exporting sequence alignments from jalview

Dear Stuart.

many thanks for your email. The Jalview applet on the MAFFT website
allows you to pass your alignment to the Jalview application by using
the 'File->View in full application' menu option. If this doesn't appear
to work, then you probably need to modify your browser's security
settings to specifically allow popups from align.bmr.kyushu-u.ac.jp, and
then try the menu option again. If all goes well, you should see a
splashscreen appear indicating that Jalview is starting up (initially it
will probably be a window with a progress bar and a label saying
something like 'downloading The Jalview Application from www.jalview.org').

I've just tried this myself, and it seems to work. However, I noticed
that there is a serious bug with the colourscheme import. Your alignment
will probably be coloured a rather sickly shade of green, rather than
the more informative colours chosen by the MAFFT server. I'll try and
post the URL of a colourscheme that you can load onto the alignment that
recreates the original MAFFT colouring.

I hope this helps!

maudsleyst@mail.nih.gov wrote:


Dear Sir/Madam,

                         I have created several sequence alignments
using the MAFFT v.6 website at Kyushu university, however using jalview
to inspect them I am unable to export the sequence alignment to any
other application to view them, e.g. powerpoint or even a printer. What
is the best way to export these visual analyses.

Any help with this would be greatly appreciated.

Best regards,

Stuart Maudsley

J. B. Procter (ENFIN/VAMSAS) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.