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5 <TITLE>JalView - Java alignment editor</TITLE>
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23 <td width="700" ><center>
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24 <table width="550" border="0">
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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>
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27 <td width="55%"><div align="center"><font size="+6"><strong><font face="Geneva, Arial, Helvetica, sans-serif">Jalview
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28 </font></strong></font> </div>
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29 <div align="center"><font size="3" face="Geneva, Arial, Helvetica, sans-serif">a
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30 multiple alignment editor</font> </div></td>
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39 <td width="197" valign="top" nowrap> <p><strong>Downloads</strong></p>
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41 <li><a href="version2/index.html">Jalview</a></li>
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43 <strong>Examples</strong> <ul>
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44 <li><a href="version2/examples/applets.html">Applet</a></li>
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45 <li><a href="version2/examples/examples.html">Application</a></li>
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47 <strong>Reference</strong> <ul>
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48 <li> <a href="jalview.pdf" target="_blank">"The Jalview Java<br>
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49 Alignment Editor,"<br>
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51 <a href="jalview.pdf"><em>Bioinformatics</em>, 12, 426-7</a>
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53 <strong>Source Code</strong> <ul>
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56 <p><strong>Feedback</strong></p>
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57 <p> <img src="help.gif" width="151" height="43"> </p>
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59 <a href="http://www.bbsrc.ac.uk/"> <img border="0"src="bbsrc.jpg"></a>
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62 <p>Jalview is a multiple alignment editor written in <a href="http://www.java.com/en/download/" target="_blank">java</a>.
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63 It is used widely in a variety of web pages (e.g. the EBI clustalw server
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64 and the PFAM protein domain database) but is available as a general
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65 purpose alignment editor. <br>
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67 <p><a href="version2/index.html">Version 2.0</a> is the latest release
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68 version of Jalview. This version has many new features compared to the
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69 original version. </p>
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70 <p>The original version of Jalview, <a target="NEW" href="version118/Jalview_118.html">version
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71 1.18</a>, can still be downloaded. Some features no longer work.</p>
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73 <em>Jalview Features</em> -- See major new developments by trying Jalview
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76 <li>Sequence feature retrieval and display on the alignment</li>
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77 <li>Reads and writes alignments in a variety of formats </li>
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78 <li>Gaps can be inserted/deleted using the mouse. </li>
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79 <li>Conservation analysis similar to that of AMAS </li>
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80 <li>Group editing (insertion deletion of gaps in groups of sequences).
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82 <li>Removal of gapped columns </li>
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83 <li>Many different colour schemes </li>
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84 <li>Alignment sorting options (by name, tree order, percent identity,
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86 <li>Linking of group colours between the alignment, tree and PCA windows.
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88 <li>UPGMA and NJ trees calculated and drawn based on percent identity
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90 <li>Sequence clustering using principal component analysis </li>
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91 <li>Removal of redundant sequences </li>
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92 <li>Smith Waterman pairwise alignment of selected sequences</li>
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93 <li>EPS, PNG files can be generated for inclusion in documents</li>
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96 Version 1.18 Michele Clamp; James Cuff; Stephen Searle; Geoff Barton<br>
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97 V ersion 2.0 Andrew Waterhouse; Jim Procter; Geoff Barton
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98 <p>Special thanks go to Alex Bateman and the Pfam team for using Jalview
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99 and making many helpful suggestions</p>
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100 <p>New JalView development has been funded for three years from 1st October
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101 2004 by the <a href="http://www.bbsrc.ac.uk/">BBSRC</a> as part of the
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102 "Visualisation and Analysis of Biological Sequences, Alignments
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103 and Structures" Project. This project is coordinated by Geoff Barton
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104 at the <a href="http://www.compbio.dundee.ac.uk">University of Dundee</a>
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105 with partners at <a href="http://www.ebi.ac.uk">EBI</a> and <a href="http://www.bioss.sari.ac.uk">BioSS</a></a>
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106 and consultancy (blessing :-) from Michele Clamp; the originator of
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