Please see also ftp://ftp.ebi.ac.uk/pub/software/clustalw2/README and http://www.clustal.org/ HOWTO COMPILE THE SOURCE AND INSTALL ---------------------------------------------------------------------- You will need a Unix environment with a working C++ compiler to compile the ClustalW source. We recommened GCC>=4.2. ICC users need to configure the package as follows: ./configure CXX=icpc For compilation under Windows you will probably need to install mingw and cygwin. Type $ ./configure $ make This will create a clustalw binary in the src directory. To install the software type $ make install (might have to be executed as superuser) or simply copy the clustalw binary to a directory of your choice.