After performing an assembly, MegAlign Pro can calculate variants between other sequences and the currently-specified reference sequence, or between all sequences and the consensus. For instance, you might download an annotated reference sequence that you found online and use this workflow to compare your own sequences to it.
- Remove a specified reference sequence (if one exists) by selecting it in a view and choosing Sequences > Stop Using as Reference.
- Perform an alignment using the Align > (Re)Align Using > (algorithm name) command for the algorithm you want to use.
- Click Compute Variants in the Variants view or choose Variants > Compute Variants. Results are displayed in the Variants view.
- Perform any type of alignment using the Align > (Re)Align Using > (algorithm name) command. If you are running a MAFFT alignment, you can optionally specify a reference sequence during setup to guide the alignment. However, this is not necessary for later variant computation.
- If you have not already done so, specify a reference sequence. If you ran a MAFFT alignment using a reference, note that you can choose a different reference in this step for use in variant analysis.
By default, the reference sequence is displayed in bold blue italics to differentiate it from the other sequences.
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