select a part of the alignment to realign | right-click the selection | Realign selection
This will open Step 2 in the "Create alignment" dialog, allowing you to set the parameters for the realignment (see Create alignment parameters).
It is possible for an alignment to become shorter or longer as a result of the realignment of a region. This is because gaps may have to be inserted in, or deleted from, the sequences not selected for realignment. This will only occur for entire columns of gaps in these sequences, ensuring that their relative alignment is unchanged.
Realigning a selection is a very powerful tool for editing alignments in several situations:
- Removing changes. If you change the alignment in a specific region by hand, you may end up being unhappy with the result. In this case you may of course undo your edits, but another option is to select the region and realign it.
- Adjusting the number of gaps. If you have a region in an alignment which has too many gaps in your opinion, you can select the region and realign it. By choosing a relatively high gap cost you will be able to reduce the number of gaps.
- Combine with fixpoints. If you have an alignment where two residues are not aligned, but you know that they should have been. You can now set an alignment fixpoint on each of the two residues, select the region and realign it using the fixpoints. Now, the two residues are aligned with each other and everything in the selected region around them is adjusted to accommodate this change.