-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

-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.