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

Frank Küster frank at kuesterei.ch
Wed Jun 18 13:57:22 EST 2003

peter_frankde at yahoo.de (Peter Frank) schrieb:

> 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?

I never used it myself (but I'm using LaTeX frequently), but there is a
LaTeX package called texshade which can do stuff like that, see 


There is also an on-line implementation, but I fear to get everything
out ouf it (e.g. arbitrary text and arrows at arbitrary places) you
would have to use it locally and add some pstricks/pdftricks stuff.

Bye, Frank
sigmentation fault

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