Hello,
this is my problem:

I used a jalview batch to incorporate jalview into an alignment program.
I put some parameters as -colour, and -png to safe the resulting file as
image.
All is ok except in the png files there is a superimposition of some
letters and numbers at the beginning of the images, as if the images were
not large enough to display correctly.
I can't find a way to set up some parameters to try to have images with
different dimensions.
To save in svg doesn't change the result.

If I use jalview desktop and I save the box as png image all is ok, not
superimposition, but i can't use it because I need to include jalview into
my code.

Any suggestion to set some parameters ?

I attached an image as example.  As you can see numbers in the left side
are not display correctly.

Thanks.

Alessandra

Attachment: Align7
Description: Binary data

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