Autotools is a collection of tools used to generate Makefiles from configure scripts. The key tools are autoscan, autoheader, automake, autoconf, libtoolize, and autoreconf. These tools take various inputs like the source code and configure.ac and generate outputs like config.h, Makefile, and configure scripts. The generated Makefiles can then be used by make to build libraries, executables, and install targets. Autotools helps manage conditional compilation and platform-specific configurations.