- Redo alignment. The original alignment will be realigned if this
checkbox is checked. Otherwise, the original alignment is kept in
its original form except for possible extra equally sized gaps in
all sequences of the original alignment. This is visualized in
Figure 19.5: The top figures shows the original alignment. In the bottom panel a single sequence with four inserted X's are aligned to the original alignment. This introduces gaps in all sequences of the original alignment. All other positions in the original alignment are fixed.
This feature is useful if you wish to add extra sequences to an existing alignment, in which case you just select the alignment and the extra sequences and choose not to redo the alignment.
It is also useful if you have created an alignment where the gaps are not placed correctly. In this case, you can realign the alignment with different gap cost parameters.