h1. BUSS 

* Beast/Beagle utility for sequence simulation*

h1. LICENSE

  This is free software; you can redistribute it and/or modify
  it under the terms of the GNU Lesser General Public License as
  published by the Free Software Foundation; either version 2
  of the License, or (at your option) any later version.
 
   This software 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 Lesser General Public License":http://www.gnu.org/licenses/lgpl.html for more details.
   
h1. PURPOSE

Fast & furious sequence simulator in Beast/Beagle.  

h1. CITING

  To cite BUSS in publications, please use:
         
          AAA
         
        A BibTeX entry for LaTeX users:
         
          article{
            author = {},
            title = {},
          }
   
h1. TODO

* PIBUSS bug with newick import (Importer line 199 read method). Does not happen if first char is newline
* boolean switch for real/log scales for the parameters of lognormal clock model 
* parser for output type should be case insensitive
* fix simulation-inference XML problem when using codons
* output type not updated after loading bussdata
* tree/taxa not set in Partitions table after loading bussdata
* simulating indels  
* command line interface
  - complex argument for partitions 
