RNA Helices Colouring

An RNA alignment loaded from a Stockholm file can be coloured based on its helices. The helices are determined from the secondary structure line in the Stockholm file (#GC SS_cons) written in WUSS notation that specifies base pairing. See Wikipedia or Jalview RNA Support Blog for more information about Stockholm files and WUSS notation.

Select "Colour" " By RNA Helices" to colour the alignment by RNA helices.