LICENSE.txt

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 pytbeaglehon/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 license occurs below the line of +++++ characters below.


++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


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  To do so, attach the following notices to the program.  It is safest
to attach them to the start of each source file to most effectively
state the exclusion of warranty; and each file should have at least
the "copyright" line and a pointer to where the full notice is found.

    <one line to give the program's name and a brief idea of what it does.>
    Copyright (C) <year>  <name of author>

    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.

    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with this program.  If not, see <http://www.gnu.org/licenses/>.

Also add information on how to contact you by electronic and paper mail.

  If the program does terminal interaction, make it output a short
notice like this when it starts in an interactive mode:

    <program>  Copyright (C) <year>  <name of author>
    This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
    This is free software, and you are welcome to redistribute it
    under certain conditions; type `show c' for details.

The hypothetical commands `show w' and `show c' should show the appropriate
parts of the General Public License.  Of course, your program's commands
might be different; for a GUI interface, you would use an "about box".

  You should also get your employer (if you work as a programmer) or school,
if any, to sign a "copyright disclaimer" for the program, if necessary.
For more information on this, and how to apply and follow the GNU GPL, see
<http://www.gnu.org/licenses/>.

  The GNU General Public License does not permit incorporating your program
into proprietary programs.  If your program is a subroutine library, you
may consider it more useful to permit linking proprietary applications with
the library.  If this is what you want to do, use the GNU Lesser General
Public License instead of this License.  But first, please read
<http://www.gnu.org/philosophy/why-not-lgpl.html>.