Sara-Coffee benchmark package

This package includes the following files and directories:

Folders:
BraliDARTS - Contains the different sequence sets.
PDBdir     - Conains all PDB files necessary.
PDBfix     - Contains the secondary structure information.
scripts    - Contains the script to run the benchmark

Files:
README                 - This README file
runBenchmark.sh        - Executing this file startes the benchmark process.
methods.txt            - File with a command line for each method to run.
TEMPLATEFILE           - File used by SARA-Coffee to link sequences and structures
TEMPLATEFILE_BESTPAIR  - File used by Best-Pair to link sequences and structures

----- Running the benchmark -----

The benchmark can be started using the runBenchmark script. All methods given
in the methods.txt script will be executed. The results are written into:

3SP.out    - Including all the 3SP scores for each cluster and for each method. On the bottom there will be a matrix showing the pairwise comparisons        
NiRMSD.out - Including all the NiRMSD scores for each cluster and for each method. On the bottom there will be a matrix showing the pairwise comparisons
OutDir     - Foder that will contain all alignments after the benchmark is run