T-Coffee is distributed as precompiled binaries for Linux and Mac OSX platforms (32-bit or 64-bit) with a guided install procedure. All results presented have been reported using a 64-bit pre-compiled version. This is the smoothest and quickest way to install T-Coffee on a local machine, since it comes with all required components and does not need any special user privilege. The default installation does not require any root privilege.
chmod +x T-COFFEE_installer_<version_xxx>.bin
Mac OS X
No T-Coffee pre-compiled installer is available for the Windows operating system. Windows users need to compile and install it using the source distribution package as described below. An easier alternative is to install a Linux guest on your Windows workstation using any virtualization tool (VMware, VirtualBox, etc) and to run the linux installer on this virtual machine. Most flavors of Linux should work, Fedora, Debian, and Ubuntu being the most thoroughly tested. It is also possible to compile the source code under the Cygwin environment although this procedure is now totally unsupported.
Compilation from source
For advanced installation (e.g. in shared environment, computation cluster, etc) it is suggested to use the T-Coffee source distribution package and compile it on your target system. It will require the GNU development tools (gcc, g77 or gfortran, make), the Perl interpreter and CPAN. You will also need the root user privileges and an Internet connection.