Jalview comes in two distinct flavours.

The main application allows connection to multiple web services provided at the University of Dundee as well as a host of additional useful features such as printing, making images from your alignment and annotating your alignment. You need to download and install this software.

The applet version runs in web browsers and is a useful interactive display for precalculated alignments, features and annotations files. It does not have the full functionality of the main application, such as making images, saving files, running web service jobs due to security restrictions imposed on applets.

For more information on how to use the applet in your website, see full list of applet parameters.

Pressing one of the buttons below will load up JalviewLite, a cut down version of Jalview, which runs within your web browser.

Ferredoxins, chloroplast precursor related UniRef50 cluster
(15 sequences x 150 residues)

User Defined Colours, loads an associated Newick format tree file which is used to sort the alignment, and group consensus and sequence logos are shown below the alignment.


Displays a features file on the alignment


Associates PDB file 1GAQ with sequence FER1_MAIZE


Displays a Multiple Sequence Alignment Based JNet Prediction for a Sequence


For more JalviewLite examples, follow the links below.