COPYRIGHT

pytbeaglthon phylogenetic likelihood caluclations using beaglelib.

With the exception of some code written by others (see below). The code is
  Copyright (C) 2010-2011
  Mark Holder, 
  Department of Ecology and Evolutionary Biology,
  The University of Kansas.
  mtholder@gmail.com


Code by others
==============
Code by others (all in the C-code in the cPhyProb/ccore directory)
C-Extension were written by adapting Alex Martelli's example code in the 
  Python Cookbook Section 17.1

Among-site rate variation code based on code from the PAML package:
Yang, Z.  2007.  PAML 4: a program package for phylogenetic analysis by 
  maximum likelihood.  Molecular Biology and Evolution 24: 1586-1591 
  (http://abacus.gene.ucl.ac.uk/software/paml.html)

Eigensystem code from MrBayes 3.2 Copyright 2002-2007
  John P. Huelsenbeck
  Fredrik Ronquist
  Paul van der Mark
updated from the CVS Repository: mrbayes from the root:
:pserver:anonymous@mrbayes.cvs.sourceforge.net:/cvsroot/mrbayes
on 2007-Oct-05
Some of that code was written (or translated from FORTRAN) by:
  David Swofford 

pytbeaglehon is only useful if you have a library installed that fulfills the 
beaglelib API for likelihood computations (
see http://code.google.com/p/beagle-lib/ ). pytbeaglehon links to your copy
of beaglelib, but does not contain code from beagle.


The code in pytbeaglehon written by Mark Holder is licensed under the 
GNU public license version 3.0 (this is because MrBayes is released under this 
license).  The full license can be found in the LICENSE.txt.