Fixpoints are added to sequences or alignments before clicking "Create alignment". To add a fixpoint, open the sequence or alignment and:
Select the region you want to use as a fixpoint | right-click the selection | Set alignment fixpoint here
This will add an annotation labeled "Fixpoint" to the sequence (see figure 20.6). Use this procedure to add fixpoints to the other sequence(s) that should be forced to align to each other.
When you click "Create alignment" and go to Step 2, check Use fixpoints in order to force the alignment algorithm to align the fixpoints in the selected sequences to each other.
In figure 20.7 the result of an alignment using fixpoints is illustrated.
Figure 20.7: Realigning using fixpoints. In the top view, fixpoints have been added to two of the sequences. In the view below, the alignment has been realigned using the fixpoints. The three top sequences are very similar, and therefore they follow the one sequence (number two from the top) that has a fixpoint.
You can add multiple fixpoints, e.g. adding two fixpoints to the sequences that are aligned will force their first fixpoints to be aligned to each other, and their second fixpoints will also be aligned to each other.