Jalview Command Line Arguments

-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

-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