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