[Jalview-discuss] Jalview command line

Julien Roux julien.roux at unil.ch
Mon Feb 7 14:31:03 GMT 2011

Dear Jalview team,
I'm new to this mailing list, please excuse me if my question has 
already been answered previously.

I am trying to create a jalview file (.jar) including an amino-acid 
alignment, the associated tree and some annotations.
To do this, I want to use the command line. I tried:

java -Djava.ext.dirs=/Applications/Jalview/lib -cp 
/Applications/Jalview/Jalview.jar jalview.bin.Jalview -open my_aln.fas 
-colour ZAPPO -annotations my_annot.jalview -tree my_tree.nwk -jalview 

This works fine and creates the test.jar file correctly. However, when I 
add the -nodisplay option to do this without User Interface, the file 
test.jar does not include the associated tree. Is this a bug or I am 
doing something wrong?

I also have 2 other questions:
- Is it possible to include (again using the command line) the 
nucleotide alignment that corresponds to the AA alignement? I have it in 
a separate fasta file.
- Is it possible to export a .html file including the alignment and the 
tree and annotations associated? From what I have seen, it seems that 
Jalview only exports the AA alignement + annotations. Also, is it 
possible to wrap the alignement using the command line?

Thanks a lot for your help.

Julien Roux, PhD
Keller group, Department of Ecology and Evolution
Biophore, University of Lausanne, 1015 Lausanne, Switzerland
tel: +41 21 692 4182    fax: +41 21 692 4165

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