**************************************************
	SIMULATIONS WITH REAL DATA
**************************************************

1. The folders are

        models/
        data/
        scripts/

        Folder contents:

        1. models/ folder contains the model files. clust.sh loads the
           modules from the cluster and calls a runall script. The
           runall script then performs the cross-validation
           experiment. The paths for the software are set in the
           runall file. Make sure that you set the right path for
           GMTK, Matlab, and PSIBLAST's PSSM files.

        2. data/ folder contains the datasets and other data files
           that are needed for the experiments.

        3. scripts/ folder contains the most of the scripts that are
           called during the experiments.


**************************************************
	SIMULATIONS WITH SYNTHETIC DATA
**************************************************

1. submit_grid_into_cluster.sh is a top level script that submits the
   jobs to the cluster


2. The folders are

        models/
        data/
        scripts/

        Folder contents:

        1. models/ folder contains the model files. The
           submit_grid_into_cluster.sh calls the clust.sh under the
           models folder. clust.sh loads the modules from the cluster
           and calls a runall script. The runall script then performs
           the synthetic data simulations. The paths for the software
           are set in the runall file. Make sure that you set the
           right paths for GMTK, Matlab, and PSIBLAST's PSSM files.

        2. data/ folder contains the datasets and other data files
           that are needed for the experiments.

        3. scripts/ folder contains the most of the scripts that are
           called during the experiments.