From 68ba1a55efa08e12e4381bb0e5bdcb70318e1dd5 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 21 Jun 2016 10:54:17 +0100
Subject: [PATCH] =?utf8?q?JAL-2089=20cleared=20out=20old=20=E2=80=98What=E2=80?=
 =?utf8?q?=99s=20new=E2=80=99?=
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---
 help/html/whatsNew.html |   55 +++--------------------------------------------
 1 file changed, 3 insertions(+), 52 deletions(-)

diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index 19be76f..d7a93c6 100755
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -27,61 +27,12 @@
     <strong>What's new ?</strong>
   </p>
   <p>
-    Jalview 2.9.0b2 is a bug fix release for Jalview 2.9.
-    The release of Jalview 2.9 in September 2015 included
-    a multitude of bug fixes and minor improvements (both small, and
-    rather big!), it also brings major new capabilities for codon-level
-    analysis of protein alignments and the retrieval and manipulation of
-    structural data.</p><p>For the patches since version 2.9 was released, see the
-    <a href="releases.html#Jalview.2.9.0b2">Jalview 2.9.0b2 Release Notes</a>.
+    Jalview 2.9.1 is the next major release in the Jalview 2.9 series. Full details are in the
+    <a href="releases.html#Jalview.2.9.1">Jalview 2.9.1 Release Notes</a>.
   </p>
   <p>
-    <strong>Highlights in Jalview 2.9</strong>
+    <strong>Highlights in Jalview 2.9.1</strong>
   <ul>
-    <li><strong>Visualisation, editing and analysis of
-        cDNA and Protein alignments</strong><br />A new <a
-      href="features/splitView.html">Split View</a> window allows linked
-      protein and nucleotide sequence alignments to be viewed, edited,
-      and analysed as one. <br />cDNA alignments can also be
-      reconstructed from protein alignments calculated by Jalview's web
-      services, and update in response to edits in the amino acid view.<br />To
-      start experimenting with cDNA/Protein analysis, jut drop a file
-      containing cDNA sequences which code for proteins in an existing
-      alignment, and Jalview will do the rest.</li>
-    <li><strong>Enhanced Integration of UCSF Chimera</strong> <br>Jalview
-      2.9 provides full support for the use of Chimera to view 3D
-      structures linked to alignment views in the Jalview Desktop. We've
-      also included support for saving Chimera sessions in Jalview
-      project files.<br />Jalview and Chimera communicate using local
-      web server connections, which may cause firewall alerts on some
-      systems, but has the advantage of allowing bidirectional
-      communication. Communication between Jalview and Chimera is now
-      much more responsive, and selected regions in Chimera are now
-      shown as highlighted regions in the Jalview desktop.</li>
-    <li><strong>Interactive querying of the PDBe</strong><br />Jalview
-      users can now <a href="features/pdbsequencefetcher.html">browse</a> and <a href="features/viewingpdbs.html">retrieve 3D structure</a> data from the PDB
-      via the <a href="http://www.ebi.ac.uk/pdbe/api/doc/search.html">PDBe
-        Search API</a> (<a href="http://dx.doi.org/10.1093%2Fnar%2Fgkt1180">Gutmanas
-        et al 2014</a>). Developed in collaboration with the PDBe group at
-      EMBL-EBI, the interface allows both structured and free-text
-      queries to be performed, and allows automatic selection of the
-      most relevant structures for an alignment acording to a variety of
-      criteria.</li>
-    <li><strong>Improved support for RNA visualisation</strong><br />Jalview
-      2.9 integrates the latest version of the <a
-      href="features/varna.html">VARNA RNA Viewer</a>, and VARNA views
-      can also now be stored in Jalview projects. We've also dealt with
-      a number of lingering bugs in the VARNA/Jalview interface,
-      including the loss of pseudoknots when RNA secondary structure is
-      shown VARNA.</li>
-    <li><strong>Protein Secondary Structure predictions
-        with JPred4</strong><br />Jalview includes a number of new features for
-      working with secondary structure predictions from the JPred4
-      server. These include new <a href="menus/popupMenu.html#hideinserts">popup menu actions</a> to automatically hide insertions and highlight
-      mutations in an alignment with respect to a <a href="calculations/referenceseq.html">Reference
-        Sequence</a>. Jalview 2.9's new <a href="io/export.html#htmlexport">scrollable
-        SVG HTML export</a> was also developed specifically for the JPred4
-      server.</li>
   </ul>
 
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