Jalview has been used for several years on many websites as a visualization tool for database search results or alignment algorithms, as well as being part of several training courses.
The following links are to projects which are actively using new features in Jalview version 2+. If you would like to add your project to the list, send a message to the usual address.

MACSIMS is a multiple alignment-based information management system that combines the advantages of both knowledge-based and ab initio sequence analysis methods.
The MACSIMS project helped to develop the input and display of sequence features in Jalview in order to display large datasets with many sequence features.

Thompson, J. D., Muller, A., Waterhouse, A. Procter, J., Barton, G. J., Plewniak, F. and Poch, O. (2006)
"MACSIMS: Multiple Alignment of Complete Sequences Information Management System",
BMC Bioinformatics.   [PubMed] [FullText] [PDF], 7, 318.

 HOMERB Homer (HOmology ModellER) is a comparative modelling server developed by Silvio Tosatto at The Biocomputing GRUP, CRIBI Biotechnology Centre, University of Padua, Italy.
The Jalview applet is used for inputting alignments to the system and to visualise predicted features on strutures and alignments.

MAFFT MAFFT is a program for the multiple alignment of nucleic acid or protein sequences developed by Kazutaka Katoh at the Bioinformatics Center, Institute for Chemical Research, Kyoto University Uji, Japan. The full Jalview application uses MAFFT running as a web service from Dundee and Katoh uses the applet with a unique user colour scheme for colouring residues.

is a database for structural alignments for proteins with non-trivial relationships being developed by Antonina Andreeva, Andreas Prlic, Tim Hubbard, Alexey Murzin at the MRC-LMB Cambridge.

Thanks to Franck Valentin for installing the Jalview applet for visualising the output of the Clustal and Muscle multiple sequence alignments at the EBI, Hinxton, Cambridge.

PFAM made extensive use of Jalview 1+, having great input on early development and continue to use the Jalview applet on the PFAM website for visualising protein families. Thanks to Benjamin Schuster-Böckler at the Wellcome Trust Sanger Institute for implementing the Stockholm parser to make this possible.

MyHits is a web based protein sequence and DNA analysis environment. It allows a user to perform motif, profile and remote homology searches on locally hosted or external databases. Results are stored in the user's own Myhits databases and can be analysed, annotated and visualized using standard bioinformatics tools. A modified version of the Jalview 2 applet is provided in Myhits for visualization and figure generation of alignments and trees.

Selectome is a database of positive selection in coding sequences. It uses the codon model branch-site from CodeML (PAML package of Ziheng Yang) to infer sites exhibiting positive selection in different lineages of vertebrate evolution. Phylogenetic data is provided by the TreeFam database. Visualization of selected sites in the protein alignment is done using the annotation feature of the Jalview 2 applet.

The ALS Online Database (ALSOD) provides both the scientific community and general public with up-to-date information on Superoxide Dismutase 1 (SOD1) associated amyotrophic lateral sclerosis (ALS). The Jalview 2 applet is used for viewing multiple alignments of the mutations collected in ALSOD.