How to draw boxes, arrows, etc. on multiple alignments?

[Peter Frank]

In journal articles I saw multiple sequence alignments which were
heavily "annotated" with text and symbols like boxes and arrows. It
was more than what is possible with software like GeneDoc.

I tried to draw such things with Word's drawing tools on the multiple
sequence alignments that I copied from GeneDoc to Word in metafile
format but it didn't work. The drawings from Word's tools always cover
everything below.

So, can anyone recommend a drawing tool for drawing simple objects on
and around multiple sequence alignments?

Peter
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