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The last version of DOTUR that was created (posted for historical reasons)
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// 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