Please see also ftp://ftp.ebi.ac.uk/pub/software/clustalw2/README HOWTO COMPILE THE SOURCE AND INSTALL ---------------------------------------------------------------------- You will need a Unix environment with a working C++ compiler and the Qt developer kit (>=version 4.3) to compile the ClustalX source. For compilation under Windows you will also need to install mingw and cygwin. Type $ qmake and then $ make This will create the clustalX binary. HOWTO INSTALL AFTER COMPILATION ---------------------------------------------------------------------- Put colprot.xml, coldna.xml, colprint.xml, clustalx.hlp and clustalX[.exe] into one folder. Add a link to the binary to your Desktop for example. On Linux you can use the installer script.