The Jalview Executable's Command Line Arguments

See running Jalview from the command line for more information.
-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
Set the colourscheme for the alignment. This can be any of the built-in colourschemes, a name of a predefined colourscheme (defined in the Jalview properties file), or an 'inline' colourscheme (see the applet's colour parameter for more information).
-annotations FILE/URL
Add precalculated annotations to the alignment. See Annotation File description.
-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