Versions of Jalview released before November 2012 did not include any special support for scoring or visualizing nucleotide sequences, although they could read, write and manipulate DNA and RNA sequences, and calculate a consensus.
Version 2.8 of Jalview was the first release to include special support for nucleic acid sequences, and included a substitution matrix that copes with both RNA and DNA symbols which can be used to calculate trees and principal component analysis plots from alignments. Nucleotide base pair patterns provided as WUSS or VIENNA dot-bracket annotation can also be visualised, and used to calculate base-pair consensus score and sequence logos. Version 2.8 of the Jalview Desktop also included VARNA for interactive exploration of 2D RNA structure. For the latest information about nucleic acid support, see the nucleic acid section of Jalview's help pages.