-nodisplay

Run Jalview without User Interface. (automatically disables questionnaire, version and usage stats checks)

-props FILE/URL

Use the given Jalview properties file instead of users default.

-features FILE/URL

Use the given file to add sequence features to an alignment. See Features File (Known as Groups file prior to 2.08) description.

-colour COLOURSCHEME

-annotations FILE/URL

-tree FILE/URL

Load the given newick format tree file onto the alignment

-questionnaire URL

Queries the given URL for information about any Jalview user questionnaires

-noquestionnaire

Turn off questionnaire check

-nonews

Disable check for Jalview news on startup (not recommended other than for classroom / demo usage)

-nousagestats

Turn off google analytics usage tracking

-[no]sortbytree

Enable or disable automatic sorting of associated view when a new tree is displayed

-dasserver nickname=URL

Add and enable a DAS server with given nickname (alphanumeric or underscores only) for retrieval of features for all alignments
Sources that also support the sequence command may be specified by prepending the URL with 'sequence:'
e.g. sequence:http://localdas.somewhere.org/das/source

-fetchfrom nickname

Query a DAS source called nickname for features for the alignments and display them

-groovy FILE/URL

Execute groovy script in FILE (where FILE may be 'STDIN' to read from the standard input) after all other arguments have been processed

-jabaws URL

Specify the URL of the preferred JABAWS server

-vdoc VAMSAS DOCUMENT FILE/URL

Import the given vamsas document into a new session.
New in 2.5

-vsess VAMSAS SESSION URL

Join the given vamsas session
If a document was also specified, this will be imported first and then committed as new data from Jalview to the specified session (Experimental - not yet enabled!).New in 2.5

-fasta FILE

Create alignment file FILE in Fasta format.

-clustal FILE

Create alignment file FILE in Clustal format.

-msf FILE

Create alignment file FILE in MSF format.

-pileup FILE

Create alignment file FILE in Pileup format.

-pir FILE

Create alignment file FILE in PIR format.

-pfam FILE

Create alignment file FILE in PFAM format.

-blc FILE

Create alignment file FILE in BLC format.

-json FILE

Create alignment file FILE in JSON format.

-jalview FILE

Create alignment file FILE in Jalview format.

-png FILE

Create PNG image FILE from alignment.

-imgMap FILE

Create HTML file FILE with image map of PNG image.

-eps FILE

Create EPS file FILE from alignment.

-svg FILE

Create Scalable Vector Graphics file FILE from alignment.

-biojsMSA FILE

Write an HTML page to display the alignment with the BioJS MSAviewer MSA