To perform a pairwise alignment:

  • MegAlign – Select two sequences in the Worktable and use Align > One Pair > Wilbur and Lipman, Align > One Pair > Martinez-NW, Align > One Pair > Lipman-Pearson, or Align > One Pair > DotPlot. In the ensuing dialog, make any desired changes to alignment parameters.

  • MegAlign Pro – Select two sequences any view and use Align > Pairwise or press the Align tool () and select Align Pairwise. In both cases, a dialog opens in which you can select the desired alignment type (Local: Smith-Waterman, Global: Needleman-Wunsch or Semi-Global: Needleman-Wunsch) and make any changes to alignment parameters. For details, see the MegAlign Pro User Guide topic Perform a Pairwise Alignment.

    The following brief video is an overview of pairwise alignment in MegAlign Pro.

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