Jalview Documentation
Jalview (2009) is a fast Java multiple alignment editor and analysis tool. It features many of the functions of AMAS, for the analysis of sub-families and the prediction of functional sites, but is fully interactive. (View the Jalview homepage at www.jalview.org).

If you use Jalview in your work, please cite the Jalview 2 paper in Bioinformatics:

Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M., Barton, G.J (2009),
"Jalview version 2: A Multiple Sequence Alignment and Analysis Workbench,"
Bioinformatics 25 (9) 1189-1191 doi: 10.1093/bioinformatics/btp033