To perform a multiple alignment:
- MegAlign – Select the sequences to align and use Align > By Jotun Hein Method, Align > By Clustal V Method, or Align > By Clustal W Method. To change parameters prior to alignment, use Align > Method Parameters, choose the tab of interest and make changes, then press the Now button.
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To edit a multiple alignment, select a portion of sequence in the Worktable and use the Straighten Columns (![]()
), Shuffle Right (![]()
) or Shuffle Left (![]()
) tools.
- MegAlign Pro – Select the sequences to align and use Align > Align Using Clustal Omega, Align > Align Using Clustal W, Align > Align Using MAFFT, or Align > Align Using MUSCLE. Alternatively, press the Align tool (
![]()
) and choose the option of the same name. To change alignment options, instead use Align > Align with Options or press the Align tool and choose the option of the same name. Select the desired method using the drop-down menu, then edit the settings and press Align. For more information, see the MegAlign Pro User Guide topic Perform an initial multiple alignment.
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The following brief video is an overview of multiple alignment in MegAlign Pro.
Additional videos highlighting multiple alignment functionality in MegAlign Pro include: Merging and realigning sequences, Aligning genomes using Mauve and Aligning multi-segment files.
), Shuffle Right (
) or Shuffle Left (
) tools. 
) and choose the option of the same name. To change alignment options, instead use Align > Align with Options or press the Align tool and choose the option of the same name. Select the desired method using the drop-down menu, then edit the settings and press Align. For more information, see the MegAlign Pro User Guide topic 
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