I have successfully built clustalx directly from source 
(ftp://ftp.ebi.ac.uk/pub/software/clustalw2/2.0.12/clustalx-2.0.12.tar.gz) 
using ubuntu karmic. 
I have installed the following packages in order to build it: qt4-dev-tools; 
build-essential; qt4-qmake.

I don't really know what the debian patches do, but are they still
required?

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Package heavily out of date
https://bugs.launchpad.net/bugs/423648
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