How to cite Jalview

  • 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

Jalview provides a large range of methods for multiple alignment, conservation analysis and prediction via JABAWS. If you use any of these, please 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 Bioinformatcis: Protein Disorder, Conservation and RNA Secondary Structure. Bioinformatics doi:10.1093/bioinformatics/bty045

as appropriate, if you use any of these methods (Don’t forget to cite the individual methods as well!)

  • Procter, JB, Carstairs, GM, Soares, B, MourĂ£o, 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, In: Multiple Sequence Alignment (book - Ed: Kazutaka Katoh), p203-224, Humana, NY, NY.
  • 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
  • Clamp M, Cuff J, Searle SM, Barton GJ (2004) The Jalview Java alignment editor. Bioinformatics 20: 426-427. doi:10.1093/bioinformatics/btg430

Papers that cite the Jalview Version 2 paper:

Papers that cite the Jalview Version 1 paper: