Peer reviewed publications

If you use Jalview 2 in your work, please cite Waterhouse et al. 
(2009). 
To cite an analysis performed with JABAWS, please use Troshin et al. 
(2011).

Troshin PV, Procter JB, Barton GJ (2011) Java bioinformatics analysis
web services for multiple sequence alignment--JABAWS:MSA.
Bioinformatics 27: 2001-2002.
http://bioinformatics.oxfordjournals.org/content/27/14/2001

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.
http://bioinformatics.oxfordjournals.org/content/25/9/1189

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.
http://www.biomedcentral.com/1471-2105/7/318

Clamp M, Cuff J, Searle SM, Barton GJ (2004) The Jalview Java
alignment editor. Bioinformatics 20: 426-427.
http://bioinformatics.oxfordjournals.org/content/20/3/426

Take a look at the citations for the Jalview 2 paper in PubMedCentral:
http://www.ncbi.nlm.nih.gov/pubmed?linkname=pubmed_pubmed_citedin&from_uid=19151095