Once you have downloaded and unpacked the apat.tar.gz source code, read the instructions in the file INSTALL. You need to install the GD library and a number of Perl packages before you can use APAT.
Installation of APAT itself is straightforward. Simply run the install.pl script. This will prompt you for the full path to your Perl executable and ask if you wish to install a web-based version. It will then ask for information about the directories into which various components should be installed.