// DOTUR: A program for calculating discriptive statistics for sequence libraries.
// Version 1.3, released on March 3, 2005
// Copyright (C) 2005 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.
//
//   LICENSE --- the GNU General Public License
//   README --- this file
//   dotur.C, otu.h, richness.h --- the source code
//
// INSTALLATION
//
// Linux users with GNU gcc can compile the program by typing:
//
//   g++ dotur.C -O4 -o dotur
//
// at the prompt.
//
// RUNNING THE PROGRAM
//	  See the manual available online.
//
// VERSION HISTORY
//
// Version 1.0
//    Released May 25, 2004
// Version 1.1
// 	  Released July 19, 2004
//	  	Fixed bug in shannon index files
//		expanded number of values to the right of the decimal point from 2 to 4
// Version 1.2
// 	  Released August 23, 2004
//		Fixed bug in calculating variance of shannon index
//		Give user the flexibility to set the number of iterations to run
//		Reverted to presenting the mean instead of 50%tile for rarefaction curve
//		Fixed a small bug that had rarefaction curves going through (1,0) instead of (1,1)
//		Changed *.r_rarefaction filename to *.rarefaction
//		Changed *.r_*.ltt to *.ltt filenames (eg. *r_chao.ltt is now *.chao.ltt)
//		Wrote first version of user manual
// Version 1.3
//	  Released March 3, 2005
//		Final release before publication of paper in March 2005 issue of AEM
//		Fixed libraries dependency error that caused compilation problems on some platforms
//		Fixed core dump error received by some users
//		Fixed bugs in reporting Shannon & Simpson Indices
//		Changed number of places to report right of the decimal point for output files
//		Streamlined terminal output
//		Added user control of whether to calculate rarefaction curve for ecological parameters
//			(still calcuates traditional rarefaction curve) - makes execution much faster
//		Fixed some problems and updated parts of user manual
// Version 1.4
//	  Released March 8, 2005
//		Fixed bug in calculating the confidence interval for the Chao1 estimator
// Version 1.5
//	  Released April 19, 2005
//		Added 95% CI for ACE richness estimator
//		Updated bias-corrected Chao1 richness estimator and standard error formulae according to Colwell and Chao
//		Allow user to set largest distance to consider (-stop)
//		Allow user to construct a rarefaction curve obtained by sampling with replacement (-wrep)
//		Fixed a problem in constructing collector's curves caused by sequence names that are a fragment of another name
// Version 1.51
//	  Released April 22, 2005
//		Support mega3 formatted distance files as input
// Version 1.53
//	  Released November XX, 2005
//		Allow user to "jumble" the order of sequences in the distance matrix (use -jumble)
//		Allow the user to input a similarity matrix, although correction is still recommended (use -sim)
//		Modified data types in otu.h making the clustering procedure use less memory and faster
//		DOTUR now produces a file containing data to construct rank-abundance plots