Yes. MegAlign Pro supports multiple ways to modify an alignment. You can:

• Trim ends at the beginning or end of an alignment.
• Realign a range of aligned sequences using different parameters or a different alignment engine.
• Merge two existing completed alignments together.
• Add all/selected sequences from the “Unaligned Sequences” area into the current alignment, while retaining all of the gaps of the original, pre-merge alignment.
• Realign existing aligned sequences plus selected unaligned sequences

MegAlign Pro provides extensive variant analysis capabilities for viral, mitochondrial, and chloroplast genomes. To analyze variants, first specify a reference sequence, either before or after alignment. Then choose Variants > Compute Variants.  Details about the variants in your alignment,  including position, feature, impact, and translation changes, can be analyzed and evaluated in the Variants view.

MegAlign Pro features three pairwise sequence alignment tools:

• Local Pairwise Alignment is designed specifically to find the highest scoring aligned segments of two sequences, even if the full extent of the two is not included in the final alignment.
• Global Pairwise Alignment doesn’t try to find the best scoring segment, but instead requires that the full extent of both sequences be included in their results. There is no requirement or guarantee that the best scoring pair of aligned segments from a local alignment will be aligned in a global alignment.
• Semi-Global Pairwise Alignment is a relatively new approach that is particularly suitable when the two sequences differ greatly in length. When that happens, the longer sequence will have overhangs on either end of the alignment. Since overhangs are represented with gaps, a global aligner will attempt to increase the match score and minimize accumulated gap penalties by aligning parts of the shorter sequence to overhanging sequence region(s). This effect can produce a number of unrealistic, usually small aligned segments spaced by gaps near the ends of the alignment. Semi-global alignment is designed to address this problem by not penalizing gaps in overhangs (aka “end gaps”).