The algorithms are implemented in:

    Src/acharnement.py

Given a newick tree, simply run: python fitchAndCompany <alg> tree.newick
where <alg> can be: 1=Fitch  2=Sankoff  3=one structure  4=two structures

Different tools in Src/
    frnakenstein_generator.py       -Generates by-stable sequences for pair of structures using frnakenstein tool
    incubator.py                    -Given a seed, target structures a tree, a mutation rate and a transition matrix,
                                     populates a tree evolving from the seed
    data_generator.py               -Executes incubator.py
    run_fitchAndCompany.py          -Executes fitchAndCompany.py
    make_rfam_tree.py               -Generates the tree to input to fitchAndCompany given BioData/
    analysis.py                     -Generates the graphs given the output of fitchAndCompany.py


The frnakenstein program is only re-distributed and under a GNU LGPL licence
in the frnakenstein.tgz tarball. 
See frnakenstein.py for the licence.