[Jalview-discuss] Help with displaying a large number of alignments

Yu Jin NG Alvin (IMCB) yjng at imcb.a-star.edu.sg
Fri Jan 18 01:27:08 GMT 2013

Dear Jalview members,

I was wondering if someone can tell me how to script/program jalview so that I can display a large number of alignments (~1k) from a fasta file and export it in a png (example attached) file with certain display preferences.
I require the alignment to be

1)      Colored by percentage identity

2)      Wrapped at around 50 residues

3)      Not have any annotation

4)      Have a scale above

5)      Remove the left scale

6)      Be species ordered

7)      Exported to a png file
I'm able to set preference for 1), 2), 3) for the first 100 I've done so that it makes it a little faster for me.

Any help/suggestions or a quick reference to the java functions? Would be much appreciated.

Thank you,
Alvin NG
BV lab

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