Whats new

If you can read this then you'll 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 will create a "selection region" which may be full sequences or groups of residues.
• To edit a sequence, the "Shift" key must be held down
• To edit groups, either the "Alt" key or the "Control" key must be held down.
• Colours maybe applied to the background, ie the whole alignment, or to selected regions. If the tickbox "Apply colour to all groups" is ticked (this is the defualt), then the colour will be applied to all groups.
• Use the right mouse button (apple and click on the mac) to define a selected region on the alignment as a new group.
• Conservation is automatically updated whenever the alignment is edited
• There is no "quick draw" option
• Edits can be undone! (and redone)