Note: This topic is not applicable to BAM-based projects.
Within the Alignment View, you may adjust small regions of sequence alignment. This function is useful where gaps may have been misplaced; in regions where one or more component sequences have G or C compression problems; or where you introduced gaps into some sequences manually and want to try to improve the alignment. For best results, the selected region should be under 30 bases
To adjust a sequence alignment:
1) Open the contig of interest in the Alignment View.
2) Highlight the consensus sequence for the region of the alignment you want to realign.
3) Select Edit > Adjust Alignment. This applies a special algorithm designed to optimize small regions of alignment.
4) To revert to the previous alignment, select Edit > Undo.
Note: To align sequences manually, use the Banana tool from the Alignment View toolbar.