EMBOSS

http://emboss.sourceforge.net/download/

wget ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.6.0.tar.gz
tar -xzf EMBOSS-6.6.0.tar.gz
cd EMBOSS-6.6.0/
./configure --prefix=`pwd` --without-x
make && make install

http://emboss.sourceforge.net/apps/cvs/emboss/apps/fuzznuc.html

fuzznuc -complement -rformat gff