The alignment view includes the options of showing a Gap Fraction Graph, providing a graphical overview of the parts of the alignment that include gaps.

The fraction score is calculated as a percentage of the total sequences in the alignment, and the amount of gaps in a given area can be shown as a gradient of colors and/or as a graph below the sequence.

The user options are

• Foreground color: Colors the letter using a gradient, where the left side color is used if there are relatively few gaps, and the right side color is used if there are relatively many gaps.
  
• Background color: Sets a background color of the residues using a gradient in the same way as described above.
  
• Graph: Displays the gap fraction as a graph at the bottom of the alignment.
  • Height
  • Type (Line plot/Bar plot/Color bar)
  • Color