Download zip Select Archive Format
Name Last Update history
File dir Src Loading commit data...
File txt README Loading commit data...
File txt frnakenstein.tgz Loading commit data...

README

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.