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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
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<p><strong>What's new ?</strong></p>
-<p><strong>Highlights in Jalview Version 2.4</strong></p>
+<p>Jalview 2.6 introduces new web services, and includes an updated
+version of the Jmol molecular graphics visualization system. See the <a
+ href="releases.html#Jalview2.6">release history</a> for the full
+details.</p>
+<p><strong>Highlights in Jalview Version 2.6</strong></p>
<ul>
- DNA and protein product highlighting<br>
- URL links generated with regular expressions<br>
- URL links for sequence database cross references<br>
- New sequence fetcher dialog and DAS Sequence Fetching<br>
- JPred Service upgraded to Jpred3<br>
- Memory monitor<br>
- PFAM full alignment retrieval<br>
- Generalised sequence database reference validation<br>
- DNA Protein Product sequence db traversal (Experimental)<br>
- VAMSAS Interoperation Client (Experimental)<br>
- export annotation rows as CSV for spreadsheet import<br>
- New application command line args and optional Groovy suport<br>
- New Applet API methods and parameters<br>
+ <li><a href="webServices/JABAWS.html">JABA Web Services</a> for
+ multiple alignment using:
+ <ul>
+ <li>ClustalW</li>
+ <li>MAFFT</li>
+ <li>Muscle</li>
+ <li>ProbCons</li>
+ <li>T-COFFEE</li>
+ </ul>
+ </li>
+ <li>User modifiable alignment service parameters</li>
+ <li>Visualization of superposed structures associated with protein
+ or nucleotide sequence alignments.</li>
+ <li>Export coordinates and projection as CSV from PCA viewer</li>
</ul>
-<p><strong>Issues Resolved (a select list)</strong></p>
+
+<p><strong>Issues Resolved (a select list - see release history for details)</strong></p>
<ul>
- Aligned cDNA translation to aligned peptide works correctly<br>
- selected region output includes visible annotations (for
- certain formats)<br>
- edit label/displaychar contains existing label/char for
- editing<br>
- Newick tree support improved for clustalW trees and preserving NHX style comments<br>
- Pathological filechooser bug avoided by not allowing
- filenames containing a ':'<br>
- Fixed exception when parsing GFF files containing global
- sequence features<br>
- Reference counting for alignment datasets<br>
- better reporting of non-fatal warnings and error messages to user when file
- parsing fails.<br>
- Save works when Jalview project is default format<br>
- Histidine should be midblue (not pink!) in Zappo<br>
- Undo recovers dataset sequence metadata when sequence
- regions are cut<br>
- PDB files without pdb ID HEADER lines (like those
- generated by MODELLER) are read in properly<br>
- Stockholm annotation parsing fixed and improved (PFAM records)<br>
- Re-instated Full AMSA support and .amsa file association (MyHits)<br>
- annotation consisting of sequence associated scores can be
- read and written correctly to annotation file<br>
- Fixed display of hidden sequence markers and non-italic font
- for representatives in Applet<br>
- Applet Menus are always embedded in applet window on Macs.</br>
- Newly shown features appear at top of stack (in Applet)</br>
- Secondary structure lines are drawn starting from first
- column of alignment<br>
- Uniprot XML import updated for new schema release in July 2008<br>
- Sequence feature to sequence ID match for Features file is case-insensitive<br>
- Sequence features read from Features file appended to all sequences with matching IDs<br>
- PDB structure coloured correctly for associated views containing a sub-sequence<br>
- Display name and local features preserved in results retrieved from web service<br>
- Visual delay indication for sequence retrieval and sequence fetcher initialisation<br>
- Updated Application to use DAS 1.53e version of dasobert DAS client
+ <li>clustalx colourscheme colours Ds preferentially when both D+E
+ are present in over 50% of the column</li>
+ <li>Prevent sequence fetcher from replacing ',' for ';' when querying DAS sequence sources</li>
+ <li>InstallAnywhere builds fail to launch on OS X java 10.5 update
+ 4 (due to apple Java 1.6 update)</li>
</ul>
-
-<p> </p>
<p>See the <a href="releases.html">Release History</a> page for
details of all new features and resolved issues.</p>
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