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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