Jalview is a free program for multiple sequence alignment editing, visualization and analysis. You can use it to view and edit sequence alignments, analyze them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation.
v2.8 [Nov 13, 2012]
-Improved JABAWS client and new JABAWS 2.0 Services:
- AACon alignment conservation
-Protein disorder - DisEMBL, RONN, GlobPlot and IUPred
-Clustal Omega for creating huge protein alignments
-Support for RNA:
-Import sequence and alignment associated WUSS or VIENNA dot-bracket notation from files and the RFAM database
-Interactive editing of RNA secondary structure annotation
-Colour scheme for purine/pyrimidine and to highlight RNA helices
-RNA canonical base pair consensus score and sequence logo
-Embedded VARNA RNA secondary structure viewer in the Desktop
