Multiple Alignment section

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
Designate the sequence to consider as the “reference”	From the Reference 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: Linear – All information for a sequence appears on a single row with no line breaks. A horizontal scrollbar is provided. Automatic wrapping – The alignment is wrapped to fit within the view. Wrapping adjusts automatically if the view’s width changes. Fixed wrapping – The alignment is wrapped at the specified number of residues. Enter a number in the Size box to wrap after a different number of residues. Vertical splits are not available in either type of wrapped view. However, any existing splits are restored if wrapping is turned off.
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: Color all residues – All residues appear in the color schemes chosen in Foreground color (dark ‘T’ icon) and Background color (white ‘T’ icon; see row below). Color only differences from reference – Only residues that differ from the consensus are colored. Color only matches to reference – Only residues that are identical to the reference sequence specified above are colored. Show only differences from reference – Only residues that differ from the consensus are displayed and colored. All other residues are shown as uncolored dashes. If you chose this option, you should select the reference sequence from the Reference drop-down menu. The reference can be the consensus or any of the aligned sequences. Choose either Color only conserved residues or Color only non-conserved residues to color according to whether or not residues are conserved. A residue is “conserved” if all sequences have the same residue in that column. Otherwise, it is “non-conserved.” If you prefer to ignore gaps when determining whether or not a residue is “conserved,” check the box next to Ignore gaps. The Ignore gaps checkbox is only enabled if you selected Color only conserved/non-conserved residues above.
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.

*Note: Once you set up styles, you can save them and apply them to future projects, either by default or when you specify.