Does Jalview work with nucleotide sequences and alignments?

Yes. All versions of Jalview after 2.8 (released Nov 2012) include special support for nucleic acid sequences, and employ a substitution matrix that copes with both RNA and DNA symbols 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 includedVARNA 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.