The user needs to provide

• color for each feature: if a feature names 'cds' is to be shown in pure red color then the line #color cds 255 0 0 should be entered in the input box. Each feature color is given on a different line. For instance, for an alignment of proteins in which two domains 'dom1', 'dom2' are being highlighted in blue and green, the user might want to start with the following:
  #color dom1 0 0 255
  #color dom2 0 255 0
  
• location of features: if dom1 stretches from amino acid 20 to amino acid 42 of protein protA, then it would be represented by the line protA 20:42:dom1. All the features of a sequence are written on a single line seperated by commas.
  #color dom1 0 0 255
  #color dom2 0 255 0
  protA 20:42:dom1,60:80:dom2
  protB 50:70:dom2
  

Yes. Start the line with #.

The color code is a r(red), g(green), b(blue) triplet in which each of the components can be set to a number between 0 and 255 (inclusive). Lower values lead to dark colors and higher values to lighter colors. Here are some useful combinations:

• (0,0,0) black
• (255,255,255) white
• (255,0,0) red
• (0,255,0) green
• (0,0,255) blue

If features are going to overlap, the user needs to specify the priority of each feature. The color of the feature with the highest priority will be used to color the region common to the overlapping features. The priority can be specified on the color line. In the following example, the color and priority of coding regions and repeats is being assigned. The priority is the last number in the color line. It has to be an integer greater than 1 (1 is used internally in the program). In this case, if part of a coding region is also part of a repeat, it will still be displayed in blue because the cds feature has a higher priority.