Aligning alignments

If you have selected an existing alignment in the first step (19.1), you have to decide how this alignment should be treated.

Image alignmentwithorwoinsert 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.