The following table describes ways to modify an initial multiple alignment:

Task See this topic
To realign a range of aligned sequences using different parameters or a different alignment engine Subalign sequences
To merge two existing completed alignments together Merge two existing alignments (“Profile alignment”)
To 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 Merge unaligned sequences into an existing alignment
To realign existing aligned sequences PLUS selected unaligned sequences Align selected unaligned sequences with an existing alignment

The following video illustrates some of these modification procedures:

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