What's new ?

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=d8ae02d413744351f8fb6da957d5a38d1b8ccfd7;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=3af69ae87bc785d2c6d10ed3974ef4c09eb807ef;hpb=6fa9683bef52d6709abb81840681e4fa452cafe7;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 3af69ae..d8ae02d 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -1,9 +1,88 @@ - - - -

Whats new

If you can read this then you'll already have seen some of the recent changes - made to Jalview.
-

- - + + + +What's new ? + + +

+ What's new ? +

+ 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.

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 Split View window allows linked + protein and nucleotide sequence alignments to be viewed, edited, + and analysed as one.
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.
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.
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 + also included support for saving Chimera sessions in Jalview + project files.
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.
Interactive querying of the PDBe
Jalview + 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 + 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.
Improved support for RNA visualisation
Jalview + 2.9 integrates the latest version of the 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 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.

+ + +