The Jalview Executable's Command Line Arguments

See running Jalview from the command line for more information.

Jalview processes arguments on the command line sequentially. If you would like to pass a 'JVL' file containing memory settings or any other launch parameters, then include it at the beginning of the command line to ensure they are processed before any remaining arguments.
Typical command line execution follows the following pattern: 
  jalview -open <Alignment File/URL> [additional import arguments] [export arguments]
-nodisplay
Run Jalview without User Interface. (automatically disables questionnaire, version and usage stats checks)
-nowebservicediscovery
Do not query configured servers to discover web services (Since 2.11.2.0)
-open FILE/URL
Specify the alignment file to open or process by providing additional arguments.
-props FILE/URL
Use the given Jalview properties file instead of users default.
-setprop PROPERTY=value
(JalviewJS ONLY) sets the given property to the given value
-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.
-no-annotation
 Do not display annotation below the alignment.
-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
-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
-jvmmempc=PERCENT
Only available with standalone executable jar or jalview.bin.Launcher. Limit maximum heap size (memory) to PERCENT% of total physical memory detected. This defaults to 90 if total physical memory can be detected. See Memory usage settings for Jalview for more details.
-jvmmemmax=MAXMEMORY
Only available with standalone executable jar or jalview.bin.Launcher. Limit maximum heap size (memory) to MAXMEMORY. MAXMEMORY can be specified in bytes, kilobytes(k), megabytes(m), gigabytes(g) or if you're lucky enough, terabytes(t). This defaults to 32g if total physical memory can be detected, or to 8g if total physical memory cannot be detected. See Memory usage settings for Jalview for more details.