Multiple Alignment Views

Multiple alignment views allow the same alignment to be viewed independently in many different ways simultaneously. Each view is an independent visualization of the same alignment, so each may have a different ordering, colouring, row and column hiding and sequence feature and annotation display setting, but alignment, feature and annotation edits are common to all, since this affects the underlying data.

Create a new view 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 a single tabbed alignment window by pressing G, or by selecting "View→Gather".

Hidden Sequence Representatives and Multiple Views

There are some unexpected interactions between hidden sequence representatives and their display in multiple views. See the corresponding entry in the documentation for hidden regions.

Structure and Analysis 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.

The results of a PCA calculation on a particular view may also be associated with other views, using the PCA Viewer's "View→Associate Nodes" submenu.

PDB Structure Viewers opened on a structure associated with a sequence in a particular view are now (as of Jalview 2.3) associated with the same sequence in all views. This means that when 'Colour by Sequence' is selected in the structure view, the colour will be updated to the colours given in the view with the current input focus.

Multiple Views were introduced in Jalview 2.2