The VARNA RNA Viewer
VARNA was integrated into Jalview 2.8 to allow interactive viewing of RNA secondary structure annotation. It is opened by selecting the "Structure→View Structure:" option in the sequence id pop-up menu (if you can't see this, then no RNA structure is associated with your sequence or alignment). In the pop-up menu all structures that are associated with this sequence and all sequences that are associated with the alignment are available.
Saving a Jalview session as a project file includes the state of any Varna viewers, which are reopened when the project is reloaded (since Jalview 2.9).
Functionality provided by VARNA
VARNA's own functions are accessed by right-clicking in the structure display area. That will open the VARNA pop-up menu, which provides access to a number of features like different draw algorithm, color highlighting or annotations.
VARNA is a very powerful RNA viewer on its own. Only the essentials have been described here - the interested reader is referred to VARNA's own comprehensive online documentation.