Compute Variants

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.

To compute variants against the consensus sequence:

1. Remove a specified reference sequence (if one exists) by selecting it in a view and choosing Sequences > Stop Using as Reference.

2. Perform an alignment using the Align > (Re)Align Using > (algorithm name) command for the algorithm you want to use.

3. Click Compute Variants in the Variants view or choose Variants > Compute Variants. Results are displayed in the Variants view.

To compute variants against a reference sequence:

1. 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.

2. 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.

3. Click Compute Variants in the Variants view or choose Variants > Compute Variants. Results are displayed in the Variants view.

*Note: If Mauve was chosen as the alignment method in either procedure above, variants are computed only for the currently-selected block. Each time you select a different block, you may choose to compute its variants, if they haven’t already been computed.