The COaLA model is implemented in the Bio++ libraries. COaLA can be employed to perform Maximum Likelihood inferences with the c++ programs (bppML, bppAncestor...) belonging to the bppSuite package, depending on the Bio++ libraries.

You have two options: either using binaries for the different programs (bppML, bppAncestor...) of the bppSuite package or install Bio++ libraries and compile the bppSuite programs with these libraries. The address to obtain the binaries is indicated below. If you choose the second option, which should allow you to have the updated version of both the libraries and the model, you first need to download and install the Bio++ libraries and then to download and install the bppSuite package.

Bio++ libraries

The main page of the Bio++ libraries is here:

http://biopp.univ-montp2.fr/

You can find all information you need to download and install the libraries here:

http://biopp.univ-montp2.fr/wiki/index.php/Installation

You can either download the stable version of the libraries (Latest Release) or the development version. COaLA is currently implemented in the Development version only, but should appear soon on the stable version, once Bio++ 2.1 is released.

BppSuite

Information on how to download and install this package is available here:

http://biopp.univ-montp2.fr/wiki/index.php/BppSuite

If you installed the development version of Bio++ (i.e. with git), the corresponding version of BppSuite is available through subversion:

http://gna.org/svn/?group=bppsuite

If you installed the stable version of Bio++, the corresponding version of BppSuite can be downloaded from here:

http://home.gna.org/bppsuite/#availability

With this address, you can also have access to the binaries of the bppSuite programs that have been pre-compiled with the stable version of Bio++.