TreeFix
http://compbio.mit.edu/treefix/
Yi-Chieh Wu, with libraries contributed from Matthew Rasmussen

=============================================================================
DEPENDENCIES

TreeFix has the following requirements:

- Python (2.5.4) -- http://python.org/
- GCC compiler (4.1.2) -- http://gcc.gnu.org/
- SWIG (1.3.29) -- http://www.swig.org/

The following programs are optional:
- Numpy (1.5.1) -- http://www.numpy.org/
  If Numpy is not found, the program uses Python's built-in 'random' module.
- Scipy (0.7.1) -- http://www.scipy.org/
  If Scipy is not found, the program uses internal libraries to approximate
  the normal distribution (so p-values may be slightly off).

Additionally, Python modules are required for computing (1) p-values for likelihood
equivalence and (2) reconciliation costs.  We have provided default modules
that compute (1) the p-value based on the Shimodaira-Hasegawa (SH) test statistic with
RAxML site-wise likelihoods and (2) the duplication-loss cost using maximum parsimony
reconciliation (MPR).  For other modules, see the website.

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INSTALL

Run

python setup.py build
python setup.py install

If you don't have permission to install software on your system, you can install
into another directory using the --prefix or --home flags to setup.py.

For example
::
python setup.py install --prefix=/home/username/python
or
python setup.py install --home=~
::

If you didn't install in the standard bin directory
you will need to set your PATH variable to the alternate location.

If you didn't install in the standard Python site-packages directory
you will need to set your PYTHONPATH variable to the alternate location.
See http://docs.python.org/inst/search-path.html for further details.

