- MegAlign – After performing a multiple alignment, select a portion of the consensus sequence in the Worktable and use Align > Create Alignment From Selection. After choosing a name for the new project, the subalignment is opened in a new MegAlign project window.
- MegAlign Pro – After performing a multiple alignment, display a Consensus track and select a portion of the consensus sequence in the Sequence view. Then use Align > Realign Subsequences. Choose the desired alignment type and parameters, then press Align. The results are shown in the current MegAlign Pro project rather than in a new project window. For more information, see the MegAlign Pro User Guide topic Subalign sequences.
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