Automake is a tool for automatically generating Makefile.ins from files called Makefile.am. Each Makefile.am is basically a series of make variable definitions1, with rules being thrown in occasionally. The generated Makefile.ins are compliant with the GNU Makefile standards.
The typical Automake input file is simply a series of variable definitions. Each such file is processed to create a Makefile.in. There should generally be one Makefile.am per directory of a project.