Realign selection

If you have created an alignment, it is possible to realign a part of it, leaving the rest of the alignment unchanged:

        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: