This program has been developped and tested on Linux (Ubuntu 10.04)
with g++ (4.4.3) and relies on the GNU scientific library (1.13) for
random number generation.  To compile this code you need the gsl
installed on your computer (check by typing "gsl-config --version").

Unzip and move into the "src" subdirectory. Then, compile the program
using the commands:

make clean 
make

This will create a binary executable with name "treemm" in the "bin"
subdirectory.

Move to the "test" subdirectory to try the program with the dataset
that served in our publication using the command line:

../bin/treemm -seq ./prom_60-40_n3242.seq -tree ./hclust_treecens.dat -nmotifs 20 -lmaxbox1 20 -lmaxbox2 10 -niter 100000 -nheur 25000

The input data files that we used in our publication can be found in
this subdirectory.