Clustalw and ncbi come with their own readme files after you unzip/untar them. You can read these, or just do the following quick start for unix: Clustalw is compiled by unpacking it, then in the clustalw directory simply type make clean make (sorry, I left old redhat8 .o files in there that need to be removed, which is why you need to "make clean" first) PSI-BLAST is compiled on unix by unpacking it then typing ./ncbi/make/makedis.csh This will give you formatdb and blastpgp (psi-blast). It takes quite a long time to compile. formatdb and blastpgp are created in ncbi/build/. You need to use formatdb to format the nr database because PSI-BLAST requires this on all its databases. There is a README.formatdb in the ncbi/doc/ directory. Unzip the nr database then do ncbi/build/formatdb -i nr -p T -o T Then finally Prof is compiled according to its readme file at http://www.aber.ac.uk/compsci/Research/bio/dss/prof/Readme Make a directory "Prof" and unzip and untar Prof into this directory. cd Prof/src make gcc trimmer10.c -o trimmer10 and then set the environment variables as described in that Readme.