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. |
-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. |
-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. |