Aligning alignments

The Redo alignment option becomes available when an alignment is provided as input to the tool (figure 24.1).

A new alignment is output, whether or not Redo alignment option is checked.

Image alignmentwithorwoinsert Figure 24.5: The original alignment is shown at the top. That alignment and a single additional sequence, with four Xs added for illustrative purposes, were used as input to Create Alignment. The "Redo alignment" option was left unchecked. The resulting alignment is shown at the bottom. Gaps have been added, compared to the original alignment, to accommodate the new sequence. All other positions are aligned as they were in the original alignment.