There are currently four third-party libraries that are being used by CERT. They are listed below with links to information and downloads. The listed versions are the only only ones that have been used to build and test CERT. Other versions may work, but would probably require changes to the project (e.g. header and library search paths) and might require changes to the code. Some of these libraries are only needed if CERT is built from source. Precompiled CERT libraries or applications may not require all third-party libraries

Boost (pre-built):
Download the boost exe installer and run it.
General information: http://boost.org
Download page: http://www.boost-consulting.com/download.html
Versions: 1.33.1
License: Boost Software License
You can also build custom for your system by compiling the code.
The CERT code uses the boost_filesystem, boost_serialization and boost_thread libraries. If using Visual Studio, install to the default directory or you will need to configure the Visual Studio project files to point to the directory you choose.

FFTW (pre-built):
General information: http://www.fftw.org
Versions: 3.1.1
License: GPL
Windows information and the download link: http://www.fftw.org/install/windows.html
Make sure to read the README-WINDOWS file for exporting the library to work with Visual Studio. 

LibXML (pre-built):
General information: http://xmlsoft.org/
Pre-built Window's libraries: http://www.zlatkovic.com/libxml.en.html
Versions: 2.6.24
License: MIT License
Additional libraries may also need to be installed (e.g. iconv and zlib). The web page with the pre-built libraries has more details.

cBlas:
General information: http://math-atlas.sourceforge.net/
Pre-built Window's libraries: https://sourceforge.net/project/showfiles.php?group_id=23725
Versions: 3.6.0
License: BSD
The Atlas project builds optimized Blas libraries with a C interface. Atlas also has downloadable binaries, although they may not be optimum for any given system.
Alternatively, the Intel Math Kernel Library also provides a cBlas interface.
The Visual studio projects are configured for the intel math kernel library. In order to use Atlas instead of the MKL, in the project configurations: (1) remove the INTELMKL symbol from the preprocessor symbols, (2) replace the mkl_c.lib library with the appropriate Atlas .lib files, and (3) replace the intel include paths with the Atlas library and include paths.

If the SOBI post processing step is being used, then the libraries produced by the ATLAS build are not sufficient. They don't contain a full implementation of the LAPACK interfaces. There are two methods to get around this. One is to not use ATLAS and instead just build the LAPACK libraries which include a default implementation of BLAS.  This won't be optimized but is much more straightforward than alternative two. Which is to first install and build ATLAS, then install and build LAPACK using the optimized ATLAS BLAS libraries, then rebuild ATLAS with the LAPACK libraries. That should give a full LAPACK implementation along with the ATLAS optimizations.

Folder layout:
$ ls
ATLAS         Documentation  WinNT_P4SSE2  featuredetector  mp_auCoder
CERT2_VS2005  MLR            aligneyes     fftw-3.1.1-dll   mptslidingwindow
CERTWrapper   Misc           eyefinder     libxml

$ ls CERT2_VS2005
CERT2_VS2005      CERT2_VS2005.sln  CERTDemo    TestImages
CERT2_VS2005.ncb  CERT2_VS2005.suo  ReadMe.txt  debug

$ ls CERT2_VS2005/debug
CERT2_VS2005.dll  CERT2_VS2005.lib  CERTDemo.exp  CERTDemo.pdb   libfftw3-3.dll
CERT2_VS2005.exp  CERT2_VS2005.pdb  CERTDemo.ilk  NewTestImages  libxml2.dll
CERT2_VS2005.ilk  CERTDemo.exe      CERTDemo.lib  iconv.dll      zlib1.dll

In addition the Boost library (headers and libraries) is installed at either C:\Program Files\boost or C:\Boost