What's new ?

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=dd536b10e9d2a48ebc4d2f6104455c8d89ea8f55;hb=c2214808f64b811a25cec10399dcff38db0c592c;hp=79cf7c98197d9c18e8884964fbeb4c5d7f93cc17;hpb=8a3915baf2a22618346a5a2ecd38f7fbca5d4a44;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 79cf7c9..dd536b1 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -1,72 +1,76 @@ + --> What's new ?

- What's new ?
Jalview 2.8.0b1 is a bugfix - release for Jalview version 2.8.
As usual you can find the - highlights below, and the comprehensive list is given in the Jalview 2.8.0b1 Release Notes. + What's new ?

+ Jalview 2.8.1 includes new features for group creation, RNA secondary + structure prediction and a host bug fixes. It also includes support + for version 2.1 + of JABA and includes a Spanish translation of its user interface.
+ The highlights are detailed below, and the full list is given in the Jalview 2.8.1 Release Notes. +

The Desktop and web based applet include new keystrokes for + defining and undefining groups, and PAM250 has been added to the range + of score models available for use by the tree and PCA calculations. + The Jalview project file format has also been extended for handling + RNA and protein secondary structure annotation, in anticipation for + new structure based secondary structure support in Jalview 2.8.2.

Internationalisation

Jalview 2.8.1 is the first release to include support for + displaying Jalview's user interface in different languages. In August + 2013, David Roldán-Martinez took on the task of + internationalising Jalview's user interface. He also recruited Sara + Hernández Díaz and Laura Ferrandis Martinez who created + Jalview's first spanish user interface translation.

+ If you notice any problems, or would like to help translate Jalview's + user interface into other languages, head over to issues.jalview.org and put in a + feature request describing the translations you can provide to the i18n + component. David has also documented + the process of creating i18n translations to help you get started. +

RNA Secondary Structure Prediction with JABA 2.1

+ This version of Jalview includes a client to access the new services available in JABA v2.1 , which + provides services for RNA consensus secondary structure prediction and + two new alignment programs (GLProbs and MSAProbs).

+ To see how to perform RNA secondary structure predictions like the one below, take a look at the RNAAliFold + client documentation.

- This bug fix release includes numerous minor enhancements made over - the last 12 months. Importantly, it is also the first release that - provides Jalview as a trusted application, signed with a certificate - donated to us by Certum. -

- Enhancements and new features -

Allow disorder predictions to be made on the current - selection (or visible selection) in the same way that JPred works
allow import of data from gzipped files
Improved per-sequence 'colour-by-annotation' performance
Support '' style escaping of quotes in Newick files
group options for JABAWS service by command line name
Select primary source when selecting authority in database - fetcher GUI
COMBINE statement uses current SEQUENCE_REF and GROUP_REF - scope to group annotation rows
add .mfa to FASTA file extensions recognised by Jalview
groovy scripting for headless jalview operation
Output in Stockholm format

- Bug fixes -

Uniprot and PDB database cross-reference fetching works - properly
'View all structures' in the desktop is more reliable
Web services parameter dialog box shows the options enabled - for different presets
Interactive creation of RNA secondary structure works more - smoothly
Keyboard mode 'P' command jumps to the right place
Improved support for parsing database cross-references via - Stockholm and Rfam database
Improved semantics in annotation files for grouping - annotation rows associated with particular sequences and groups
More robust DNA->Amino acid translation
Improved Headless-mode operation for DAS annotation - retrieval, groovy script execution and alignment figure generation
annotation label tooltip text needs to be wrapped

The RNAalifold client was implemented by Jalview's 2013 + summer student, Dan Barton. +