We've posted an update with some features that should make it easier to use the Alignment Tool with multiple templates.

Sequences are now split into two groups, the "working sequences", which you can realign and thread from, essentially as sequences did before. In addition, it is now possible to move sequences in and out
of your "reserve sequences". Reserve sequences are template sequences that are stored outside of the alignment you are working on so you can focus on one (or a few) template(s) at a time. Reserve sequences show up at the bottom of the alignment tool window.

Use the red arrows on the left of each working sequence to move it to the reserve sequences. Use the single green arrow in the bottom left to move a reserve sequence into the working sequences, or the green and red arrow in the bottom left to make a reserve sequence the only working sequence. Use the blue arrows above the reserve sequences to look through them.

The information displayed to the right of each sequence can now be toggled between the alignment score and the name of each sequence, using the button in the top right.

When threading from an alignment, any time a good threading is found, it will be taken and copied over to your protein. Threading will continue looking for better threadings, but you can stop it at any
time, and undo to previous threadings. Threading will still stop on its own when it is done trying threadings.

You can highlight and select sequences on the 3D structure as well as the 2D sequence.

The sequence alignment levels have been moved to be earlier.