Jalview related publications include both ‘canonical’ papers and work describing services and methodologies related to Jalview.
If you use Jalview then please cite the most recent canonical paper:
Waterhouse AM, Procter JB, Martin DMA, Clamp M, Barton GJ (2009) Jalview Version 2 - A multiple sequence alignment editor and analysis workbench. Bioinformatics 25 1189-1191. (doi:10.1093/bioinformatics/btp033)
Citing alignment and analysis services
Jalview’s range of methods for multiple alignment, conservation analysis and prediction are provided by JABAWS. If you use any of these, please remember to copy and paste the method’s citation from the Jalview webservices window, and also cite:
Troshin PV, Procter JB, Barton GJ (2011) Java bioinformatics analysis web services for multiple sequence alignment–JABAWS:MSA. Bioinformatics 27 2001-2002. ( doi:10.1093/bioinformatics/btr304)
Troshin PV, Procter JB, Sherstnev A, Barton DL, Madeira F, Barton GJ (2018) JABAWS 2.2 Distributed Web Services for Bioinformatics: Protein Disorder, Conservation and RNA Secondary Structure. Bioinformatics 34 1939–1940. (doi:10.1093/bioinformatics/bty045)
Other Jalview related publications
Procter JB, Carstairs GM, Soares B, Mourão K, Ofoegbu T, Barton D, Lui L, Menard A, Sherstnev N, Roldan-Martinez D, Duce, S, Martin DMA, Barton GJ, (2021), Alignment of biological sequences with Jalview
This is an open access ‘Methods in Molecular Biology’ paper included in the book Multiple Sequence Alignment edited by Kazutaka Katoh as part of the series published by Humana, NY, USA.
Thompson JD, Muller A, Waterhouse A, Procter J, Barton GJ, et al. (2006) MACSIMS: multiple alignment of complete sequences information management system. BMC Bioinformatics 7: 318. ( doi:10.1186/1471-2105-7-318)