The NEAT software is based on the NeuroEvolution of Augmenting Topologies
method of evolving artificial neural networks, by Stanley and
Miikkulainen (2001).  A paper describing the method and some associated
findings is available:

@TechReport{stanley:utcstr01,
  author       = "Kenneth Stanley and Risto
                  Miikkulainen",
  title        = "Evolving Neural Networks through Augmenting Topologies",
  institution  = UTCS,
  year         = 2001,
  number       = "AI2001-290",
  url          = "http://www.cs.utexas.edu/users/nn/pages/publications/abstracts.html#stanley.utcstr01.ps.gz",
  bibauthor    = "kstanley",
}

Also, see:
http://www.cs.utexas.edu/users/nn/pages/research/ne-methods.html#NEAT

Detailed documentation of this software is included in the
postscript file NEATDOC.ps.  Reading this documentation is
highly recommended before attempting to use the system.
The text file USERDOC includes a brief description of every file 
included in this distribution.

This program is free software; you can redistribute it and/or modify it
under the terms of the GNU General Public License version 2 as published
by the Free Software Foundation. This program is distributed in the hope
that it will be useful, but without any warranty; without even the
implied warranty of merchantability or fitness for a particular purpose.
See the GNU General Public License for more details.

We hope that this software will be a useful starting point for your own
explorations in Neuroevolution. The software is provided as is,
however, we will do our best to maintain it and accommodate
suggestions. If you want to be notified of future releases of the
software or have questions, comments, bug reports or suggestions, send
email to kstanley@cs.utexas.edu.