[Jalview-discuss] exporting sequence alignments from jalview

[James Procter]

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!
Jim.

maudsleyst at 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
> 
>  
> 
>  
> 


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J. B. Procter  (ENFIN/VAMSAS)  Barton Bioinformatics Research Group
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