// 
// S-LIBSHUFF: A program for pairwise comparison of sequence libraries.
// Version 1.22, released on May 17, 2006
// Copyright (C) 2003, 2004, 2005, 2006 Bret Larget and Patrick D. Schloss 
//
// 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 2 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, write to the Free Software
// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
//
// This distribution contains the following files.
//
//   COPYING --- the GNU General Public Licence
//   makefile --- file useful for easy compilation of the software
//   README --- this file
//   s-libshuff.C --- the source code
//
// INSTALLATION
//
// Linux users with GNU gcc can compile the program by typing:
//
//   make
//
// at the prompt.  Others may need to edit the makefile.
//
// RUNNING THE PROGRAM
//
//  Usage: s-libshuff [-s1 seedOne] [-s2 seedTwo] [-n numPermutations] [-d] [-z size] [-e numFamilyPermutations] <file>
//  Options:
//  -s1: first seed for random number generator, any positive integer (default is 1234).
//  -s2: second seed for random number generator, any positive integer (default is 5678).
//  -n: number of permutations for each permutation test (default is 10000).
//  -d: use the discrete approximation for calculation (default is integral form).
//  -z: size of increment for discrete calculation (only used if -d set; default is 0.01).
//  -l: lower triangular distance matrix (default is a square matrix).
//  -e: number of complete permutations to estimate family-wise error rate (default is 0).
//  <file> is a symmetric distance matrix as produced by PHYLIP.
//
// VERSION HISTORY
//
// Version 1.22
//   outputs delCxy values
//	 Released May 16, 2006
// Version 1.21
//	 supports lower-triangular mega3 formatted distance matrices
//	 Released April 22, 2005
// Version 1.2
// 	 corrected a small bug that has gone largely undetected that behaves poorly when numGroups > 9
// 	 added output file feature that contains coverage values for input distance matrix
// 	 released initial version of manual
// 	 Released November 5, 2004
// Version 1.1
// 	 added ability to use lower triangular matrix for input file
// 	 Released May 25, 2004
// Version 1.0
//   fixed error in sCalculate (forgetting j!=i)
//   changed the output format
// Version 0.2
//   Released January 16, 2003
// Version 0.1 written by Bret Larget and Patrick D. Schloss
//   Released January 9, 2003
// Version 0.0 written by Bret Larget and Patrick D. Schloss
//   Released December 28, 2003