You can export sequences and alignments to classic MegAlign, where you may realign using a different method, perform bootstrapping, or view alignment reports.

Timing Command Notes
Before performing an alignment File > Send Sequences to MegAlign Creates and opens a new MegAlign project containing the same sequences and sequence order as in the MegAlign Pro project.
After performing an alignment File > Send Aligned Sequences to MegAlign Sequences retain their MegAlign Pro alignment.
After performing an alignment and selecting a portion of the consensus File > Send Aligned Subsequences to MegAlign Sequences retain their MegAlign Pro alignment.
After performing a Mauve alignment and selecting an alignment block in the Overview File > Send Active Block to MegAlign Exports only the sequences in the active block.

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