What's new ?

If you are reading this then you will already have seen some of the recent changes made to Jalview.
Jalview takes advantage of some of the more recent user interface developments in the Java programming language. For instance Jalview is now a multi windowed application, this keeps all your Jalview windows neatly together in one main application window.

If you were familiar with the original Jalview, here is a list of important features you should know about the current development:

• Editing sequences is no longer the default when mouse clicking the alignment. Instead, mouse clicking on the alignment creates a "selection region" which may be full sequences or groups of residues.
• To insert or edit the gaps in one sequence in alignment, the "Shift" key must be held down when dragging the mouse.
• To insert or edit gaps for a group of sequences, the "Alt" key (or in X windows the "Control" key) must be held down.
• Selecting colour schemes in the colour menu either sets just the "background" colourscheme for the alignment, or - when the tickbox "Apply colour to all groups" is ticked, applies the scheme to the background and all groups defined on the alignment.
• Use the right mouse button (apple and click on the Mac) whilst the pointer is within the selection area to access the "define" region menu to define a new region, give it a name, and change its colourscheme and display properties.
• Conservation is automatically updated whenever the alignment is edited
• There is no "quick draw" option
• Edits can be undone, and redone!