-nodisplay

Run Jalview without User Interface. (automatically disables questionnaire, version and usage stats checks)

-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

-tree FILE

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

-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.