The RNAalifold client was implemented by Jalview's 2013 + summer student, Dan Barton. +
What's new ?
- -Jalview Version 2.2
-Multiple views with different styles, colours, hidden regions for one alignment -
-Easily add, amend and delete sequence features -
-"Reload" alignment from File or URL to revert to original -
-"Save" to current filename or "Save As" to new filename -
-Set different text colour for dark or light background -
-Right align sequence ids -
-Set colour of lower case residues in a user defined colour scheme -
-Menu Rearrangements: New Format for alignment layout and Select for region selection. -
-Menu item accelerator keys added -
-Control-V pastes sequences to active window, Control-Shift-V pastes to a new window. -
-Raise/Minimise alignment and all associated windows from desktop window's window menu -
-Select and colour whole branches of a tree
-'New Window' button on the 'Output to Text box' alignment output -option to open a new alignment window after editing.
-Issues Resolved
- --Optimisations for large alignments: faster multithreaded calculations and Undo/Redo system. -
-Remove empty columns - if empty columns exist at the end of the -alignment bug fixed. -
-DAS feature fetching slowed down, doesn't overload DAS servers -
-DAS feature fetching can be cancelled -
-Correct display of > and < symbols for feature descriptions without explicit <html> tags. -
-Zoom working in PCA viewer -
-Sequence Descriptions retained after running a web service -
--
See the Release History page for details of all - new features and resolved issues.
++ 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. +
+