polyphony_Ete2_tree.py
==========

    Polyphony. Python code for the analysis of protein structure ensembles.
    
    Copyright (C) 2013  William R. Pitt

    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/>.

No module named MySQLdb
Usage: Calculate dendrogram (tree) of structures based upon clustering by provided property. Plot tree using Ete2 module and write out Newick format file. REQUIRES Ete2

Options:
  -h, --help            show this help message and exit
  -f FILE, --file=FILE  name of a fasta file created with create_fasta_file.py
  -p PROPERTY, --property=PROPERTY
                        type of property to calculate, can be [backbone|sidech
                        ain|phipsi|bfactor|sequence|calphas|crystal_contacts|p
                        ockets|distance1000]
  -u, --update          use this option if you want to recalculate property
                        data