install freebayes

install bamtools
sudo apt-get install cmake
wget http://clavius.bc.edu/~erik/freebayes/freebayes-5d5b8ac0.tar.gz
tar xzvf freebayes-5d5b8ac0.tar.gz
cd freebayes
make

Now that freebayes is built, we can run it:

bin/freebayes        # default summary
bin/freebayes -h     # verbose help text, summary of options