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.

  • Use the Layout drop-down menu to specify the wrapping style for rows in the Sequences view. 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.

  • Use the Comparison drop-down menu to specify how to color the sequences and the consensus to facilitate visual comparisons. Sequence comparisons can only be performed with aligned sequences. Choose between:

    • None – All residues appear in the color schemes chosen in Color foreground and Color background (see row above).

    • Color only differences from reference – Only residues that differ from the consensus are colored. 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.

    • Color only matches to reference – Only residues that are identical to the consensus are colored. 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.

    • 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.

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