MegAlign Pro provides the option to specify a reference sequence and then use it to guide a MAFFT alignment or act as the comparison sequence for variant analysis. By default, the reference sequence is displayed as a track in the Overview and/or Sequences view headers. The sequence name is shown in bold blue font.

To show/hide this reference sequence, check or uncheck the Reference boxes in the Tracks panel. Checking the box will not do anything unless you have already specified a reference sequence.

To change Reference options:

These options let you change the font style and color for the reference sequence’s name in the Sequences view and Overview.

  • To control bolding and italicization, check the Text box and use the B and/or I buttons. Uncheck the box if you want to use normal font.
  • To control the font color, check the Color box and click on the A to open the color picker. Uncheck the box if you want the font color to be black.

You can also add white space above and/or below the reference track using sliders in the Layout section.

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