so, get the NCBI toolkit and unpack it in , for example, /var/tmp. I have /var/tmp/ncbi. I put mpiBLAST in /opt/mpiBLAST and from that dir I do $ ./configure --with-ncbi=/var/tmp/ncbi --prefix=/usr/local/mpiblast This should build the config with a knowledge of the location of the NCBI files. $ make $ make -n install (to see what it will do without actually doing it) $ make install Steve Pittard | http://catalina.bimcore.emory.edu (HOME PAGE) Emory University | wsp@emory.edu, wsp@bimcore.emory.edu (INTERNET) BIMCORE Support | 404 727 0038