A Makefile is a good solution when you are always going to build and run your software on the same system, and things like glibc and gcc versions and the available library versions are known. However, most software need to be built and run in a variety of systems.
The GNU build system, or autotools, is a set of tools whose aim is to create a Makefile for your software in a variety of systems. It's made up of three main tools:
autoconf: This parses the contents of aconfigure.acfile that describes the source code to be built and creates aconfigurescript. This script will then be used to generate the finalMakefile.automake: This parses the contents of aMakefile.amfile and converts it into aMakefile.infile. This is then used by theconfigurescript generated earlier to obtain aconfig.statusscript that gets automatically executed to obtain the finalMakefile.libtools: This manages the creation of both static and dynamic libraries.