Some of the code is from publically available source by Paul Lewis, Ziheng Yang, 
John Huelsenbeck, David Swofford , and others  (as noted in the code).
In fact the main structure of the program was created by modifying Paul Lewis' 
basiccmdline.cpp from his NCL

Other code is: Copyright (C) 2008 Mark T. Holder

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/>.