This error:

configure.in:14: error: possibly undefined macro: AC_PROG_LIBTOOL
If this token and others are legitimate, please use m4_pattern_allow.
See the Autoconf documentation.
autoreconf: /usr/bin/autoconf failed with exit status: 1

Occurs on Debian when attempting to automake a source program, to fix this we need to install libtool by running:

apt-get install libtool

Now re-run that automake or autogen.sh and it should work fine