Advanced use of fixpoints

Fixpoints with the same names will be aligned to each other, which gives the opportunity for great control over the alignment process. It is only necessary to change any fixpoint names in very special cases.

One example would be three sequences A, B, and C where sequences A and B has one copy of a domain while sequence C has two copies of the domain. You can now force sequence A to align to the first copy and sequence B to align to the second copy of the domains in sequence C. This is done by inserting fixpoints in sequence C for each domain, and naming them 'fp1' and 'fp2' (for example). Now, you can insert a fixpoint in each of sequences A and B, naming them 'fp1' and 'fp2', respectively. Now, when aligning the three sequences using fixpoints, sequence A will align to the first copy of the domain in sequence C, while sequence B would align to the second copy of the domain in sequence C.

You can name fixpoints by:

        right-click the Fixpoint annotation | Edit Annotation () | type the name in the 'Name' field