[Jalview-discuss] obtaining conservation data using command line

[Rachel.Hawken at csiro.au]

Hi,
I am a new user to Jalview.
I would like to pull out the conservation information from a multiple sequence alignment using the command line.
I have installed Jalview via the java webstart.

when I use the command line arguments:
-open cfos.fasta -nodisplay -jalview out.txt
I get an application error.  'unable to launch application' and these details:

InvalidArgumentException[ Invalid arguments supplied: {out.txt, http://www.jalview.org/webstart/jalview.jnlp }]
 at com.sun.javaws.Main.launchApp(Unknown Source)
 at com.sun.javaws.Main.continueInSecureThread(Unknown Source)
 at com.sun.javaws.Main$1.run(Unknown Source)
 at java.lang.Thread.run(Unknown Source)

How can I use the command line version of jalview to create the jalview output containing conservation
information without manually running jalview and exporting?

thanks for your help.

cheers
Rachel