Dear Andrew,
I’m glad you are finding jalview useful in your studies. I’m not sure which particular site you are referring to when you say the Jalview applet embedded in T-Coffee. Jalview is used on many sites as an applet including alignment methods at EBI and elsewhere. If you join and reply to the jalview-discuss@jalview.org mailing list then someone should be able to help you more.
Kind regards,
Geoff
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Geoff Barton, Professor of Bioinformatics, College of Life Sciences
University of Dundee, Scotland, UK. [g.j.barton@dundee.ac.uk](mailto:g.j.barton@dundee.ac.uk)
Tel:+44 1382 385860/388731 (Fax:385764) [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk)
The University of Dundee is registered Scottish charity: No.SC015096
Hi all,
I think that Andrew is referring to the T-Coffee web server http://tcoffee.crg.cat in which I’ve recently added Jalview as an option to display the alignment produced by T-Coffee.
To render the applet in a similar way we do in our web server, you can use the following applet definition:
The alignment to be showed have to specified using the parameter “file”.
You can find the explanation for all the available applet parameters at this page: http://www.jalview.org/examples/appletParameters.html
Regarding the second part of your question, frankly I haven’t understood which is your goal.
Cheers,
Paolo
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Geoff Barton, Professor of Bioinformatics, College of Life Sciences
University of Dundee, Scotland, UK. [g.j.barton@dundee.ac.uk](mailto:g.j.barton@dundee.ac.uk)
Tel:+44 1382 385860/388731 (Fax:385764) [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk/)
The University of Dundee is registered Scottish charity: No.SC015096