X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=19be76f59844b47234a5a9550d2f6275656530d3;hb=7182b83bcc2d48f6335ac0ca16528607cee81408;hp=d124cc8d5de3e7904164dc87fd7fd9e7f48271db;hpb=9a881df532ecf49063d4f032144533b9a1a89319;p=jalview.git
diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index d124cc8..19be76f 100755
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -27,16 +27,16 @@
What's new ?
- Jalview 2.9 has been in development since December 2014. In addition
- to a multitude of bug fixes and minor improvements (both small, and
+ 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 manipulation of structural
- data.
For the full list of changes, see the Jalview 2.9 Release Notes.
+ analysis of protein alignments and the retrieval and manipulation of
+ structural data.
For the patches since version 2.9 was released, see the
+ Jalview 2.9.0b2 Release Notes.
Highlights in Jalview 2.9
-
- Visualisation, editing and analysis of
cDNA and Protein alignments
A new To
start experimenting with cDNA/Protein analysis, jut drop a file
- containing cDNA sequences which code for, and have IDs matching
- proteins in an existing alignment, and Jalview will do the rest.
+ containing cDNA sequences which code for proteins in an existing
+ alignment, and Jalview will do the rest.
- Enhanced Integration of UCSF Chimera
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
@@ -59,7 +59,7 @@
much more responsive, and selected regions in Chimera are now
shown as highlighted regions in the Jalview desktop.
- Interactive querying of the PDBe
Jalview
- users can now browse and retrieve 3D structure data from the PDB
+ users can now browse and retrieve 3D structure data from the PDB
via the PDBe
Search API (Gutmanas
et al 2014). Developed in collaboration with the PDBe group at
@@ -69,18 +69,19 @@
criteria.
- Improved support for RNA visualisation
Jalview
2.9 integrates the latest version of the VARNA RNA Viewer, and VARNA views
+ href="features/varna.html">VARNA RNA Viewer, 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.
- Protein Secondary Structure predictions
- with JPred4Jalview includes a number of new features for working
- with secondary structure predictions from the JPred4 server. These
- include the ability to automatically hide insertions and highlight
- mutations in an alignment with respect to a reference sequence.
- Jalview 2.9's new scrollable SVG HTML export mode was also
- developed specifically for the JPred4 server.
+ with JPred4
Jalview includes a number of new features for
+ working with secondary structure predictions from the JPred4
+ server. These include new popup menu actions to automatically hide insertions and highlight
+ mutations in an alignment with respect to a Reference
+ Sequence. Jalview 2.9's new scrollable
+ SVG HTML export was also developed specifically for the JPred4
+ server.