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
|
-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
|