Multiple alignment views allow's the same alignment to be viewed in many different ways, either as multiple alignment tabs, or simultaneously in linked alignment windows. A view is an independent visualization of the same alignment, so each may have a different ordering, colouring, row and column hiding and seuqence feature and annotation display setting, but alignment, feature and annotation edits are common to all, since this affects the underlying data.

A new view is created using the "View→New View" menu item, or by pressing Control+T. A newly created view will be identical to the view it was created from, but any changes to the way the alignment is coloured or displayed will only affect the new view.

A particular view may focus on some specific aspect of an alignment - for example, hiding all but the region of an alignment containing a particular domain. Right-clicking a view's tab opens the View Name dialog box, allowing it to be renamed to something more meaningful.

Viewing Multiple Views Simultaneously

Multiple views of an alignment are, by default, gathered together as tabs within a single alignment window. They can be viewed simultanously by pressing X (or via "View→Expand") to expand each view into its own linked alignment window. Expanded views are gathered back into into a single tabbed alignment window by pressing G, or by selecting "View→Gather").

Tree Viewers and Multiple Views

A tree calculated on a particular view, or loaded onto it, is by default associated with just that view. However, the Tree Viewer's "View→Associate leaves" submenu allows a tree's view association to be changed to to any or all other views.

Multiple Views were introduced in Jalview 2.2