Download the applet jar file from here. Parameters are described below, and the javascript API is described here.

Useful to know!!

  • Package all your data files into a single (or multiple) zip / jar files. This is very useful to reduce download time of large data files. The applet archive tag can take multiple entries separated by commas, eg
    <applet code="jalview.bin.JalviewLite" archive="jalviewApplet.jar,">
  • Use Jalview for input to a HTML form. For an example of how to code this using Javascript, click here.
  • Embed Jalview into the web page, without the "Start Jalview" button by setting the embed parameter to true;
    <param name="embedded" value="true">

**NEW FEATURES** in Jalview 2.5

  • New parameters to control display of tree annotation, width of alignment columns, and to disable the jalview button and check for Jmol on startup.

**NEW FEATURES** in Jalview 2.4

  • New applet API methods for feature display control, views, and obtaining current selection via javascript.
  • Group show and hide parameters: "showfeaturegroups" and "hidefeaturegroups". Both take a list of feature group names (separarated by "|" by default) to hide or show on the displayed alignment.
  • Regular expressions can be used in URL links for sequence IDs.
  • "debug" parameter to control verbosity of the applet's console output.
  • "showbutton" parameter to disable launch button and open JalviewLite immediatly.
  • "nojmol" parameter to disable check for Jmol classes.

**NEW FEATURES** in Jalview 2.3

  • Note that Parameter "PDBFile" now takes the PDB file followed by a space separated list of alignment sequence ids to associate the structure to. It is also possible to associate multiple PDB files by adding an incremental value to PDBFile (up to 10). It is also possible to map specific sequences to specific chains by using the following notation:

    <param name="PDBFile" value="First.pdb SeqA SeqB SeqC">

    <param name="PDBFile2" value="Second.pdb A=SeqA B=SeqB C=SeqC">
    <param name="PDBFile3" value="Third.pdb D=SeqX B=SeqY C=SeqZ">
  • Note parameter "PDBSeq" is no longer required.
  • To use Jmol as the structure viewer for Jalview, you must include the jar file in the applet archive argument thus:
  • Jmol 11.0.2 is not Java 1.1 compatible, and requires at least Java 1.4 plugin in the clients web browser. If the client does not have Java 1.4, or if the Jmol-11.0.2.jar is not added to the archive, the original Jalview structure viewer will still be available.
  • Jalview 2.3 currently works only with Jmol 11.0.2, and it is recommended that you use the Jmol jar file located here


**NEW FEATURES** in Jalview 2.1
  • Jalview Applet can read and display JNet secondary structure annotation directly via the jnetfile parameter.
  • Param UserDefinedColour - specify your own colours for each residue using a semi colon separated list. Multiple residues can be assigned the same colour using commas. eg:
    <param name="userDefinedColour" value="D,E=red; K,R,H=0022FF; C=yellow">
  • Param showFeatureSettings - this will display the feature settings window when the applet starts.
  • Param Application_URL value=""
    This calls a servlet which creates a JNLP file with the alignment file, annotations file and features file of the applet as arguments. If the user has Java installed, the returned JNLP file should start up the full Jalview Application. BUT this does not currently work for alignment files added to the applet in a zip file.
  • Alignment file can be a series of parameters using eg PFAM format
    <param name="sequence1" value="Q93XJ9_SOLTU/11-26 TSFLPRKPVVTSLKAI">
    <param name="sequence2" value="FER1_PEA/14-29 TSFLRTQPMPMSVTTT">
    (All the usual Jalview File formats are valid, however each new line in an alignment file must be entered as a parameter)
<param name="" value=""> Description
file fileName The file to open, must be on same server as the applet.
sequence in (preferably) PFAM or Fasta format The alignment can be added as a series of sequences instead of from a file.
tree fileName Tree file in Newick format
features fileName Jalview Features file to be applied to the alignment
annotations fileName Jalview Annotation file will be added to the alignment
jnetfile fileName Secondary structure predictions from a Jnet Concise file will be added to the first sequence in the alignment.

fileName seq1 seq2 seq3


fileName A=seq1 B=seq2 C=seq3

PDB file which is to be associated with a sequence, followed by space separated list of alignment sequence ids. PDB chains can be specifed to map to particular sequence by using A=SeqA notation

*Not needed post Jalview 2.3, use PDBFile instead

SequenceId The sequence to associate a PDB file with. Note the value is case sensitive.
defaultColour One of:
Clustal, Blosum62, % Identity, Hydrophobic, Zappo, Taylor, Helix Propensity, Strand Propensity, Turn Propensity, Buried Index, Nucleotide
Default is no colour.

D,E=red; K,R,H=0022FF; c=yellow

Define residue colours
showFullId true or false if true displays start and end residue at the end of sequence Id.
showAnnotation true or false If true shows the annotation panel below the alignment.
showConservation true or false Default is true.
showQuality true or false Default is true.
showConsensus true or false Default is true.
sortBy Id , Pairwise Identity, or Length Sorts the alignment on startup
RGB colour as hex string Background colour for applet button - purely cosmetic to blend in with your web page. For orange, enter the value FF6600
embedded true or false The applet is embedded in the web page, the "Start Jalview" button is not displayed.
windowWidth value frame width
windowHeight value frame height
label label text Change text for the Launch Jalview Button
wrap true or false Opens new windows in wrapped mode
linkLabel_1 Uniprot

Right click on sequence id to see list of available links. Any new links MUST have $SEQUENCE_ID$ as part of the linkURL_n value. For multiple links, increment the label and url name by 1. ie
<param name="linkLabel_2" ...,
<param name="linkUrl_2"....

Regular expressions may also be used (since Jalview 2.4) to process the ID string inserted into the URL:
$SEQUENCE_ID=/<regex to extract ID>/=$
Use the debug flag to check parsing and make sure that special symbols are properly escaped (particularly when generating applet tags from CGI scripts).
Regex URL links are also applied to the description line (since Jalview 2.4.+).


showFeatureSettings true or false Shows the feature settings window when starting the applet
showfeaturegroups separator separated list of feature groups Display the features in the given groups on the alignment
hidefeaturegroups separator separated list of feature groups Hide the features in the given groups on the alignment (will be overridden by showfeaturegroups for group names found in both lists)

URL of dynamic JNLP servlet,

Launches full application with original alignment, features and annotations files used in applet
separator non-empty separator string
default: |
string used to separate fields in list parameters (such as showfeaturegroups)
debug true Instruct the applet to output additional debug messages to the java console
nojmol false When set, do not try to find Jmol classes. Set this to supress URL not found errors appearing in server logs when Jmol is not available.
showbutton true Show the jalview button on the page. When false, JalviewLite will open immediately.
sortByTree true or false (default is false) automatically sort the associated alignment view by the tree when a new tree is opened.
showTreeBootstrapstrue or false (default is true)show or hide branch bootstraps
showTreeDistancestrue or false (default is true)show or hide branch lengths
showUnlinkedTreeNodestrue or false (default is false)indicate if unassociated nodes should be highlighted in the tree view
heightScale 1.0 or greater Adjust the height of each cell in the alignment grid relative to the height of a character in the alignment font.
widthScale 1.0 or greater Adjust the width of each cell in the alignment grid relative to the width of a character in the alignment font.