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The algorithms are implemented in:


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/       -Generates by-stable sequences for pair of structures using frnakenstein tool                    -Given a seed, target structures a tree, a mutation rate and a transition matrix,
                                     populates a tree evolving from the seed               -Executes          -Executes               -Generates the tree to input to fitchAndCompany given BioData/                     -Generates the graphs given the output of

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