEVILYPQ AIFKDPFR.N \r
-AJDHQ           .......... .......... .......... .......... .......... \r
-AJMSQ           TR.TLDCEPK CVEELPEWNF DGSSTFQSEG SNSDMYLHPV AMFRDPFR.P \r
-AJMSQ3          TCRTLDCEPK CVEELPEWNF DGSSTFQSEG SNSNMYLHPV AMFRDPFR.. \r
-AJHYQ           TR.TLDCEPK CVEELPEWNF DGSSTFQSEG SNSDMYLSPV AMFRDPFR.P \r
-AJRTQ           TR.TLDCDPK CVEELPEWNF DGSSTFQSEG SNSDMYLHPV AMFRDPFR.P \r
-AJHUQ           TR.TLDSEPK CVEELPEWNF DGSSTLQSEG SNSDMYLVPA AMFRDPFR.P \r
-AJCHQ           TR.TLDHEPK SLEDLPEWNF DGSSTFQAEG SNSDMYLRPA AMFRDPFR.P \r
-AJFF2C          DR.TLDFIPQ SPKELPVWNY DGSSCYQAEG SNSDTYLYPV AIYKDPFR.N \r
-AJFF1M          DR.VLDKVPS SVEDLPDWQY DGSSTYQAHG ENSDTTLKPR AIYRDPFKKN \r
-AJSM2V          TKIITGQPAG .LDALPIWGF DGSSTNQAEG HSSDCVLKPV FTCPDPIRGD \r
-AJSM2H          TKILSDGSR. ....LPRWGF DGSSTNQAEG HASDLVLEPV FSCPDPIRGD \r
-AJKXQ           TRIIKDGKE. ....PEIWGF DGSSTNQAPG SNSDCVLRPV FETPDPIRGD \r
-AJZJQ2          TQIKEFASFP TLEHVPLWGF DGSSTQQAEG HSSDCVLKPV AVFPDAARTN \r
-\r
-\r
-AJPMQA          NILVICDVYT PAGEP.LPTN KRYNAAKIFS HPDVAAEVPW YGIEQELLQK \r
-AJFBQA          NILVICDVYT PAGEP.LPTN KRYDAAKIFS HPDVVAEVPW YGIEQELLQK \r
-AJAAQ           NILVMCDAYT PAGEP.IPTN KRHAAAKIFS HPDVVAEVPW YGIEQELLQK \r
-AJFBQB          NILVICDAYT PAGEP.IPTN KRHNAAKIFS NPDVVAEEPW YGIEQELLQK \r
-AJPMQ1          HILVMCDAYS PAGEP.IPTN KRHAAAKVFS HPDVVAEETW YGIEQELLQK \r
-AJFBQ           NILVMCDAYT PAGEP.IPTN KRHNAAKIFS NPEVVAEEPW YGIEQELLQK \r
-AJYLNB          NILVICDTYT PSGKP.IPTN KRHAAAKIFS HPDVAAEEPW FGIEQELLQK \r
-AJRZQG          NILVMCDCYT PAGEP.IPTN KRHNAAKIFS SPEVASEEPW YGIEQELLQK \r
-AJLCQB          HILVMCDAYT PAGEP.IPTN KRAAAAKIFS NPEVEKEVTW YGIEQELLQK \r
-AJRZQB          NILVMCDCYT PQGEP.IPTN KRHSAAKIFS HPDVVAEVPW YGIEQELLQK \r
-AJFBQD          NILVICDAYT PAGEP.IPTN KRHRAAEVFS NPRVIAEVPW FGIEQELLQT \r
-AJPMQ2          NILVVCDAYT PAGEP.IPTN KRHRAAEIFS NPKVEAEIPW YGIEQELLQT \r
-AJRZQD          NILVMCDTYT PAGEP.IPTN KRNRAAQVFS DPKVVSQVPW FGIEQELLQR \r
-AJBHQ           NILVICDTYT PQGEP.IPTN KRHMAAQIFS DPKVTSQVQW FGIEQELMQR \r
-AJDHQ           .......... .......... .......... ....KAQEPW FGIEQELLNS \r
-AJMSQ           NKLVLCEVFK YNRKP.AETN LRH..ICKRI MDMVSNQHPW FGMEQELMGT \r
-AJMSQ3          NKLVLCEVFK YNRKP.AETN LRH..ICKRI MDMVSNQHPW FGMEQELMGT \r
-AJHYQ           NKLVFCEVFK YNRKP.AETN LRH..SCKRI MDMVSNQHPW FGMEQELMGT \r
-AJRTQ           NKLVFCEVFK YNRKP.AETN LRH..SCKRI MDMVSSQHPW FGMEQELMGT \r
-AJHUQ           NKLVLCEVFK YNRRP.AETN LRH..TCKRI MDMVSNQHPW FGMEQELMGT \r
-AJCHQ           NKLVLCEVFK YNRQS.ADTN LRH..TCRRI MDMVSNQHPW FGMEQELLGT \r
-AJFF2C          NILVMCDTYK FDGTP.TDTN KRK..TCLEV ANKCAAEEPW FGIEQESDFD \r
-AJFF1M          DVIVLCDTYS ADGKP.TASN KRA..AFQAA IDLISDQEPW FGIEQELLRR \r
-AJSM2V          DILVLCEVLN IDLTPH.ASN TRAALAEVAE RFAA..QEPI FGIEQEFFQD \r
-AJSM2H          HLLVLCEVLH TDLTPH.PSN TRALLRPVAE RFAG..QEPI FGIEQEFLKG \r
-AJKXQ           NRLVLCEVQL TDFTP..PTN TRAAALGVAE RYAD..MSPM FGIEQEFFKD \r
-AJZJQ2          GVLVMCEVMM PDGKTPHASN KRATILDDAG ........AW FGFEQEFYKD \r
-\r
-\r
-AJPMQA          DINWPLGWPI GG..YPGKQG PYYCGIGADK AY..GRDIVD AHYKAFAGIN \r
-AJFBQA          DVNWPLGWPL GG..YPGPQG PYYCGVGADK AY..GRDIVD AHYKAYAGIN \r
-AJAAQ           DINWPLGWPV GG..FPGPQG PYYCGAGADK AF..GRDIVD SHYKAYAGIN \r
-AJFBQB          EVNWPVGWPV GG..FPGPQG PYYCGVGADK AF..GRDIVD AHYKAYAGIN \r
-AJPMQ1          DINWPLGWPA GG..YPGPQG PYYCSVGADK AF..GRDVVE AHYKAFAGIN \r
-AJFBQ           DVQWPVGWPL GG..FPGPQG PYYCGIGANK AF..GRDIVD SHYKAYAGIN \r
-AJYLNB          DIHWPIGMAL GG..FPGPQG PYYCGTGAEK AF..GRDIVD SHYKAYAGIN \r
-AJRZQG          DINWPLGWPV GG..FPGPQG PYYCGIGADK SF..GRDIVD SHYKAYAGIN \r
-AJLCQB          DTNWPLGWPL GG..FPGPQG PYYCGIGADK AF..GRDIVH AHYKAYAGVN \r
-AJRZQB          DVNWPLGWPV GG..FPGPQG PYYCAAGAEK AF..GRDIVD AHYKAYAGIN \r
-AJFBQD          NVNWPLGWPV GG..YPGPQG PYYCSAGADK SF..GRDISD AHYKAFAGIN \r
-AJPMQ2          NVKWPLGWPV GG..YPGPQG PYYCAAGADK SF..GRDISD AHYKAYAGIN \r
-AJRZQD          DVNWPLGWPV GG..YPGPQG PYYCAVGSDK SF..GRDISD AHYKAYAGIN \r
-AJBHQ           DVNWPLGWPV GG..YPGPQG PYYCAVGSDK SF..GRDISD AHYKAYAGIE \r
-AJDHQ           VTKWPLGWPK GG..YPAGQG PYYCSVGAGR SI..GRDIPE VHYRCHAGIQ \r
-AJMSQ           DG.HPFGWPS NG..FPGPQG PYYCGVGADK AY..GRDIVE AHYRAYAGVK \r
-AJMSQ3          DG.HPFGWPF NG..FPGPQG PYYCGVGADK AY..GRDIVE AHYRAYAGVK \r
-AJHYQ           DG.HPFGWPS NG..FPGPQG PYYCGVGADK AY..GRDIVE AHYRAYAGVK \r
-AJRTQ           DG.HPFGWPS NG..FPGPQG PYYCGVGADK AY..GRDIVE AHYRAYAGIK \r
-AJHUQ           DG.HPFGWPS NG..FPGPQG PYYCGVGADR AY..GRDIVE AHYRAYAGVK \r
-AJCHQ           DG.HPFGWPS NC..FPGPQG PYYCGVGADK AY..GRDIVE AHYRAYAGVK \r
-AJFF2C          G....HHWAG QEW.FPDP.G PYYCGVGANK SS..PR.HKD AHYAPYAGTQ \r
-AJFF1M          GR.TSFGWPE NG..FPAPQG PYYCGVGADR VY..ARDLVE AHVVAYAGID \r
-AJSM2V          GY..PLGFPK GG..FPAPQG GYYCGVGADE IF..GRDVVE AHLDNKAGLA \r
-AJSM2H          DR..PLGFPE GGG.YPAPQA DYYCGVGADA IF..GREIVE KHLDLAAGLG \r
-AJKXQ           GR..PYGWPE VG..YPAPQG PYYCGVGGSK MP..GRQIVE RHTQADAGLA \r
-AJZJQ2          GR..PLGFPT SG..YPAPQG PYYTGVGFSN VGDVARKIVE EHLDLAAGIN \r
-\r
-\r
-AJPMQA          ISGINGEVMP GQWEFQVGPS VGISAGDEIW AARYILERIT EIAVVSFDPK \r
-AJFBQA          ISGINGEVMP GQWEFQVGPS VGISAGDEVW AARYILERIT ELAVVSFDPK \r
-AJAAQ           ISGINGEVMP GQWEFQVGPS VGISAGDEIW VARYILERIT EVAVLSFDPK \r
-AJFBQB          ISGINGEVMP GQWEFQVGPA VGISAGDELW VARYILERIT EVAVLSFDPK \r
-AJPMQ1          ISGINGEVMP GQWEFQVGPS VGISAGDEIW VARYILERIT EVAVLTFDPK \r
-AJFBQ           ISGINGEVMP GQWEFQVGPS VGISAADELW VARYILERIT EIAVLSFDPK \r
-AJYLNB          ISGINAEVMP GQWEFQVGPS IGISAGDELW VARYILERIT EIAVLSLDPK \r
-AJRZQG          ISGINGEVMP GQWEFQVGPS VGISAGDQVW VARYILERIT EIAVVSFDPK \r
-AJLCQB          ISGINGEVMP GQWEFQVGPS VGIAAADQIW VARYILERIT EIYVVSFDPK \r
-AJRZQB          ISGINGEVMP GQWEFQVGPS VGIAAADQVW VARYILERVT EVAVLSLDPK \r
-AJFBQD          ISGTNGEVMP GQWEYQVGPS VGIEAGDHIW ASRYILERIT EQAVLSLDPK \r
-AJPMQ2          ISGTNGEVMP GQWEYQVGPS VGIEAGDHIW ASRYILERIT EQAVLTLDPK \r
-AJRZQD          ISGTNGEVMP GQWEYQVGPS VGIEAGDHIW ISRYILERIT EQAVLTLDPK \r
-AJBHQ           ISGTNGEVMP GQWEYQVGPS VGIDAGDHIW ASRYILERIT EQAVLTLDPK \r
-AJDHQ           ISGVNGEVLP SQWEYQVGPV EGIAMGDQMW MSRYLMYRVA ELFEVTFDPK \r
-AJMSQ           ITGTNAEVMP AQWEFQIGPC EGIRMGDHLW IARFILHRVC EDFIATFDPK \r
-AJMSQ3          ITGTNAEVMP AQW....... .......... .......... .......... \r
-AJHYQ           ITGTNAEVMP AQWEFQIGPC EGIRMGDHLW VARFILHRVC EDFIATFDPK \r
-AJRTQ           ITGTNAEVMP AQWEFQIGPC EGIRMGDHLW VARFILHRVC EDFIATFDPK \r
-AJHUQ           IAGTNAEVMP AQWEFQIGPC EGISMGDHLW VARFILHRVC EDFIATFDPK \r
-AJCHQ           IGGTNAEVMP AQWEFQVGPC EGIEMGDHLW IARFILHRVC EDFIVSFDPK \r
-AJFF2C          GVPTNAEVMP AQWEFQVGPC EGISIGDDLW MARFLLHRIS EEFVSTLDPK \r
-AJFF1M          FAGTNAEVMP AQWEFQIGPA G.IKACDDLW VSRYILQRIA EEYVVTFDPK \r
-AJSM2V          ISGINAEVMP GQWEFQVGPV SPLEVSDHLW VARWLLYRTA EDFAATLDPK \r
-AJSM2H          LSGINAEVMP GQWEFQVGAL PPLEVSDHMW VARWLLHRVA EEFTASLDAK \r
-AJKXQ           IEGTNAEVMM GQWEFQIGVL PAPAIGDQIW LGRWLLHRIA EDYEVSFAAK \r
-AJZJQ2          HEGINAEVAK GQWEFQIFGK GSKKAADEMW MARYLMLRLT EKYDIEFHCK \r
-\r
-\r
-AJPMQA          PIPG.DWNGA GAHANFSTKS MRENGGYEVI KKAIEKLGLR HHIAAYGE.. \r
-AJFBQA          PIPG.DWNGA GAHSNYSTKS MREEGGYEVI KKAIEKLGLR HHIAAYGK.. \r
-AJAAQ           PIKG.DWNGA GAHTNYSTKS MREDGGYEVI LKAIEKLGKK HHIAAYGE.. \r
-AJFBQB          PIKG.DWNGA GAHTNYSTKT MRNDGGYEEI KSAIQKLGKR HHIAAYGE.. \r
-AJPMQ1          PIKG.DWNGA GAHTNYSTKS MREDGGYEII KKAIEKLGKR LHISAYGE.. \r
-AJFBQ           PIQG.DWNGA GAHTNYSTKS MRNDGGYEVI KKAITKLEKR HHIAAYGE.. \r
-AJYLNB          PIPG.DWNGA GAHTNYSTKS MRNDGGYEVI KQAIEKLEKR HHIAAYGE.. \r
-AJRZQG          PIPG.DWNGA GAHTNYSTKS MRNDGGYEII KSAIEKLKLR HHISAYGE.. \r
-AJLCQB          PIPG.DWNGA GAHTNYSTKT MREEGGYEVI KKAIEKLGLR HHIAAYGE.. \r
-AJRZQB          PIPG.DWNGA GAHTNFSTKS MREPGGYEVI KKAIDKLALR HHIAAYGE.. \r
-AJFBQD          PIEG.DWNGA GCHTNYSTKS MREDGGFEVI KKAILNLSLR HHISAYGE.. \r
-AJPMQ2          PIEG.DWNGA GCHTNYSTKS MREDGGFEVI KKAILNLSLR HHIEAYGE.. \r
-AJRZQD          PIQG.DWNGA GCHTNYSTKS MREDGGFEVI KKAILNLSLR HHISAYGE.. \r
-AJBHQ           PIQG.DWNGA GCHTNYSTLS MREDGGFDVI KKAILNLSLR HHIAAYGE.. \r
-AJDHQ           PIPG.DWNGS GGHVNFSNRQ PESPPAGKQS RSSAKKLGKR HHIAAYGE.. \r
-AJMSQ           PIPG.NWNVA GCHTNFSTKA MREENGLKCI EEAIDKLSKR HHIRAYDPKG \r
-AJMSQ3          .......... .......... .......... .......... .......... \r
-AJHYQ           PIPG.NWNGA GCHTNFSTKA MREENGLKHI EEAIEKLSKR HHIRAYDPKG \r
-AJRTQ           PIPG.NWNGA GCHTNFSTKA MREENGLRCI EEAIDKLSKR HHIRAYDPKG \r
-AJHUQ           PIPG.NWNGA GCHTNFSTKA MREENGLKYI EEAIEKLSKR HHIRAYDPKG \r
-AJCHQ           PIPG.NWNGA GCHTNFSTKN MREDGGLKHI EEAIEKLSKR HHIRAYDPKG \r
-AJFF2C          PMPG.DWNGA GAHTNVSTNA MREDGGIRDI EKAVAKLSKC HHIRAYDPKQ \r
-AJFF1M          PMEG.QWNGA GAHTNFSTKE MRADGGIKAI EEAIEKLSKR HHIKAYYPKE \r
-AJSM2V          PVKG.DWNGA GAHTNFSTKA MRESYDAIIT AAESLGEGSK PHVKNYGA.. \r
-AJSM2H          PAKG.DWNGA GAHTNFSTRA MREGYDPIIT ACEALGQDDK PHVRQYGT.. \r
-AJKXQ           PIPG.DWNGA GAHTNFSTKQ TMEGWDAIVT CCEALG..TR VHVTHYGK.. \r
-AJZJQ2          PLGDTDWNGS GMHANFSTEY MRTVGGKEYF EALMAAFDKN LHIAVYGP.. \r
-\r
-\r
-AJPMQA          ..GNERRLTG KHETADINVF SWGVANRGSS IRVGRDTEKG KGYFEDRRPA \r
-AJFBQA          ..GNERRLTG RHETADINTF SWGVANRGSS VRVGRDTEKG KGYFEDRRPA \r
-AJAAQ           ..GNERRLTG RHETADINTF LWGVANRGAS IRVGRDTEKG KGYFEDRRPS \r
-AJFBQB          ..GNERRLTG RHETADINTF LWGVANRGAS IRVGRDTEKG KGYFEDRRPA \r
-AJPMQ1          ..GNERRLTG KHETADINTF SWGVANRGAS VRVGRDTEKG KGYFEDRRPA \r
-AJFBQ           ..GNERRLTG KHETADMNTF IWGVANRGAS IRVGRDTEKG KGYFEDRRPA \r
-AJYLNB          ..GNERRLTG RHETADISTF SWGVANRGAS I......... .......... \r
-AJRZQG          ..GNERRLTG RHETADINTF SWGVANRGAS VRVGRETEQG KGYFEDRRPA \r
-AJLCQB          ..GNERRLTG RHETADINTF LWGVANRGAS IRVGRDTEKG KGYFEDRRPA \r
-AJRZQB          ..GNERRLTG RHETADINTF KWGVANRGAS IRVGRDTEKG KGYFEDRRPA \r
-AJFBQD          ..GNERRLTG KHETASINTF SWGVANRGCS IRVGRDTEKG KGYLEDRRPA \r
-AJPMQ2          ..GNERRLTG KHETASINDF SWGVANRGCS IRVGRDTEKG KGYLEDRRPA \r
-AJRZQD          ..GNERRLTG LHETASIDNF SWGVANRGCS IRVGRDTEAG KGYLEDRRPA \r
-AJBHQ           ..GNERRLTG LHETASISDF SWGVANRGCS IRVGRDTEAG KGYLEDRRPA \r
-AJDHQ           ..GNERRLTG KHETSSMNDF SWGVANRGCS IRVGRMVPVK CGYYEDRRPS \r
-AJMSQ           GLDNARALTG FHETSNINDF SAGVANRGAS IRIPRTVGQK KGYFEDRRLR \r
-AJMSQ3          .......... .......... .......... .......... .......... \r
-AJHYQ           GLDNARGLTG FHETSNINDF SAGVANRSAS IRIPRTVGQK KGYFEDRRPS \r
-AJRTQ           GLDNARRLTG FHETSNINDF SAGVANRSAS IRIPRIVGQK KGYFEDRRPS \r
-AJHUQ           GLDNARRLTG FHETSNINDF SAGVANRSAR LRIPRTVGQK KGYFEDRRPS \r
-AJCHQ           GLDNARRLTG FHETSSIHEF SAGVANRGAS IRIPRNVGHK KGYFEDRGPS \r
-AJFF2C          GQDNARRLTG KHETSSINDF SAGVANRGCS IRIPRGVNDG KGYFEDRCPS \r
-AJFF1M          GKDNERRLVG RLETSSIDKF SWGVANRAVS VRVPRGVATG KGYLEDRRPS \r
-AJSM2V          ..GIDDRLTG LHETAPWNEY SYGVSDRGAS VRIPWQVEKG KGYIEDRRPN \r
-AJSM2H          ..GIEDRLTG AHETAPWDAY SYGASDRGAS VRIPWQVEVK KGYIEDRRPN \r
-AJKXQ           ..GIEDRLTG KHETAPWNKY SWGASDRGAS VRIPWAVEKK KGWLEDRRPN \r
-AJZJQ2          ..DNDKRLTG KHETAPWNKF SYGVADRGAS IRVPHSFVNY KGYLEDRRPN \r
-\r
-\r
-AJPMQA          SNMDPYVVTS MIAETTILWK KP........ .........\r
-AJFBQA          SNMDPYVVTS MIAETTILWK P......... .........\r
-AJAAQ           SNMDPYVVTS MIADTTILWK P......... .........\r
-AJFBQB          SNMDPYVVTS MIADTTILWK P......... .........\r
-AJPMQ1          SNMDPYVVTS MIAETTILLK P......... .........\r
-AJFBQ           SNMDPYVVTS MIAETTLLWK P......... .........\r
-AJYLNB          .......... .......... .......... .........\r
-AJRZQG          SNMDPYIVTS MIAETTIIWK P......... .........\r
-AJLCQB          SNMDPYVVTS MIAETTILWD NKS....... .........\r
-AJRZQB          SNMDPYVVTG MIAETTLLWK QN........ .........\r
-AJFBQD          SNMDPYVVTS LLAESTLLWE PTLEAEALAA QKLALKV..\r
-AJPMQ2          SNMDPYVVTA LLAESTLLWE PTLEAEALAA QKIALKV..\r
-AJRZQD          SNMDPYVVTA LLAETTILWE PTLEAEVLAA KKLALKV..\r
-AJBHQ           SNMDPYTVTA LLAETTILWE PTLEAEALAA KKLALKV..\r
-AJDHQ           SNLDPYVVTR LLVETTLL.. .......... .........\r
-AJMSQ           ANCDPYAVTE AIVRTCLLNE TGDEPFQYKN .........\r
-AJMSQ3          .......... .......... .......... .........\r
-AJHYQ           ANCDPFAVTE AIVRTCLLNE TGDEPFQYKN .........\r
-AJRTQ           ANCDPYAVTE AIVRTCLLNE TGDEPFQYKN .........\r
-AJHUQ           ANCEPFSVTE ALIRTCLLNE TGDEPFQYKN .........\r
-AJCHQ           ANCDPYAVTE ALVRTCLLNE TGDEPFEYKN .........\r
-AJFF2C          SNCDPYSVVE AILRTICLDE .......... .........\r
-AJFF1M          SNCDPYAVCN AIVRTCLLNE .......... .........\r
-AJSM2V          ANVDPYVVTR LLVDTCCSAL EK.......A GQV......\r
-AJSM2H          ANVDPYVVTR LMVDTCCTEL AR.......R EQI......\r
-AJKXQ           ANMDPYLVTA LMIDTCCSAL AGDKPTLFVP SQTTPAPAS\r
-AJZJQ2          SQGDPYQIVR RS........ .......... .........\r
-\r
-\r
diff --git a/website/version2/examples/glut.newick b/website/version2/examples/glut.newick
deleted file mode 100755 (executable)
index d1f965b..0000000
--- a/website/version2/examples/glut.newick
+++ /dev/null
@@ -1 +0,0 @@
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r
diff --git a/website/version2/examples/jalviewlite.jar b/website/version2/examples/jalviewlite.jar
deleted file mode 100755 (executable)
index 99b506e..0000000
Binary files a/website/version2/examples/jalviewlite.jar and /dev/null differ
diff --git a/website/version2/examples/jpred.jpg b/website/version2/examples/jpred.jpg
deleted file mode 100755 (executable)
index 011c982..0000000
Binary files a/website/version2/examples/jpred.jpg and /dev/null differ
diff --git a/website/version2/examples/jpredQ.jpg b/website/version2/examples/jpredQ.jpg
deleted file mode 100755 (executable)
index 8e1a4b7..0000000
Binary files a/website/version2/examples/jpredQ.jpg and /dev/null differ
diff --git a/website/version2/examples/lipase.msf b/website/version2/examples/lipase.msf
deleted file mode 100755 (executable)
index f737753..0000000
--- a/website/version2/examples/lipase.msf
+++ /dev/null
@@ -1,207 +0,0 @@
-PileUp\r
-\r
-\r
-\r
-   MSF:  487  Type: P    Check:  4627   .. \r
-\r
- Name: LIP1_CANFA oo  Len:  487  Check:   678  Weight:  1.00\r
- Name: LIP2_MOUSE oo  Len:  487  Check:  2632  Weight:  1.00\r
- Name: LIPH_HUMAN oo  Len:  487  Check:  2807  Weight:  1.00\r
- Name: LIPH_MOUSE oo  Len:  487  Check:  1096  Weight:  1.00\r
- Name: LIPH_RAT oo  Len:  487  Check:  1917  Weight:  1.00\r
- Name: LIPL_BOVIN oo  Len:  487  Check:  3520  Weight:  1.00\r
- Name: LIPL_CAVPO oo  Len:  487  Check:  9282  Weight:  1.00\r
- Name: LIPL_CHICK oo  Len:  487  Check:  7040  Weight:  1.00\r
- Name: LIPL_HUMAN oo  Len:  487  Check:  3879  Weight:  1.00\r
- Name: LIPL_MOUSE oo  Len:  487  Check:  5123  Weight:  1.00\r
- Name: LIPL_RAT oo  Len:  487  Check:  3636  Weight:  1.00\r
- Name: LIPP_HORSE oo  Len:  487  Check:  3071  Weight:  1.00\r
- Name: LIPP_HUMAN oo  Len:  487  Check:   243  Weight:  1.00\r
- Name: LIPP_PIG oo  Len:  487  Check:  3267  Weight:  1.00\r
- Name: LIPP_RABIT oo  Len:  487  Check:  5962  Weight:  1.00\r
- Name: LIPP_RAT oo  Len:  487  Check:   474  Weight:  1.00\r
-\r
-//\r
-\r
-\r
-\r
-LIP1_CANFA      KEVCYEQIGC FSDAEPWAG. TAIRPLKVLP WSPERIGTRF LLYTNKNP.N \r
-LIP2_MOUSE      KEVCYGHLGC FSNDKPWAG. MIQRPSKIFP WSPEDIDTRF LLYTNENP.N \r
-LIPH_HUMAN      SSALGQSLKP EPFGRRAQA. ......VETN KTLHEMKTRF LLFGETN... \r
-LIPH_MOUSE      SSACGQGVGT EPFGRSLGA. ......TEAS KPLKKPETRF LLFQDEND.R \r
-LIPH_RAT        SSACGQGVGT EPFGRNLGA. ......TEER KPLQKPEIRF LLFKDESD.R \r
-LIPL_BOVIN      LDPAGPNFEY AEDRITGG.. .......... KDFRDIESKF ALRTPEDTAE \r
-LIPL_CAVPO      MNIDRKILNK ALAKEKVAN. ........CQ KDYTDIESKF ARRTPENTVE \r
-LIPL_CHICK      KTALLAVLCL CLRGAAGSD. ......PEAE MNFEGIESKF SLRTPAEPDE \r
-LIPL_HUMAN      LAVWLQSLTA SRGGVAAAD. ........QR RDFIDIESKF ALRTPEDTAE \r
-LIPL_MOUSE      LGVWLQSLTA FRGGVAAAD. ........AG RDFSDIESKF ALRTPEDTAE \r
-LIPL_RAT        LGVWLQSLTA FRGGVAAAD. ........GG RDFSDIESKF ALRTPEDTAE \r
-LIPP_HORSE      NEVCYERLGC FSDDSPWAG. IVERPLKILP WSPEKVNTRF LLYTNENP.D \r
-LIPP_HUMAN      KEVCYERLGC FSDDSPWSG. ITERPLHILP WSPKDVNTRF LLYTNENP.N \r
-LIPP_PIG        SEVCFPRLGC FSDDAPWAG. IVQRPLKILP PD.KDVDTRF LLYTNQNQ.N \r
-LIPP_RABIT      LEVCYERLGC FGNRIPWSGG TLERPFSTLP STPKIVNTRF LLYTNENP.N \r
-LIPP_RAT        KEVCFDKLGC FSDDAPWSG. TIDRPLKALP WSPAQINTRF LLYTNENQ.D \r
-\r
-\r
-LIP1_CANFA      NFQTLLPSDP STIEASNFQT DKKTRFIIHG FIDKGE.ENW LLDMCKNMFK \r
-LIP2_MOUSE      NYQIISATDP ATINASNFQL DRKTRFIIHG FIDKGE.EGW LLDMCKKMFQ \r
-LIPH_HUMAN      QGCQIRINHP DTLQECGFNS SLPLVMIIHG WSVDGVLENW IWQMVAALKS \r
-LIPH_MOUSE      LGCRLRPQHP ETLQECGFNS SQPLIMIIHG WSVDGLLENW IWKIVSALKS \r
-LIPH_RAT        LGCQLRPQHP ETLQECGFNS SHPLVMIIHG WSVDGLLETW IWKIVGALKS \r
-LIPL_BOVIN      DTCHLIPGVT ESVANCHFNH SSKTFVVIHG WTVTGMYESW VPKLVAALYK \r
-LIPL_CAVPO      DTCHLIPGVT ESVANCHFNH SSKTFMVIHG WTVTGMYESW VPKLVAALYK \r
-LIPL_CHICK      DVCYLVPGQM DSLAQCNFNH TSKTFVVIHG WTVTGMYESW VPKLVDALYK \r
-LIPL_HUMAN      DTCHLIPGVA ESVATCHFNH SSKTFMVIHG WTVTGMYESW VPKLVAALYK \r
-LIPL_MOUSE      DTCHLIPGLA DSVSNCHFNH SSKTFVVIHG WTVTGMYESW VPKLVAALYK \r
-LIPL_RAT        DTCHLIPGLA DSVSNCHFNH SSKTFVVIHG WTVTGMYESW VPKLVAALYK \r
-LIPP_HORSE      NFQEIV.ADP STIQSSNFNT GRKTRFIIHG FIDKGE.ESW LSTMCQNMFK \r
-LIPP_HUMAN      NFQEVA.ADS SSISGSNFKT NRKTRFIIHG FIDKGE.ENW LANVCKNLFK \r
-LIPP_PIG        NYQELV.ADP STITNSNFRM DRKTRFIIHG FIDKGE.EDW LSNICKNLFK \r
-LIPP_RABIT      NFQEIS.ADA STIRGSNFRT DRKTRFIIHG FTDKGE.ENW LSNLCENLFQ \r
-LIPP_RAT        NYQKIT.SDA SSIRNSNFKT NRKTRIIIHG FIDKGE.ENW LSDMCKNMFK \r
-\r
-\r
-LIP1_CANFA      V...EEVNCI CVDWKKGSQT SYTQAANNVR VVGAQVAQML SMLSANYSYS \r
-LIP2_MOUSE      V...EKVNCI CVDWKRGSRT EYTQASYNTR VLGAEIAFLV QVLSTEMGYS \r
-LIPH_HUMAN      QPAQP.VNVG LVDWITLAHD HYTIAVRNTR LVGKEVAALL RWLEESVQLS \r
-LIPH_MOUSE      RQSQP.VNVG LVDWISLAYQ HYTIAVQNTR IVGQDVAALL LWLEESAKFS \r
-LIPH_RAT        RQSQP.VNVG LVDWISLAYQ HYAIAVRNTR VVGQEVAALL LWLEESMKFS \r
-LIPL_BOVIN      R..EPDSNVI VVDWLSRAQQ HYPVSAGYTK LVGQDVAKFM NWMADEFNYP \r
-LIPL_CAVPO      R..EPDSNVI VVDWLRRAQH HYPESADYTK LVGEDVARFI NWMEDEFKYS \r
-LIPL_CHICK      R..EPDSNVI VVDWLVRAQQ HYPVSAAYTK LVGKDVAMFI DWMEEKFNYP \r
-LIPL_HUMAN      R..EPDSNVI VVDWLSRAQE HYPVSAGYTK LVGQDVARFI NWMEEEFNYP \r
-LIPL_MOUSE      R..EPDSNVI VVDWLYRAQQ HYPVSAGYTK LVGNDVARFI NWMEEEFNYP \r
-LIPL_RAT        R..EPDSNVI VVDWLYRAQQ HYPVSAGYTK LVGNDVARFI NWLEEEFNYP \r
-LIPP_HORSE      V...ESVNCI CVDWKSGSRT AYSQASQNVR IVGAEVAYLV GVLQSSFDYS \r
-LIPP_HUMAN      V...ESVNCI CVDWKGGSRT GYTQASQNIR IVGAEVAYFV EFLQSAFGYS \r
-LIPP_PIG        V...ESVNCI CVDWKGGSRT GYTQASQNIR IVGAEVAYFV EVLKSSLGYS \r
-LIPP_RABIT      V...ETVNCI CVDWKGGSRT TYPQATQNIR IVGAEVAYLV GTLQSSLGYS \r
-LIPP_RAT        V...ESVNCI CVDWKGGSRA TYTQATQNVR VVGAEVALLV NVLKSDLGHP \r
-\r
-\r
-LIP1_CANFA      PSQVQLIGHS LGAHVAGEAG SRTPG...LG RITGLDPVEA SFQGTPEEVR \r
-LIP2_MOUSE      PENVHLIPHS LGSHVAGEAG RRLEGH..VG RITGLDPAEP CFQGLPEEVR \r
-LIPH_HUMAN      RSHVHLIGYS LGAHVSGFAG SSIGGTHKIG RITGLDAAGP LFEGSAPSNR \r
-LIPH_MOUSE      RSKVHLIGYS LGAHVSGFAG SSMDGKNKIG RITGLDPAGP MFEGTSPNER \r
-LIPH_RAT        RSKVHLIGYS LGAHVSGFAG SSMGGKRKIG RITGLDPAGP MFEGTSPNER \r
-LIPL_BOVIN      LGNVHLLGYS LGAHAAGIAG SLTN..KKVN RITGLDPAGP NFEYAEAPSR \r
-LIPL_CAVPO      VDNVHLLGYS LGAHAAGVAG SRTN..TKVS RITGLDPAGP NFEYAEATSR \r
-LIPL_CHICK      LNNVHLLGYS LGAHAAGIAG SLTK..KKVN RITGLDPAGP TFEYADAPIR \r
-LIPL_HUMAN      LDNVHLLGYS LGAHAAGIAG SLTN..KKVN RITGLDPAGP NFEYAEAPSR \r
-LIPL_MOUSE      LDNVHLLGYS LGAHAAGVAG SLTN..KKVN RITGLDPAGP NFEYAEAPSR \r
-LIPL_RAT        LDNVHLLGYS LGAHAAGVAG SLTN..KKVN RITGLDPAGP NFEYAEAPSR \r
-LIPP_HORSE      PSNVHIIGHS LGSHAAGEAG RRTNGA..VG RITGLDPAEP CFQGTPELVR \r
-LIPP_HUMAN      PSNVHVIGHS LGAHAAGEAG RRTNGT..IG RITGLDPAEP CFQGTPELVR \r
-LIPP_PIG        PSNVHVIGHS LGSHAAGEAG RRTNGT..IE RITGLDPAEP CFQGTPELVR \r
-LIPP_RABIT      PSNIHVIGHS LGAHAAGEVG RRTNGT..IG RITGLDPAEP YFQGTPEIVR \r
-LIPP_RAT        PDNVHLIGHS LGSHVAGEAG KRTFGA..IG RITGLDAAEP YFQGTPEEVR \r
-\r
-\r
-LIP1_CANFA      LDPTDADFVD VIHTDAAPLI PFLGFGTSQQ MGHLDFFPNG GEEMPGCKKN \r
-LIP2_MOUSE      LDPSDAMFVD VIHTDSAPII PYLGFGMSQK VGHLDFFPNG GKEIPGCQKN \r
-LIPH_HUMAN      LSPDDANFVD AIHTFTR.EH MGLSVGIKQP IGHYDFYPNG GSFQPGCHFL \r
-LIPH_MOUSE      LSPDDANFVD AIHTFTR.EH MGLSVGIKQP IAHYDFYPNG GSFQPGCHFL \r
-LIPH_RAT        LSPDDANFVD AIHTFTR.EH MGLSVGIKQP IAHYDFYPNG GSFQPGCHFL \r
-LIPL_BOVIN      LSPDDADFVD VLHTFTR.GS PGRSIGIQKP VGHVDIYPNG GTFQPGCNIG \r
-LIPL_CAVPO      LSPDDAQFVD VLHTFTR.GS PGRSIGIQKP VGHVDIYPNG GSFQPGCNIQ \r
-LIPL_CHICK      LSPDDADFVD VLHTYTR.GS PDRSIGIQKP VGHIDIYPNG GGFQPGCNLG \r
-LIPL_HUMAN      LSPDDADFVD VLHTFTR.GS PGRSIGIQKP VGHVDIYPNG GTFQPGCNIG \r
-LIPL_MOUSE      LSPDDADFVD VLHTFTR.GS PGRSIGIQKP VGHVDIYPNG GTFQPGCNIG \r
-LIPL_RAT        LSPDDADFVD VLHTFTR.GS PGRSIGIQKP VGHVDIYPNG GTFQPGCNIG \r
-LIPP_HORSE      LDPSDAQFVD VIHTDIAPFI PNLGFGMSQT AGHLDFFPNG GKEMPGCQKN \r
-LIPP_HUMAN      LDPSDAKFVD VIHTDGAPIV PNLGFGMSQV VGHLDFFPNG GVEMPGCKKN \r
-LIPP_PIG        LDPSDAKFVD VIHTDAAPII PNLGFGMSQT VGHLDFFPNG GKQMPGCQKN \r
-LIPP_RABIT      LDPSDAQFVD VIHTDAAPMV PNLGFGMSQT VGHLDFFPNG GKEMPGCQKN \r
-LIPP_RAT        LDPTDAQFVD AIHTDAAPII PNLGFGMSQT VGHLDFFPNG GMEMPGCQKN \r
-\r
-\r
-LIP1_CANFA      ALSQIVDLDG IWEGTRDFVA CNHLRSYKYY SESILNPDG. FASYPCASYR \r
-LIP2_MOUSE      ILSTIVDING IWEGTRNFAA CNHLRSYKYY ASSILNPDG. FLGYPCSSYE \r
-LIPH_HUMAN      ELYRHIAQHG FNAITQ.TIK CSHERSVHLF IDSLLHAGTQ SMAYPCGDMN \r
-LIPH_MOUSE      ELYKHIAEHG LNAITQ.TIK CAHERSVHPF IDSLQHSDLQ SIGFQCSDMG \r
-LIPH_RAT        ELYKHIAEHG LNAITQ.TIN CAHERSVHLF IDSLQHSNLQ NTGFQCSNMD \r
-LIPL_BOVIN      EALRVIAERG LGDVDQ.LVK CSHERSVHLF IDSLLNEENP SKAYRCNSKE \r
-LIPL_CAVPO      DALRVISQKG FGDMDQ.LVK CSHERSIHLF IDSLLNEENP SKAYRCNSKE \r
-LIPL_CHICK      EALRLIAEKG FSDVDQ.LVK CSHERSIHLF IDSLLYEEKP SMAYRCNTKE \r
-LIPL_HUMAN      EAIRVIAERG LGDVDQ.LVK CSHERSIHLF IDSLLNEENP SKAYRCSSKE \r
-LIPL_MOUSE      EAIRVIAERG LGDVDQ.LVK CSHERSIHLF IDSLLNEENP SKAYRCNSKE \r
-LIPL_RAT        EAIRVIAEKG LGDVDQ.LVK CSHERSIHLF IDSLLNEENP SKAYRCNSKE \r
-LIPP_HORSE      VLSQIVDIDG IWQGTRDFAA CNHLRSYKYY TDSILNPDG. FAGFSCASYS \r
-LIPP_HUMAN      ILSQIVDIDG IWEGTRDFAA CNHLRSYKYY TDSIVNPDG. FAGFPCASYN \r
-LIPP_PIG        ILSQIVDIDG IWEGTRDFVA CNHLRSYKYY ADSILNPDG. FAGFPCDSYN \r
-LIPP_RABIT      VLSQIVDING VWEGTRDFVA CNHLRSYKYY ADSIVNPNG. FAGFSCASYT \r
-LIPP_RAT        ILSQIVDIDG IWEGTRDFAA CNHLRSYKYY TDSIVNPTG. FSGFSCSSYN \r
-\r
-\r
-LIP1_CANFA      AFESNKCFPC PDQGCPQMGH YADKFAVKTS DETQKYFLNT GDSSNFARWR \r
-LIP2_MOUSE      KFQHNDCFPS PEQGCPKMGH YADQFEGKTA TVEQTFFLNT ADTGNFTRWR \r
-LIPH_HUMAN      SFSQGLCLSC KKGRCNTLGY HVRQEPRSKS ...KRLFLVT RAQSPFKVYH \r
-LIPH_MOUSE      SFSQGLCLSC KKGRCNTLGY DIRKDRSGKS ...KRLFLIT RAQSPFKVYH \r
-LIPH_RAT        SFSQGLCLNC KKGRCNSLGY DIRRIGHVKS ...KTLFLIT RAQSPFKVYH \r
-LIPL_BOVIN      AFEKGLCLSC RKNRCNNMGY EINKVRAKRS ...SKMYLKT RSQMPYKVFH \r
-LIPL_CAVPO      AFEKGLCLSC RKNRCNNVGY EINKVRAKRS ...SKMYLKT RSQMPYKVFH \r
-LIPL_CHICK      AFEKGLCLSC RKNRCNNLGY KVNRVRTKRN ...TKMYLKT RAQMPYKVFH \r
-LIPL_HUMAN      AFEKGLCLSC RKNRCNNLGY EINKVRAKRS ...SKMYLKT RSQMPYKVFH \r
-LIPL_MOUSE      AFEKGLCLSC RKNRCNNLGY EINKVRAKRS ...SKMYLKT RSQMPYKVFH \r
-LIPL_RAT        AFEKGLCLSC RKNRCNNVGY EINKVRAKRS ...SKMYLKT RSQMPYKVFH \r
-LIPP_HORSE      DFTANKCFPC SSEGCPQMGH YADRFPGRTK GVGQLFYLNT GDASNFARWR \r
-LIPP_HUMAN      VFTANKCFPC PSGGCPQMGH YADRYPGKTN DVGQKFYLDT GDASNFARWR \r
-LIPP_PIG        VFTANKCFPC PSEGCPQMGH YADRFPGKTN GVSQVFYLNT GDASNFARWR \r
-LIPP_RABIT      AFSANKCFPC SN.GCPQMGH YADRFSRKTD GVGQTFYLNT GDSSNFARWR \r
-LIPP_RAT        VFSANKCFPC GSEGCPQMGH YADKYPGKTK ELYQKFYLNT GDKSNFARWR \r
-\r
-\r
-LIP1_CANFA      YGVSITLSG. ..KR.ATGQA KVALFGSKGN THQFNIFKGI .LKPGSTHSN \r
-LIP2_MOUSE      YKVSVTLSGP ..KK.LSGYI LVALYGCNAN SKQYEVFKGS .LQPEARYIR \r
-LIPH_HUMAN      YQLKIQFINQ TETP.IQTTF TMSLLGTKEK MQKIPITLGK GIASNKTYSF \r
-LIPH_MOUSE      YQFKIQFINQ IEKP.VEPTF TMSLLGTKEE IKRIPITLGE GITSNKTYSF \r
-LIPH_RAT        YQFKIQFINQ MEKP.MEPTF TMTLLGTKEE IKKIPITLGE GITSNKTYSL \r
-LIPL_BOVIN      YQVKIHFSGT ESNTYTNQAF EISLYGTVAE SENIPFTLPE .VSTNKTYSF \r
-LIPL_CAVPO      YQVKIYFSGT ETTTYTNQAF EISLYGTVAE SENIPFTLPE .VSANNTYSF \r
-LIPL_CHICK      YQVKIHFFGK TNVTKVDQPF LISLYGTLDE SENIPFTLPE .VSSNKTFSF \r
-LIPL_HUMAN      YQVKIHFSGT ESETHTNQAF EISLYGTVAE SENIPFTLPE .VSTNKTYSF \r
-LIPL_MOUSE      YQVKIHFSGT ENGKQHNQAF EISLYGTVAE SENIPFTLPE .VSTNKTYSF \r
-LIPL_RAT        YQVKIHFSGT ENDKQNNQAF EISLYGTVAE SENIPFTLPE .VATNKTYSF \r
-LIPP_HORSE      YRVDVTLSG. ..KK.VTGHV LVSLFGNKGN SRQYEIFQGT .LKPDNTYSN \r
-LIPP_HUMAN      YKVSVTLSG. ..KK.VTGHI LVSLFGNKGN SKQYEIFKGT .LKPDSTHSN \r
-LIPP_PIG        YKVSVTLSG. ..KK.VTGHI LVSLFGNEGN SRQYEIYKGT .LQPDNTHSD \r
-LIPP_RABIT      YQVAVTLSG. ..RR.VTGHV LVSLYGSKGN SKQYEIFTGL .LKPGDTHLN \r
-LIPP_RAT        YQVTVTLSG. ..QK.VTGHI LVSLFGNGGN SKQYEVFKGS .LHPGDTHVK \r
-\r
-\r
-LIP1_CANFA      EFDAKLDVGT IEKVKFLWNN N..VVNPTFP KVG....... ........AA \r
-LIP2_MOUSE      DIDVDVNVGE IQKVKFLWNN K..VINLFRP TMG....... ........AS \r
-LIPH_HUMAN      LITLDVDIGE LIMIKFKWEN S..AVWANVW DTVQTIIPWS TGPRHSGLVL \r
-LIPH_MOUSE      LITLDKDIGE LILLKFKWEN S..AVWANVW NTVQTIMLWG IEPHHSGLIL \r
-LIPH_RAT        LITLNKDIGE LIMLKFKWEN S..AVWANVW NTVQTIMLWD TEPHYAGLIV \r
-LIPL_BOVIN      LLYTEVDIGE LLMLKLKWIS DSYFSWSNWW SSP....... ......GFDI \r
-LIPL_CAVPO      LIYTEVDIGE LLMLKLKWIT ESYFSWSSWW GRP....... ......TFTI \r
-LIPL_CHICK      LIYTEVDIGD LLMLKLQWEK DTFFSWSDWW TPF....... ......AFTI \r
-LIPL_HUMAN      LIYTEVDIGE LLMLKLKWKS DSYFSWSDWW SSP....... ......GFAI \r
-LIPL_MOUSE      LIYTEVDIGE LLMMKLKWMS DSYFSWPDWW SSP....... ......SFVI \r
-LIPL_RAT        LIYTEVDIGE LLMMKLKWKN DSYFRWSDWW SSP....... ......SFVI \r
-LIPP_HORSE      EFDSDVEVGD LEKVKFIWYN N..VINLTLP KVG....... ........AS \r
-LIPP_HUMAN      EFDSDVDVGD LQMVKFIWYN N..VINPTLP RVG....... ........AS \r
-LIPP_PIG        EFDSDVEVGD LQKVKFIWYN NN.VINPTLP RVG....... ........AS \r
-LIPP_RABIT      EFDSDVDVGD VQKVKFVWYN N..VINPTLP KVG....... ........AS \r
-LIPP_RAT        EFDSDMDVGD LQKVKFIWYN N..VINPTLP KVG....... ........AS \r
-\r
-\r
-LIP1_CANFA      KITVQK.GEE KTVHSFCSES TVR....EDV LLTLTPC\r
-LIP2_MOUSE      QITLQR.AKD GKEFNFCTSN TVH....EDV LQSLYPC\r
-LIPH_HUMAN      KTIRVKAGET QQRMTFCSEN TDDLLLRPTQ EKIFVKC\r
-LIPH_MOUSE      KTIWVKAGET QQRMTFCPEN LDDLQLHPSQ EKVFVNC\r
-LIPH_RAT        KTIWVKAGET QQRMTFCPDN VDDLQLHPTQ EKVFVKC\r
-LIPL_BOVIN      GKIRVKAGET QKKVIFCSRE KMSYLQKGKS PVIFVKC\r
-LIPL_CAVPO      EKIRVKAGET QKKIVFCSRE KVSKLQKGKE APVFVKC\r
-LIPL_CHICK      QRVRVKSGET QKKVVFCSRD GSSRLGKGEE AAIFVKC\r
-LIPL_HUMAN      QKIRVKAGET QKKVIFCSRE KVSHLQKGKA PAVFVKC\r
-LIPL_MOUSE      ERIRVKAGET QKKVIFCARE KVSHLQKGKD SAVFVKC\r
-LIPL_RAT        EKIRVKAGET QKKVIFCARE KVSHLQKGKD AAVFVKC\r
-LIPP_HORSE      KITVER.NDG .SVFNFCSEE TVR....EDV LLTLTAC\r
-LIPP_HUMAN      KIIVET.NVG .KQFNFCSPE TVR....EEV LLTLTPC\r
-LIPP_PIG        KITVER.NDG .KVYDFCSQE TVR....EEV LLTLNPC\r
-LIPP_RABIT      QITVEQ.NDG .RVFKFCSTD TVR....EDI LLTLTPC\r
-LIPP_RAT        RISVER.NDG .RVFNFCSQD TVR....EDV LLTLSAC\r
-\r
-\r
diff --git a/website/version2/examples/muscle.jpg b/website/version2/examples/muscle.jpg
deleted file mode 100755 (executable)
index 5f89239..0000000
Binary files a/website/version2/examples/muscle.jpg and /dev/null differ
diff --git a/website/version2/examples/overview.gif b/website/version2/examples/overview.gif
deleted file mode 100755 (executable)
index e961650..0000000
Binary files a/website/version2/examples/overview.gif and /dev/null differ
diff --git a/website/version2/examples/pca.gif b/website/version2/examples/pca.gif
deleted file mode 100755 (executable)
index 6192c3b..0000000
Binary files a/website/version2/examples/pca.gif and /dev/null differ
diff --git a/website/version2/examples/pdb.gif b/website/version2/examples/pdb.gif
deleted file mode 100755 (executable)
index 7e1e739..0000000
Binary files a/website/version2/examples/pdb.gif and /dev/null differ
diff --git a/website/version2/examples/search.gif b/website/version2/examples/search.gif
deleted file mode 100755 (executable)
index 4d98c44..0000000
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diff --git a/website/version2/examples/serprot.msf b/website/version2/examples/serprot.msf
deleted file mode 100755 (executable)
index cc5b9b4..0000000
--- a/website/version2/examples/serprot.msf
+++ /dev/null
@@ -1,65 +0,0 @@
-PileUp\r
-\r
-\r
-\r
-   MSF:  279  Type: P    Check:  9995   .. \r
-\r
- Name: KYBOA oo  Len:  279  Check:  4492  Weight:  1.00\r
- Name: TRBOTR oo  Len:  279  Check:  6670  Weight:  1.00\r
- Name: ELPG oo  Len:  279  Check:  6037  Weight:  1.00\r
- Name: PRRTG oo  Len:  279  Check:  3057  Weight:  1.00\r
- Name: KQHUP oo  Len:  279  Check:  6499  Weight:  1.00\r
- Name: TRSMG oo  Len:  279  Check:  3240  Weight:  1.00\r
-\r
-//\r
-\r
-\r
-\r
-KYBOA           .CGVP..... AIQPVLSGLS .........R IVNGEEAVPG SWPWQVSLQD \r
-TRBOTR          .......... .....VDDDD .........K IVGGYTCGAN TVPYQVSLN. \r
-ELPG            .......... .......... .......... VVGGTEAQRN SWPSQISLQY \r
-PRRTG           .......... .......... .......... IIGGVESIPH SRPYMAHLDI \r
-KQHUP           AYGTQGSSGY SLRLCNTGDN SVCTTKTSTR IVGGTNSSWG EWPWQVSLQV \r
-TRSMG           .......... .......... .......... VVGGTRAAQG EFPFMVRLS. \r
-\r
-\r
-KYBOA           K...TGFHFC GGSLINENWV VTAAHCG... ..VTTSDVVV AGEFDQGSSS \r
-TRBOTR          ....SGYHFC GGSLINSQWV VSAAHCY... ..KSGIQVRL G.EDNINVVE \r
-ELPG            RSGSSWAHTC GGTLIRQNWV MTAAHCVD.. .RELTFRVVV G.EHNLNQNN \r
-PRRTG           VTEKGLRVIC GGFLISRQFV LTAAHCK... ..GREITVIL G.AHDVRKRE \r
-KQHUP           K.LTAQRHLC GGSLIGHQWV LTAAHCFDGL PLQDVWRIYS G.ILNLSDIT \r
-TRSMG           .......MGC GGALYAQDIV LTAAHCVS.. ..GSGNNTSI TATGGVVDLQ \r
-\r
-\r
-KYBOA           EKIQKLKIAK VFKNSKYNSL TINN..DITL LKLSTAASFS QTVSAVCLPS \r
-TRBOTR          GNEQFISASK SIVHPSYNSN TLNN..DIML IKLKSAASLN SRVASISLPT \r
-ELPG            GTEQYVGVQK IVVHPYWNTD DVAAGYDIAL LRLAQSVTLN SYVQLGVLPR \r
-PRRTG           STQQKIKVEK QIIHESYNSV PNLH..DIML LKLEKKVELT PAVNVVPLPS \r
-KQHUP           KDTPFSQIKE IIIHQNYKVS EGNH..DIAL IKLQAPLNYT EFQKPICLPS \r
-TRSMG           S.AVKVRSTK VLQAPGYNGT G.K...DWAL IKLAQPINQ. P.....TLKI \r
-\r
-\r
-KYBOA           ASDDFAAGTT CVTTGWGLTR YTNANTPDRL QQASLPLLSN TNCKK..YWG \r
-TRBOTR          S..CASAGTQ CLISGWGNTK SSGTSYPDVL KCLKAPILSD SSCKS..AYP \r
-ELPG            AGTILANNSP CYITGWGLTR .TNGQLAQTL QQAYLPTVDY AICSSSSYWG \r
-PRRTG           PSDFIHPGAM CWAAGWGKTG .VRDPTSYTL REVELRIMDE KACVD...YR \r
-KQHUP           KGDTSTIYTN CWVTGWGFSK .EKGEIQNIL QKVNIPLVTN EECQKR.YQD \r
-TRSMG           ATTTAYNQGT FTVAGWGANR .EGGSQQRYL LKANVPFVSD AACRS.AYGN \r
-\r
-\r
-KYBOA           TKIKDAMICA G...ASGVSS .CMGDSGGPL VCKK.NGAWT LVGIVSWGS. \r
-TRBOTR          GQITSNMFCA GY.LEGGKDS .CQGDSGGPV VCS...G..K LQGIVSWGS. \r
-ELPG            STVKNSMVCA G...GNGVRS GCQGDSGGPL HCLV.NGQYA VHGVTSFVSR \r
-PRRTG           YYEYKFQVCV G..SPTTLRA AFMGDSGGPL LCA...G..V AHGIVSYGH. \r
-KQHUP           YKITQRMVCA GY.KEGGKDA .CKGDSGGPL VCKH.NGMWR LVGITSWGE. \r
-TRSMG           ELVANEEICA GYPDTGGVDT .CQGDSGGPM FRKDNADEWI QVGIVSWGY. \r
-\r
-\r
-KYBOA           .STCSTSTPG VYARVTALVN WVQQTLAAN\r
-TRBOTR          .GCAQKNKPG VYTKVCNYVS WIKQTIASN\r
-ELPG            LGCNVTRKPT VFTRVSAYIS WINNVIASN\r
-PRRTG           ...PDAKPPA IFTRVSTYVP TINAVIN..\r
-KQHUP           .GCARREQPG V......... .........\r
-TRSMG           .GCARPGYPG VYTEVSTFAS AIASAARTL\r
-\r
-\r
diff --git a/website/version2/examples/tree.gif b/website/version2/examples/tree.gif
deleted file mode 100755 (executable)
index e4619dd..0000000
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diff --git a/website/version2/examples/uniprot.gif b/website/version2/examples/uniprot.gif
deleted file mode 100755 (executable)
index a643904..0000000
Binary files a/website/version2/examples/uniprot.gif and /dev/null differ
diff --git a/website/version2/examples/wrap.gif b/website/version2/examples/wrap.gif
deleted file mode 100755 (executable)
index b67a78b..0000000
Binary files a/website/version2/examples/wrap.gif and /dev/null differ
diff --git a/website/version2/index.html b/website/version2/index.html
deleted file mode 100755 (executable)
index 8acf398..0000000
--- a/website/version2/index.html
+++ /dev/null
@@ -1,100 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">\r
-<html><!-- InstanceBegin template="/Templates/jtemplate.dwt" codeOutsideHTMLIsLocked="false" -->\r
-<head>\r
-<!-- InstanceBeginEditable name="doctitle" -->\r
-<TITLE>JalView - Java alignment editor</TITLE>\r
-<!-- InstanceEndEditable -->\r
-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">\r
-<!-- InstanceBeginEditable name="head" --><!-- InstanceEndEditable -->\r
-<style type="text/css">\r
-<!--\r
-td {\r
-       font-family: Geneva, Arial, Helvetica, sans-serif;\r
-       font-size: 12px;\r
-}\r
--->\r
-</style>\r
-</head>\r
-\r
-<body>\r
-<div align="left">\r
-  <table border="0">\r
-    <tr>\r
-      <td width="700" ><center>\r
-          <table width="550" border="0">\r
-            <tr>\r
-              <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
-              <td width="55%"><div align="center"><font size="+6"><strong><font face="Geneva, Arial, Helvetica, sans-serif">Jalview\r
-                  </font></strong></font> </div>\r
-                <div align="center"><font size="3" face="Geneva, Arial, Helvetica, sans-serif">a\r
-                  multiple alignment editor</font> </div></td>\r
-            </tr>\r
-          </table>\r
-          </center></td>\r
-    </tr>\r
-  </table>\r
- <br>\r
-  <table border="0">\r
-    <tr>\r
-      <td width="197" valign="top" nowrap> <p><strong>Downloads</strong></p>\r
-        <ul>\r
-          <li><a href="index.html">Jalview</a></li>\r
-        </ul>\r
-        <strong>Examples</strong> <ul>\r
-          <li><a href="examples/applets.html">Applet</a></li>\r
-          <li><a href="examples/examples.html">Application</a></li>\r
-        </ul>\r
-        <strong>Reference</strong> <ul>\r
-          <li> <a href="../jalview.pdf" target="_blank">&quot;The Jalview Java<br>\r
-            Alignment Editor,&quot;<br>\r
-            </a></li>\r
-          <a href="../jalview.pdf"><em>Bioinformatics</em>, 12, 426-7</a>\r
-        </ul>\r
-        <strong>Source Code</strong> <ul>\r
-          <li>Jalview 2</li>\r
-        </ul>\r
-        <p><strong>Feedback</strong></p>\r
-        <p>&nbsp;&nbsp;&nbsp;<img src="../help.gif" width="151" height="43"> </p>\r
-        <p><br>\r
-          <a href="http://www.bbsrc.ac.uk/"> <img border="0"src="../bbsrc.jpg"></a>\r
-        </p></td>\r
-      <td width="499" valign="top"><!-- InstanceBeginEditable name="Contents" -->\r
-        <p>Key features of Jalview Version 2:\r
-        <ul>\r
-          <li>Remote tools implemented as web services</li>\r
-          <li>Remote alignments (<a href="http://www.ebi.ac.uk/clustalw/" target="CLUSTAL">Clustal</a>, <a href="http://www.drive5.com/muscle/" target="MUSCLE">Muscle</a>...)</li>\r
-          <li>Remote alignment annotation (<a href="http://www.compbio.dundee.ac.uk/~www-jpred/" target="JPRED">JPred Secondary Structure Prediction</a>)</li>\r
-          <li>Printing</li>\r
-          <li>PNG, HTML, Encapsulated PostScript output</li>\r
-        </ul>\r
-        <p>Current development allows the Jalview Application to be distributed\r
-          using Java Web Start which is installed with <a href="http://www.java.com/en/download/" target="JAVA">Java.</a>\r
-          Each time the application is started via Java Web Start an automatic\r
-          update is performed so that you will always be running the latest code.<br>\r
-          <br>\r
-          N.B. if you have a local installation of Java and clicking on the link\r
-          below prompts the question &quot;Open using application...&quot;, locate\r
-          your installation of Java Web Start - its called "javaws". Your web browser will now associate .jnlp\r
-          files with Java Web Start<br>\r
-          <br>\r
-          Try it now.\r
-        <center>\r
-          <h2><a href="http://www.compbio.dundee.ac.uk/~andrew/JalviewWebsite/version2/webstart/JalviewX.jnlp">Start\r
-            Jalview</a> </h2>\r
-          <p>&nbsp;</p>\r
-        </center>\r
-        If you are having difficulties installing Java or would prefer not to\r
-        use Java Web Start you could try installing Jalview from the following\r
-        link.\r
-        <p>\r
-        <center>\r
-          <h2><a  target="NEW" href="Web_Installers/install.htm">Install with InstallAnywhere</a>\r
-          </h2>\r
-        </center>\r
-        <!-- InstanceEndEditable -->\r
-      </td>\r
-    </tr>\r
-  </table>\r
-</div>\r
-</body>\r
-<!-- InstanceEnd --></html>\r
diff --git a/website/version2/webstart/JalviewX.jar b/website/version2/webstart/JalviewX.jar
deleted file mode 100755 (executable)
index 96d4a5c..0000000
Binary files a/website/version2/webstart/JalviewX.jar and /dev/null differ
diff --git a/website/version2/webstart/JalviewX.jnlp b/website/version2/webstart/JalviewX.jnlp
deleted file mode 100755 (executable)
index 16c4b60..0000000
--- a/website/version2/webstart/JalviewX.jnlp
+++ /dev/null
@@ -1,43 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>   \r
-<jnlp codebase="http://www.compbio.dundee.ac.uk/~andrew/JalviewWebsite/version2/webstart" \r
-      href="http://www.compbio.dundee.ac.uk/~andrew/JalviewWebsite/version2/webstart/JalviewX.jnlp">\r
-       <information>\r
-               <title>Jalview</title>\r
-               <vendor>The Barton Group</vendor>\r
-               <homepage href="www.jalview.org"/>\r
-               <description>Jalview Multiple Alignment Editor</description>\r
-               <description kind="short">Jalview</description>\r
-               <icon href="logo_big.gif"/>\r
-               <association mime-type="application-x/ext-file" extensions="fa"/>\r
-               <association mime-type="application-x/ext-file" extensions="fasta"/>\r
-               <association mime-type="application-x/ext-file" extensions="fastq"/>\r
-               <association mime-type="application-x/ext-file" extensions="blc"/>\r
-               <association mime-type="application-x/ext-file" extensions="msf"/>\r
-               <association mime-type="application-x/ext-file" extensions="pfam"/>\r
-               <association mime-type="application-x/ext-file" extensions="aln"/>\r
-               <association mime-type="application-x/ext-file" extensions="pir"/>\r
-       </information>\r
-       <resources>\r
-               <j2se version="1.3+"/>\r
-               <jar href="JalviewX.jar"/>\r
-               <jar href="regex.jar"/>\r
-               <jar href="jhall.jar"/>\r
-               <jar href="axis.jar"/>\r
-               <jar href="jaxrpc.jar"/>\r
-               <jar href="commons-logging.jar"/>\r
-               <jar href="commons-discovery.jar"/>\r
-               <jar href="saaj.jar"/>  \r
-               <jar href="wsdl4j.jar"/>\r
-               <jar href="log4j-1.2.8.jar"/>\r
-               <jar href="mail.jar"/>\r
-               <jar href="activation.jar"/>\r
-               <jar href="xercesImpl.jar"/>\r
-               <jar href="castor.zip"/>\r
-               <jar href="xml-apis.jar"/>\r
-       </resources>\r
-       <application-desc main-class="jalview.bin.Jalview"/>\r
-       <security>\r
-               <all-permissions/>\r
-       </security>\r
-</jnlp>\r
-\r
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