The Jalview Executable's Command Line Arguments
See running Jalview from the command line for more information.-nodisplay |
Run Jalview without User Interface. |
-props FILE |
Use the given Jalview properties file instead
of users default. |
-features FILE |
Use the given file to add sequence features to an alignment. See Features File (Known as Groups file prior to 2.08) description. |
-annotations FILE
|
Add precalculated annotations to the alignment. See Annotation File description. |
-nodisplay
|
Run Jalview without User Interface
|
-props FILE
|
Use the given Jalview properties file instead
of users default
|
-tree FILE
|
Load the given newick format tree file onto
the alignment
|
-features FILE
|
Use the given file to mark features on the
alignment
|
-questionnaire URL
|
Queries the given URL for information about
any Jalview user questionnaires
|
-noquestionnaire
|
Turn off questionnaire check
|
-nousagestats
|
Turn off google analytics usage tracking
|
-dasserver nickname=URL
|
Add and enable a das server with given
nickname (alphanumeric or underscores only) for retrieval of features
for all alignments
|
-fetchfrom nickname
|
Query nickname for features for the alignments
and display them
|
-groovy FILE
|
Execute groovy script in FILE (where FILE may be 'STDIN' to read from the standard input) after all other
arguments have been processed
|
-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. |
-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. |