--- /dev/null
+<!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="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">"The Jalview Java<br>\r
+ Alignment Editor,"<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> <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>Jalview is a multiple alignment editor written in <a href="http://www.java.com/en/download/" target="_blank">java</a>. \r
+ It is used widely in a variety of web pages (e.g. the EBI clustalw server \r
+ and the PFAM protein domain database) but is available as a general \r
+ purpose alignment editor. <br>\r
+ </p>\r
+ <p><a href="version2/index.html">Version 2.0</a> is the latest release \r
+ version of Jalview. This version has many new features compared to the \r
+ original version. </p>\r
+ <p>The original version of Jalview, <a target="NEW" href="version118/Jalview_118.html">version \r
+ 1.18</a>, can still be downloaded. Some features no longer work.</p>\r
+ <p><br>\r
+ <em>Jalview Features</em> -- See major new developments by trying Jalview \r
+ Version 2 -- </p>\r
+ <ul>\r
+ <li>Sequence feature retrieval and display on the alignment</li>\r
+ <li>Reads and writes alignments in a variety of formats </li>\r
+ <li>Gaps can be inserted/deleted using the mouse. </li>\r
+ <li>Conservation analysis similar to that of AMAS </li>\r
+ <li>Group editing (insertion deletion of gaps in groups of sequences). \r
+ </li>\r
+ <li>Removal of gapped columns </li>\r
+ <li>Many different colour schemes </li>\r
+ <li>Alignment sorting options (by name, tree order, percent identity, \r
+ group) </li>\r
+ <li>Linking of group colours between the alignment, tree and PCA windows. \r
+ </li>\r
+ <li>UPGMA and NJ trees calculated and drawn based on percent identity \r
+ distances. </li>\r
+ <li>Sequence clustering using principal component analysis </li>\r
+ <li>Removal of redundant sequences </li>\r
+ <li>Smith Waterman pairwise alignment of selected sequences</li>\r
+ <li>EPS, PNG files can be generated for inclusion in documents</li>\r
+ </ul>\r
+ Authors :<br>\r
+ Version 1.18 Michele Clamp; James Cuff; Stephen Searle; Geoff Barton<br>\r
+ V ersion 2.0 Andrew Waterhouse; Jim Procter; Geoff Barton \r
+ <p>Special thanks go to Alex Bateman and the Pfam team for using Jalview \r
+ and making many helpful suggestions</p>\r
+ <p>New JalView development has been funded for three years from 1st October \r
+ 2004 by the <a href="http://www.bbsrc.ac.uk/">BBSRC</a> as part of the \r
+ "Visualisation and Analysis of Biological Sequences, Alignments \r
+ and Structures" Project. This project is coordinated by Geoff Barton \r
+ at the <a href="http://www.compbio.dundee.ac.uk">University of Dundee</a> \r
+ with partners at <a href="http://www.ebi.ac.uk">EBI</a> and <a href="http://www.bioss.sari.ac.uk">BioSS</a></a> \r
+ and consultancy (blessing :-) from Michele Clamp; the originator of \r
+ JalView. </p>\r
+ <!-- InstanceEndEditable --> \r
+ </td>\r
+ </tr>\r
+ </table>\r
+</div>\r
+</body>\r
+<!-- InstanceEnd --></html>\r
git://source.jalview.org / jalview.git / commitdiff
