To access options affecting the display of multiple alignments in the Sequences view, click on the Style panel expand bar entitled Multiple Alignment, or choose View > Style > Multiple Alignment.
Task | How To |
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Designate the sequence you want to compare the other sequences to | From the Compare to drop-down menu, choose Consensus or any of the aligned sequences by name. This menu is disabled until you have performed an alignment. |
Specify the wrapping style for rows | Use the Layout drop-down menu. Choose between:
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Specify how to color the sequences and the consensus to facilitate visual comparisons | Use the Alignment coloring drop-down menu to s. Sequence comparisons can only be performed with aligned sequences. Choose between:
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Specify the color of sequence characters | Use the Foreground color tools to the right of . To display the letters in a single solid color of your choice, check the upper box. Then click on the ‘A’ tool to the right of the checkbox and choose a color from the color picker. To instead choose a preset color scheme, check the lower box and make a selection from the drop-down menu. Color scheme choices are described in Available color schemes. |
Specify the background color (boxes around each letter) | Use the Background color tools to the right of . To use a single solid color of your choice, check the upper box. Then click on the ‘highlighter pen’ tool to the right of the checkbox and choose a color from the color picker. To instead choose a preset color scheme, check the lower box and make a selection from the drop-down menu (see image in row above). Color scheme choices are described in Available color schemes. |
Specify the background color for gaps | Use the Background color for gaps tool to the right of .To use a single solid color of your choice, check the box next to Solid. Then click on the ‘highlighter pen’ tool to the right of the checkbox and choose a color from the color picker. If you do not wish to use a background color for gaps, check the Default box. |
Specify a font style for residues that differ from the reference | To display a specialized font, check the box next to Differences from reference and then choose B for bold, I for italic, and/or U for underline. Multiple selections can be made, if desired. Note that the font style display can be used alone, or in addition to text color and background color options described above. If you do not wish to use a specific font for differences from the reference, leave the box unchecked. |
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