changes to chop.seqs

author westcott <westcott>

Thu, 27 May 2010 12:47:59 +0000 (12:47 +0000)

committer westcott <westcott>

Thu, 27 May 2010 12:47:59 +0000 (12:47 +0000)
author westcott <westcott>
Thu, 27 May 2010 12:47:59 +0000 (12:47 +0000)
committer westcott <westcott>
Thu, 27 May 2010 12:47:59 +0000 (12:47 +0000)
diff --git a/bayesian.cpp b/bayesian.cpp

index 63f8716dc0ee4fd243a21c06dd41c30f648228c9..57b8e20def801dffdf90f7e49d061d90d8c7a576 100644 (file)
--- a/bayesian.cpp
+++ b/bayesian.cpp
@@ -213,7 +213,7 @@ string Bayesian::getTaxonomy(Sequence* seq) {
                 int index = getMostProbableTaxonomy(queryKmers);
                 
                 if (m->control_pressed) { return tax; }
-                                       
+//cout << seq->getName() << '\t' << index << endl;                                     
                 //bootstrap - to set confidenceScore
                 int numToSelect = queryKmers.size() / 8;
                 tax = bootstrapResults(queryKmers, index, numToSelect);
@@ -249,10 +249,10 @@ string Bayesian::bootstrapResults(vector<int> kmers, int tax, int numToSelect) {
                         
                         //get taxonomy
                         int newTax = getMostProbableTaxonomy(temp);
-                       TaxNode taxonomy = phyloTree->get(newTax);
-                       
+                       TaxNode taxonomyTemp = phyloTree->get(newTax);
+       
                         //add to confidence results
-                       while (taxonomy.level != 0) { //while you are not at the root
+                       while (taxonomyTemp.level != 0) { //while you are not at the root
                                 
                                 itBoot2 = confidenceScores.find(newTax); //is this a classification we already have a count on
                                 
@@ -262,8 +262,8 @@ string Bayesian::bootstrapResults(vector<int> kmers, int tax, int numToSelect) {
                                         confidenceScores[newTax]++;
                                 }
                                 
-                               newTax = taxonomy.parent;
-                               taxonomy = phyloTree->get(taxonomy.parent);
+                               newTax = taxonomyTemp.parent;
+                               taxonomyTemp = phyloTree->get(newTax);
                         }
         
                 }
diff --git a/chopseqscommand.cpp b/chopseqscommand.cpp

index adf0910589c7d65161027bedae6cc74236e2ef5f..9020d2b4763515e1b6e1ead544247e676b043f41 100644 (file)
--- a/chopseqscommand.cpp
+++ b/chopseqscommand.cpp
@@ -21,7 +21,7 @@ ChopSeqsCommand::ChopSeqsCommand(string option)  {
                 
                 else {
                         //valid paramters for this command
-                       string Array[] =  {"fasta","end","outputdir","inputdir"};
+                       string Array[] =  {"fasta","end","fromend","outputdir","inputdir"};
                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                         
                         OptionParser parser(option);
@@ -57,13 +57,14 @@ ChopSeqsCommand::ChopSeqsCommand(string option)  {
                         if (fastafile == "not open") { abort = true; }
                         else if (fastafile == "not found") {  m->mothurOut("You must provide a fasta file."); m->mothurOutEndLine(); abort = true; }    
                         
-                       string temp = validParameter.validFile(parameters, "end", false);       
-                       if (temp == "not found") {  m->mothurOut("You must provide an end for the chops.seqs command."); m->mothurOutEndLine(); abort = true; } 
-                       else {  
-                               convert(temp, end);   
-                               if (end < 0) { m->mothurOut("End must be positive."); m->mothurOutEndLine(); abort = true;  }
-                       }
-                       
+                       string temp = validParameter.validFile(parameters, "end", false);       if (temp == "not found") { temp = "0"; } 
+                       convert(temp, end);   
+               
+                       temp = validParameter.validFile(parameters, "fromend", false);          if (temp == "not found") { temp = "0"; } 
+                       convert(temp, fromend);   
+                               
+                       if ((end == 0) && (fromend == 0))  { m->mothurOut("You must provide either end or fromend for the chops.seqs command."); m->mothurOutEndLine(); abort = true;  }
+                       if ((end != 0) && (fromend != 0))  { m->mothurOut("You must provide either end or fromend for the chops.seqs command, not both."); m->mothurOutEndLine(); abort = true;  }
                 }
  
         }
@@ -77,8 +78,10 @@ ChopSeqsCommand::ChopSeqsCommand(string option)  {
  void ChopSeqsCommand::help(){
         try {
                 m->mothurOut("The chop.seqs command reads a fasta file and outputs a .chop.fasta with sequences trimmed to the end position.\n");
-               m->mothurOut("The chop.seqs command parameters are fasta and end, both are required.\n");
+               m->mothurOut("The chop.seqs command parameters are fasta, end and fromend, fasta is required.\n");
                 m->mothurOut("The chop.seqs command should be in the following format: chop.seqs(fasta=yourFasta, end=yourEnd).\n");
+               m->mothurOut("The end parameter allows you to specify an end base position for your sequences, default = 0.\n");
+               m->mothurOut("The fromend parameter allows you to remove the last X bases from the end of the sequence, default = 0.\n");
                 m->mothurOut("Example chop.seqs(fasta=amazon.fasta, end=200).\n");
                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
         }
@@ -96,38 +99,53 @@ int ChopSeqsCommand::execute(){
                 if (abort == true) { return 0; }
                 
                 string outputFileName = outputDir + getRootName(getSimpleName(fastafile)) + "chop.fasta";
+               string outputFileNameAccnos = outputDir + getRootName(getSimpleName(fastafile)) + "chop.accnos";
                 
                 ofstream out;
                 openOutputFile(outputFileName, out);
                 
+               ofstream outAcc;
+               openOutputFile(outputFileNameAccnos, outAcc);
+               
                 ifstream in;
                 openInputFile(fastafile, in);
                 
-               while (!in.eof()) {
+               bool wroteAccnos = false;
                 
-                       Sequence seq(in, "no align");
+               while (!in.eof()) {
+                       
+                       Sequence seq(in);
                         
-                       if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0;  }
+                       if (m->control_pressed) { in.close(); out.close(); outAcc.close(); remove(outputFileName.c_str()); remove(outputFileNameAccnos.c_str()); return 0;  }
                         
                         if (seq.getName() != "") {
-                               string temp = seq.getUnaligned();
-                               
-                               //output sequence name
-                               out << ">" << seq.getName() << endl;
-                               
-                               //if needed trim sequence
-                               if (temp.length() > end) {  temp = temp.substr(0, end);         }
+                               string newSeqString = "";
+                               if (seq.getIsAligned()) { //sequence is aligned
+                                       newSeqString = getChoppedAligned(seq);
+                               }else{
+                                       newSeqString = getChoppedUnaligned(seq);
+                               }
                                 
-                               //output trimmed sequence       
-                               out << temp << endl;
+                               //output trimmed sequence
+                               if (newSeqString != "") {
+                                       out << ">" << seq.getName() << endl << newSeqString << endl;
+                               }else{
+                                       outAcc << seq.getName() << endl;
+                                       wroteAccnos = true;
+                               }
                         }
                 }
                 in.close();
                 out.close();
+               outAcc.close();
                 
                 m->mothurOutEndLine();
                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
                 m->mothurOut(outputFileName); m->mothurOutEndLine();    
+               
+               if (wroteAccnos) { m->mothurOut(outputFileNameAccnos); m->mothurOutEndLine();  }
+               else {  remove(outputFileNameAccnos.c_str());  }
+               
                 m->mothurOutEndLine();
                 
                 return 0;               
@@ -138,7 +156,74 @@ int ChopSeqsCommand::execute(){
                 exit(1);
         }
  }
+//**********************************************************************************************************************
+string ChopSeqsCommand::getChoppedUnaligned(Sequence seq) {
+       try {
+               string temp = seq.getUnaligned();
+                               
+               //if needed trim sequence
+               if (end != 0) {
+                       if (temp.length() > end) {  temp = temp.substr(0, end);         }
+                       else { temp = "";  }
+               }else { //you are using fromend
+                       if (temp.length() > fromend) { temp = temp.substr(0, (temp.length()-fromend));  }
+                       else {  temp = ""; } //sequence too short
+               }
+
+               return temp;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ChopSeqsCommand", "getChoppedUnaligned");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+string ChopSeqsCommand::getChoppedAligned(Sequence seq) {
+       try {
+               string temp = seq.getAligned();
+               string tempUnaligned = seq.getUnaligned();
+                               
+               //if needed trim sequence
+               if (end != 0) {
+                       if (tempUnaligned.length() > end) { //you have enough bases to remove some
+                               
+                               int stopSpot = 0;
+                               int numBases = 0;
+                               
+                               for (int i = 0; i < temp.length(); i++) {
+                                       if(isalpha(temp[i])) { numBases++; }
  
+                                       if (numBases >= end) { stopSpot = i; break; }
+                               }
+                               
+                               temp = temp.substr(0, stopSpot);                
+                       }else { temp = ""; } //sequence too short
+                       
+               }else { //you are using fromend
+               
+                       if (tempUnaligned.length() > fromend) { 
+                               
+                               int stopSpot = 0;
+                               int numBases = 0;
+                               
+                               for (int i = (temp.length()-1); i >= 0; i--) {
+                                       if(isalpha(temp[i])) { numBases++; }
+
+                                       if (numBases >= fromend) { stopSpot = i; break; }
+                               }
+                               
+                               temp = temp.substr(0, stopSpot);
+                       }
+                       else {  temp = ""; } //sequence too short
+               }
+
+               return temp;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ChopSeqsCommand", "getChoppedUnaligned");
+               exit(1);
+       }
+}
  //**********************************************************************************************************************
  
  
diff --git a/chopseqscommand.h b/chopseqscommand.h

index 5d8d6c4a87223dd1ec5573563f64b0b658cfcc1d..2da134e4660202410c86f86d6c1ef1e1139bff5e 100644 (file)
--- a/chopseqscommand.h
+++ b/chopseqscommand.h
@@ -12,6 +12,7 @@
  
  
  #include "command.hpp"
+#include "sequence.hpp"
  
  class ChopSeqsCommand : public Command {
         
@@ -25,7 +26,10 @@ class ChopSeqsCommand : public Command {
         private:
                 string fastafile, outputDir;
                 bool abort;
-               int end;
+               int end, fromend;
+               
+               string getChoppedAligned(Sequence);
+               string getChoppedUnaligned(Sequence);
  };
  
  #endif
diff --git a/classify.cpp b/classify.cpp

index e07344d4678a0ca263008e4b10d4d125ad8ef122..7f451261550a949b3a1cbb7ab72fd374122597bb 100644 (file)
--- a/classify.cpp
+++ b/classify.cpp
@@ -128,7 +128,7 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
                                 gobble(fastaFile);
                         
                                 names.push_back(temp.getName());
-                                                               
+                                                       
                                 database->addSequence(temp);    
                         }
                         fastaFile.close();
@@ -153,6 +153,11 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
  #endif         
                 database->setNumSeqs(names.size());
                 
+               //sanity check
+               bool okay = phyloTree->ErrorCheck(names);
+               
+               if (!okay) { m->control_pressed = true; }
+               
                 m->mothurOut("DONE."); m->mothurOutEndLine();
                 m->mothurOut("It took " + toString(time(NULL) - start) + " seconds generate search database. "); m->mothurOutEndLine();
  
diff --git a/clustersplitcommand.cpp b/clustersplitcommand.cpp

index 1e4e42fa6f4e3e4a3eb4fab97bcf35472bfe5d67..ab8bdcfdfa6ea950745c857efe482352bbc19d4c 100644 (file)
--- a/clustersplitcommand.cpp
+++ b/clustersplitcommand.cpp
@@ -27,7 +27,7 @@ ClusterSplitCommand::ClusterSplitCommand(string option)  {
                 
                 else {
                         //valid paramters for this command
-                       string Array[] =  {"phylip","column","name","cutoff","precision","method","showabund","timing","hard","processors","splitcutoff","outputdir","inputdir"};
+                       string Array[] =  {"phylip","column","name","cutoff","precision","method","showabund","timing","hard","processors","outputdir","inputdir"};
                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                         
                         OptionParser parser(option);
@@ -121,11 +121,6 @@ ClusterSplitCommand::ClusterSplitCommand(string option)  {
                         convert(temp, cutoff); 
                         if (!hard) {    cutoff += (5 / (precision * 10.0));  }
                         
-                       temp = validParameter.validFile(parameters, "splitcutoff", false);
-                       if (temp == "not found") { temp = "0.10"; }
-                       convert(temp, splitcutoff); 
-                       if (!hard) {    splitcutoff += (5 / (precision * 10.0));  }
-                       
                         method = validParameter.validFile(parameters, "method", false);
                         if (method == "not found") { method = "furthest"; }
                         
@@ -208,7 +203,7 @@ int ClusterSplitCommand::execute(){
                 time_t estart = time(NULL);
                 
                 //split matrix into non-overlapping groups
-               SplitMatrix* split = new SplitMatrix(distfile, namefile, splitcutoff);
+               SplitMatrix* split = new SplitMatrix(distfile, namefile, cutoff);
                 split->split();
                 
                 if (m->control_pressed) { delete split; return 0; }
diff --git a/commandfactory.cpp b/commandfactory.cpp

index 0bca8c0ee3db3706404b3fc5c4ff42b8c8f99388..4d2b0ae2b93a6e205ae8b8d24a86dea37c2f6606 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -164,7 +164,7 @@ CommandFactory::CommandFactory(){
         commands["clearcut"]                    = "clearcut";
         commands["catchall"]                    = "catchall";
         commands["split.abund"]                 = "split.abund";
-       commands["cluster.split"]               = "cluster.split";
+       //commands["cluster.split"]             = "cluster.split";
         commands["classify.seqs"]               = "MPIEnabled"; 
         commands["dist.seqs"]                   = "MPIEnabled";
         commands["filter.seqs"]                 = "MPIEnabled";
@@ -287,7 +287,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                 else if(commandName == "clearcut")                              {       command = new ClearcutCommand(optionString);                            }
                 else if(commandName == "catchall")                              {       command = new CatchAllCommand(optionString);                            }
                 else if(commandName == "split.abund")                   {       command = new SplitAbundCommand(optionString);                          }
-               else if(commandName == "cluster.split")                 {       command = new ClusterSplitCommand(optionString);                        }
+               //else if(commandName == "cluster.split")                       {       command = new ClusterSplitCommand(optionString);                        }
                 else                                                                                    {       command = new NoCommand(optionString);                                          }
  
                 return command;
diff --git a/makefile b/makefile

index 566c6b0381a3549778d6209d9579d67a5232df0d..fdcef2794c06cb81c399376aaf79518246c23aca 100644 (file)
--- a/makefile
+++ b/makefile
@@ -1,1701 +1,1701 @@
-###################################################
-#
-# Makefile for mothur
-# Creator [Xcode -> Makefile Ver: Feb 14 2007 09:18:41]
-# Created: April 16, 2010
-#
-###################################################
-
-#
-# Macros
-#
-
-CC = g++
-CC_OPTIONS = -O3
-
-# if you do not want to use the readline library set to no, default yes.
-# make sure you have the library installed
-
-USEREADLINE ?= yes
-
-ifeq  ($(strip $(USEREADLINE)),yes)
-    CC_OPTIONS += -DUSE_READLINE
-       LNK_OPTIONS += \
-      -lreadline\
-      -lncurses\
-      -L../readline-6.0
-endif
-
-USEMPI ?= no
-
-ifeq  ($(strip $(USEMPI)),yes)
-       CC = mpic++
-    CC_OPTIONS += -DUSE_MPI
-endif
-
-#
-# INCLUDE directories for mothur
-#
-
-     INCLUDE = -I.
-
-#
-# Build mothur
-#
-
-mothur : \
-               ./sharedutilities.o\
-               ./treegroupscommand.o\
-               ./bootstrapsharedcommand.o\
-               ./matrixoutputcommand.o\
-               ./getoturepcommand.o\
-               ./screenseqscommand.o\
-               ./chimera.o\
-               ./decalc.o\
-               ./readotucommand.o\
-               ./readdistcommand.o\
-               ./commandfactory.o\
-               ./alignment.o\
-               ./alignmentcell.o\
-               ./gotohoverlap.o\
-               ./overlap.o\
-               ./needlemanoverlap.o\
-               ./blastalign.o\
-               ./noalign.o\
-               ./suffixdb.o\
-               ./suffixnodes.o\
-               ./suffixtree.o\
-               ./blastdb.o\
-               ./nast.o\
-               ./nastreport.o\
-               ./boneh.o\
-               ./efron.o\
-               ./solow.o\
-               ./unifracweightedcommand.o\
-               ./weighted.o\
-               ./unweighted.o\
-               ./unifracunweightedcommand.o\
-               ./getsabundcommand.o\
-               ./getrabundcommand.o\
-               ./bellerophon.o\
-               ./pintail.o\
-               ./sharedanderbergs.o\
-               ./venncommand.o\
-               ./venn.o\
-               ./fullmatrix.o\
-               ./heatmap.o\
-               ./heatmapcommand.o\
-               ./libshuffcommand.o\
-               ./nocommands.o\
-               ./sharedbraycurtis.o\
-               ./sharedkulczynski.o\
-               ./sharedlennon.o\
-               ./sharedkulczynskicody.o\
-               ./sharedmorisitahorn.o\
-               ./sharedochiai.o\
-               ./readcolumn.o\
-               ./readotu.o\
-               ./readphylip.o\
-               ./consensuscommand.o\
-               ./heatmapsimcommand.o\
-               ./heatmapsim.o\
-               ./optionparser.o\
-               ./filterseqscommand.o\
-               ./goodscoverage.o\
-               ./sequencedb.o\
-               ./sharedjackknife.o\
-               ./sharedmarczewski.o\
-               ./aligncommand.o\
-               ./treemap.o\
-               ./parsimonycommand.o\
-               ./parsimony.o\
-               ./seqsummarycommand.o\
-               ./chimeraccodecommand.o\
-               ./chimerabellerophoncommand.o\
-               ./chimeracheckcommand.o\
-               ./chimeraslayercommand.o\
-               ./chimerapintailcommand.o\
-               ./chimeraseqscommand.o\
-               ./sharedlistvector.o\
-               ./tree.o\
-               ./readtree.o\
-               ./sharedsobscollectsummary.o\
-               ./deconvolutecommand.o\
-               ./listseqscommand.o\
-               ./getseqscommand.o\
-               ./removeseqscommand.o\
-               ./systemcommand.o\
-               ./binsequencecommand.o\
-               ./distancecommand.o\
-               ./ace.o\
-               ./averagelinkage.o\
-               ./bootstrap.o\
-               ./calculator.o\
-               ./chao1.o\
-               ./cluster.o\
-               ./clustercommand.o\
-               ./collect.o\
-               ./collectcommand.o\
-               ./collectsharedcommand.o\
-               ./commandoptionparser.o\
-               ./completelinkage.o\
-               ./database.o\
-               ./engine.o\
-               ./fastamap.o\
-               ./fileoutput.o\
-               ./globaldata.o\
-               ./groupmap.o\
-               ./helpcommand.o\
-               ./makegroupcommand.o\
-               ./chopseqscommand.o\
-               ./clearcutcommand.o\
-               ./catchallcommand.o\
-               ./splitabundcommand.o\
-               ./splitmatrix.o\
-               ./clustersplitcommand.o\
-               ./inputdata.o\
-               ./jackknife.o\
-               ./kmer.o\
-               ./kmerdb.o\
-               ./listvector.o\
-               ./mothur.o\
-               ./nameassignment.o\
-               ./npshannon.o\
-               ./ordervector.o\
-               ./progress.o\
-               ./quitcommand.o\
-               ./rabundvector.o\
-               ./rarecalc.o\
-               ./raredisplay.o\
-               ./rarefact.o\
-               ./rarefactcommand.o\
-               ./rarefactsharedcommand.o\
-               ./sabundvector.o\
-               ./sequence.o\
-               ./shannon.o\
-               ./sharedace.o\
-               ./sharedchao1.o\
-               ./sharedcommand.o\
-               ./sharedjabund.o\
-               ./sharedjclass.o\
-               ./sharedjest.o\
-               ./sharedordervector.o\
-               ./sharedrabundvector.o\
-               ./sharedsabundvector.o\
-               ./sharedsobs.o\
-               ./sharedsorabund.o\
-               ./sharedsorclass.o\
-               ./sharedsorest.o\
-               ./sharedthetan.o\
-               ./sharedthetayc.o\
-               ./simpson.o\
-               ./singlelinkage.o\
-               ./sparsematrix.o\
-               ./summarycommand.o\
-               ./summarysharedcommand.o\
-               ./uvest.o\
-               ./validcalculator.o\
-               ./validparameter.o\
-               ./treenode.o\
-               ./readtreecommand.o\
-               ./reversecommand.o\
-               ./trimseqscommand.o\
-               ./slibshuff.o\
-               ./libshuff.o\
-               ./dlibshuff.o\
-               ./mergefilecommand.o\
-               ./coverage.o\
-               ./whittaker.o\
-               ./preclustercommand.o\
-               ./otuhierarchycommand.o\
-               ./setdircommand.o\
-               ./getgroupcommand.o\
-               ./getlabelcommand.o\
-               ./secondarystructurecommand.o\
-               ./mothurout.o\
-               ./parselistscommand.o\
-               ./readblast.o\
-               ./chimeracheckrdp.o\
-               ./hclustercommand.o\
-               ./hcluster.o\
-               ./getlistcountcommand.o\
-               ./readcluster.o\
-               ./ccode.o\
-               ./taxonomyequalizer.o\
-               ./phylotypecommand.o\
-               ./classifyseqscommand.o\
-               ./parsesffcommand.o\
-               ./classify.o\
-               ./phylotree.o\
-               ./phylodiversity.o\
-               ./phylodiversitycommand.o\
-               ./bayesian.o\
-               ./phylosummary.o\
-               ./alignmentdb.o\
-               ./knn.o\
-               ./distancedb.o\
-               ./chimeraslayer.o\
-               ./slayer.o\
-               ./pcacommand.o\
-               ./formatcolumn.o\
-               ./formatphylip.o\
-               ./mgclustercommand.o\
-               ./getsharedotucommand.o\
-               ./maligner.o\
-               ./chimerarealigner.o\
-               ./bergerparker.o\
-               ./bstick.o\
-               ./sharedkstest.o\
-               ./qstat.o\
-               ./shen.o\
-               ./logsd.o\
-               ./geom.o\
-               ./setlogfilecommand.o
-       $(CC) $(LNK_OPTIONS) \
-               ./sharedutilities.o\
-               ./treegroupscommand.o\
-               ./bootstrapsharedcommand.o\
-               ./matrixoutputcommand.o\
-               ./getoturepcommand.o\
-               ./screenseqscommand.o\
-               ./chimera.o\
-               ./decalc.o\
-               ./readotucommand.o\
-               ./readdistcommand.o\
-               ./commandfactory.o\
-               ./alignment.o\
-               ./alignmentcell.o\
-               ./gotohoverlap.o\
-               ./overlap.o\
-               ./needlemanoverlap.o\
-               ./blastalign.o\
-               ./noalign.o\
-               ./suffixdb.o\
-               ./suffixnodes.o\
-               ./suffixtree.o\
-               ./blastdb.o\
-               ./nast.o\
-               ./nastreport.o\
-               ./boneh.o\
-               ./efron.o\
-               ./solow.o\
-               ./unifracweightedcommand.o\
-               ./weighted.o\
-               ./unweighted.o\
-               ./unifracunweightedcommand.o\
-               ./getsabundcommand.o\
-               ./getrabundcommand.o\
-               ./bellerophon.o\
-               ./pintail.o\
-               ./sharedanderbergs.o\
-               ./venncommand.o\
-               ./venn.o\
-               ./fullmatrix.o\
-               ./heatmap.o\
-               ./heatmapcommand.o\
-               ./libshuffcommand.o\
-               ./nocommands.o\
-               ./sharedbraycurtis.o\
-               ./sharedkulczynski.o\
-               ./sharedlennon.o\
-               ./sharedkulczynskicody.o\
-               ./sharedmorisitahorn.o\
-               ./sharedochiai.o\
-               ./readcolumn.o\
-               ./readotu.o\
-               ./readphylip.o\
-               ./consensuscommand.o\
-               ./heatmapsimcommand.o\
-               ./heatmapsim.o\
-               ./optionparser.o\
-               ./filterseqscommand.o\
-               ./goodscoverage.o\
-               ./sequencedb.o\
-               ./sharedjackknife.o\
-               ./sharedmarczewski.o\
-               ./aligncommand.o\
-               ./treemap.o\
-               ./parsimonycommand.o\
-               ./parsimony.o\
-               ./seqsummarycommand.o\
-               ./chimeraccodecommand.o\
-               ./chimerabellerophoncommand.o\
-               ./chimeracheckcommand.o\
-               ./chimeraslayercommand.o\
-               ./chimerapintailcommand.o\
-               ./chimeraseqscommand.o\
-               ./sharedlistvector.o\
-               ./tree.o\
-               ./readtree.o\
-               ./sharedsobscollectsummary.o\
-               ./deconvolutecommand.o\
-               ./listseqscommand.o\
-               ./getseqscommand.o\
-               ./removeseqscommand.o\
-               ./systemcommand.o\
-               ./binsequencecommand.o\
-               ./distancecommand.o\
-               ./ace.o\
-               ./averagelinkage.o\
-               ./bootstrap.o\
-               ./calculator.o\
-               ./chao1.o\
-               ./cluster.o\
-               ./clustercommand.o\
-               ./collect.o\
-               ./collectcommand.o\
-               ./collectsharedcommand.o\
-               ./commandoptionparser.o\
-               ./completelinkage.o\
-               ./database.o\
-               ./engine.o\
-               ./fastamap.o\
-               ./fileoutput.o\
-               ./globaldata.o\
-               ./groupmap.o\
-               ./helpcommand.o\
-               ./makegroupcommand.o\
-               ./chopseqscommand.o\
-               ./clearcutcommand.o\
-               ./catchallcommand.o\
-               ./splitabundcommand.o\
-               ./splitmatrix.o\
-               ./clustersplitcommand.o\
-               ./inputdata.o\
-               ./jackknife.o\
-               ./kmer.o\
-               ./kmerdb.o\
-               ./listvector.o\
-               ./mothur.o\
-               ./nameassignment.o\
-               ./npshannon.o\
-               ./ordervector.o\
-               ./progress.o\
-               ./quitcommand.o\
-               ./rabundvector.o\
-               ./rarecalc.o\
-               ./raredisplay.o\
-               ./rarefact.o\
-               ./rarefactcommand.o\
-               ./rarefactsharedcommand.o\
-               ./sabundvector.o\
-               ./sequence.o\
-               ./shannon.o\
-               ./sharedace.o\
-               ./sharedchao1.o\
-               ./sharedcommand.o\
-               ./sharedjabund.o\
-               ./sharedjclass.o\
-               ./sharedjest.o\
-               ./sharedordervector.o\
-               ./sharedrabundvector.o\
-               ./sharedsabundvector.o\
-               ./sharedsobs.o\
-               ./sharedsorabund.o\
-               ./sharedsorclass.o\
-               ./sharedsorest.o\
-               ./sharedthetan.o\
-               ./sharedthetayc.o\
-               ./simpson.o\
-               ./singlelinkage.o\
-               ./sparsematrix.o\
-               ./summarycommand.o\
-               ./summarysharedcommand.o\
-               ./uvest.o\
-               ./validcalculator.o\
-               ./validparameter.o\
-               ./treenode.o\
-               ./readtreecommand.o\
-               ./reversecommand.o\
-               ./trimseqscommand.o\
-               ./slibshuff.o\
-               ./libshuff.o\
-               ./dlibshuff.o\
-               ./mergefilecommand.o\
-               ./coverage.o\
-               ./whittaker.o\
-               ./preclustercommand.o\
-               ./otuhierarchycommand.o\
-               ./setdircommand.o\
-               ./getgroupcommand.o\
-               ./getlabelcommand.o\
-               ./secondarystructurecommand.o\
-               ./mothurout.o\
-               ./parselistscommand.o\
-               ./readblast.o\
-               ./chimeracheckrdp.o\
-               ./hclustercommand.o\
-               ./hcluster.o\
-               ./getlistcountcommand.o\
-               ./readcluster.o\
-               ./ccode.o\
-               ./taxonomyequalizer.o\
-               ./phylotypecommand.o\
-               ./classifyseqscommand.o\
-               ./parsesffcommand.o\
-               ./classify.o\
-               ./phylotree.o\
-               ./phylodiversity.o\
-               ./phylodiversitycommand.o\
-               ./bayesian.o\
-               ./phylosummary.o\
-               ./alignmentdb.o\
-               ./knn.o\
-               ./distancedb.o\
-               ./chimeraslayer.o\
-               ./slayer.o\
-               ./pcacommand.o\
-               ./formatcolumn.o\
-               ./formatphylip.o\
-               ./mgclustercommand.o\
-               ./getsharedotucommand.o\
-               ./maligner.o\
-               ./chimerarealigner.o\
-               ./bergerparker.o\
-               ./bstick.o\
-               ./sharedkstest.o\
-               ./qstat.o\
-               ./shen.o\
-               ./logsd.o\
-               ./geom.o\
-               ./setlogfilecommand.o\
-               -o mothur
-
-clean : 
-               rm \
-               ./sharedutilities.o\
-               ./treegroupscommand.o\
-               ./bootstrapsharedcommand.o\
-               ./matrixoutputcommand.o\
-               ./getoturepcommand.o\
-               ./screenseqscommand.o\
-               ./chimera.o\
-               ./decalc.o\
-               ./readotucommand.o\
-               ./readdistcommand.o\
-               ./commandfactory.o\
-               ./alignment.o\
-               ./alignmentcell.o\
-               ./gotohoverlap.o\
-               ./overlap.o\
-               ./needlemanoverlap.o\
-               ./blastalign.o\
-               ./noalign.o\
-               ./suffixdb.o\
-               ./suffixnodes.o\
-               ./suffixtree.o\
-               ./blastdb.o\
-               ./nast.o\
-               ./nastreport.o\
-               ./boneh.o\
-               ./efron.o\
-               ./solow.o\
-               ./unifracweightedcommand.o\
-               ./weighted.o\
-               ./unweighted.o\
-               ./unifracunweightedcommand.o\
-               ./getsabundcommand.o\
-               ./getrabundcommand.o\
-               ./bellerophon.o\
-               ./pintail.o\
-               ./sharedanderbergs.o\
-               ./venncommand.o\
-               ./venn.o\
-               ./fullmatrix.o\
-               ./heatmap.o\
-               ./heatmapcommand.o\
-               ./libshuffcommand.o\
-               ./nocommands.o\
-               ./sharedbraycurtis.o\
-               ./sharedkulczynski.o\
-               ./sharedlennon.o\
-               ./sharedkulczynskicody.o\
-               ./sharedmorisitahorn.o\
-               ./sharedochiai.o\
-               ./readcolumn.o\
-               ./readotu.o\
-               ./readphylip.o\
-               ./consensuscommand.o\
-               ./heatmapsimcommand.o\
-               ./heatmapsim.o\
-               ./optionparser.o\
-               ./filterseqscommand.o\
-               ./goodscoverage.o\
-               ./sequencedb.o\
-               ./sharedjackknife.o\
-               ./sharedmarczewski.o\
-               ./aligncommand.o\
-               ./treemap.o\
-               ./parsimonycommand.o\
-               ./parsimony.o\
-               ./seqsummarycommand.o\
-               ./chimeraccodecommand.o\
-               ./chimerabellerophoncommand.o\
-               ./chimeracheckcommand.o\
-               ./chimeraslayercommand.o\
-               ./chimerapintailcommand.o\
-               ./chimeraseqscommand.o\
-               ./sharedlistvector.o\
-               ./tree.o\
-               ./readtree.o\
-               ./sharedsobscollectsummary.o\
-               ./deconvolutecommand.o\
-               ./listseqscommand.o\
-               ./getseqscommand.o\
-               ./removeseqscommand.o\
-               ./systemcommand.o\
-               ./binsequencecommand.o\
-               ./distancecommand.o\
-               ./ace.o\
-               ./averagelinkage.o\
-               ./bootstrap.o\
-               ./calculator.o\
-               ./chao1.o\
-               ./cluster.o\
-               ./clustercommand.o\
-               ./collect.o\
-               ./collectcommand.o\
-               ./collectsharedcommand.o\
-               ./commandoptionparser.o\
-               ./completelinkage.o\
-               ./database.o\
-               ./engine.o\
-               ./fastamap.o\
-               ./fileoutput.o\
-               ./globaldata.o\
-               ./groupmap.o\
-               ./helpcommand.o\
-               ./makegroupcommand.o\
-               ./chopseqscommand.o\
-               ./clearcutcommand.o\
-               ./catchallcommand.o\
-               ./splitabundcommand.o\
-               ./splitmatrix.o\
-               ./clustersplitcommand.o\
-               ./inputdata.o\
-               ./jackknife.o\
-               ./kmer.o\
-               ./kmerdb.o\
-               ./listvector.o\
-               ./mothur.o\
-               ./nameassignment.o\
-               ./npshannon.o\
-               ./ordervector.o\
-               ./progress.o\
-               ./quitcommand.o\
-               ./rabundvector.o\
-               ./rarecalc.o\
-               ./raredisplay.o\
-               ./rarefact.o\
-               ./rarefactcommand.o\
-               ./rarefactsharedcommand.o\
-               ./sabundvector.o\
-               ./sequence.o\
-               ./shannon.o\
-               ./sharedace.o\
-               ./sharedchao1.o\
-               ./sharedcommand.o\
-               ./sharedjabund.o\
-               ./sharedjclass.o\
-               ./sharedjest.o\
-               ./sharedordervector.o\
-               ./sharedrabundvector.o\
-               ./sharedsabundvector.o\
-               ./sharedsobs.o\
-               ./sharedsorabund.o\
-               ./sharedsorclass.o\
-               ./sharedsorest.o\
-               ./sharedthetan.o\
-               ./sharedthetayc.o\
-               ./simpson.o\
-               ./singlelinkage.o\
-               ./sparsematrix.o\
-               ./summarycommand.o\
-               ./summarysharedcommand.o\
-               ./uvest.o\
-               ./validcalculator.o\
-               ./validparameter.o\
-               ./treenode.o\
-               ./readtreecommand.o\
-               ./reversecommand.o\
-               ./trimseqscommand.o\
-               ./slibshuff.o\
-               ./libshuff.o\
-               ./dlibshuff.o\
-               ./mergefilecommand.o\
-               ./coverage.o\
-               ./whittaker.o\
-               ./preclustercommand.o\
-               ./otuhierarchycommand.o\
-               ./setdircommand.o\
-               ./getgroupcommand.o\
-               ./getlabelcommand.o\
-               ./secondarystructurecommand.o\
-               ./mothurout.o\
-               ./parselistscommand.o\
-               ./readblast.o\
-               ./chimeracheckrdp.o\
-               ./hclustercommand.o\
-               ./hcluster.o\
-               ./getlistcountcommand.o\
-               ./readcluster.o\
-               ./ccode.o\
-               ./taxonomyequalizer.o\
-               ./phylotypecommand.o\
-               ./classifyseqscommand.o\
-               ./parsesffcommand.o\
-               ./classify.o\
-               ./phylotree.o\
-               ./phylodiversity.o\
-               ./phylodiversitycommand.o\
-               ./bayesian.o\
-               ./phylosummary.o\
-               ./alignmentdb.o\
-               ./knn.o\
-               ./distancedb.o\
-               ./chimeraslayer.o\
-               ./slayer.o\
-               ./pcacommand.o\
-               ./formatcolumn.o\
-               ./formatphylip.o\
-               ./mgclustercommand.o\
-               ./getsharedotucommand.o\
-               ./maligner.o\
-               ./chimerarealigner.o\
-               ./bergerparker.o\
-               ./bstick.o\
-               ./sharedkstest.o\
-               ./qstat.o\
-               ./shen.o\
-               ./logsd.o\
-               ./geom.o\
-               ./setlogfilecommand.o\
-               mothur
-
-install : mothur
-               #cp mothur ../Release/mothur
-
-#
-# Build the parts of mothur
-#
-
-
-# Item # 1 -- sharedutilities --
-./sharedutilities.o : sharedutilities.cpp
-       $(CC) $(CC_OPTIONS) sharedutilities.cpp -c $(INCLUDE) -o ./sharedutilities.o
-
-
-# Item # 2 -- treegroupscommand --
-./treegroupscommand.o : treegroupscommand.cpp
-       $(CC) $(CC_OPTIONS) treegroupscommand.cpp -c $(INCLUDE) -o ./treegroupscommand.o
-
-
-# Item # 3 -- bootstrapsharedcommand --
-./bootstrapsharedcommand.o : bootstrapsharedcommand.cpp
-       $(CC) $(CC_OPTIONS) bootstrapsharedcommand.cpp -c $(INCLUDE) -o ./bootstrapsharedcommand.o
-
-
-# Item # 4 -- matrixoutputcommand --
-./matrixoutputcommand.o : matrixoutputcommand.cpp
-       $(CC) $(CC_OPTIONS) matrixoutputcommand.cpp -c $(INCLUDE) -o ./matrixoutputcommand.o
-
-
-# Item # 5 -- getoturepcommand --
-./getoturepcommand.o : getoturepcommand.cpp
-       $(CC) $(CC_OPTIONS) getoturepcommand.cpp -c $(INCLUDE) -o ./getoturepcommand.o
-
-
-# Item # 6 -- screenseqscommand --
-./screenseqscommand.o : screenseqscommand.cpp
-       $(CC) $(CC_OPTIONS) screenseqscommand.cpp -c $(INCLUDE) -o ./screenseqscommand.o
-
-
-# Item # 7 -- chimera --
-./chimera.o : chimera.cpp
-       $(CC) $(CC_OPTIONS) chimera.cpp -c $(INCLUDE) -o ./chimera.o
-
-
-# Item # 8 -- decalc --
-./decalc.o : decalc.cpp
-       $(CC) $(CC_OPTIONS) decalc.cpp -c $(INCLUDE) -o ./decalc.o
-
-
-# Item # 9 -- readotucommand --
-./readotucommand.o : readotucommand.cpp
-       $(CC) $(CC_OPTIONS) readotucommand.cpp -c $(INCLUDE) -o ./readotucommand.o
-
-
-# Item # 10 -- readdistcommand --
-./readdistcommand.o : readdistcommand.cpp
-       $(CC) $(CC_OPTIONS) readdistcommand.cpp -c $(INCLUDE) -o ./readdistcommand.o
-
-
-# Item # 11 -- commandfactory --
-./commandfactory.o : commandfactory.cpp
-       $(CC) $(CC_OPTIONS) commandfactory.cpp -c $(INCLUDE) -o ./commandfactory.o
-
-
-# Item # 12 -- alignment --
-./alignment.o : alignment.cpp
-       $(CC) $(CC_OPTIONS) alignment.cpp -c $(INCLUDE) -o ./alignment.o
-
-
-# Item # 13 -- alignmentcell --
-./alignmentcell.o : alignmentcell.cpp
-       $(CC) $(CC_OPTIONS) alignmentcell.cpp -c $(INCLUDE) -o ./alignmentcell.o
-
-
-# Item # 14 -- gotohoverlap --
-./gotohoverlap.o : gotohoverlap.cpp
-       $(CC) $(CC_OPTIONS) gotohoverlap.cpp -c $(INCLUDE) -o ./gotohoverlap.o
-
-
-# Item # 15 -- overlap --
-./overlap.o : overlap.cpp
-       $(CC) $(CC_OPTIONS) overlap.cpp -c $(INCLUDE) -o ./overlap.o
-
-
-# Item # 16 -- needlemanoverlap --
-./needlemanoverlap.o : needlemanoverlap.cpp
-       $(CC) $(CC_OPTIONS) needlemanoverlap.cpp -c $(INCLUDE) -o ./needlemanoverlap.o
-
-
-# Item # 17 -- blastalign --
-./blastalign.o : blastalign.cpp
-       $(CC) $(CC_OPTIONS) blastalign.cpp -c $(INCLUDE) -o ./blastalign.o
-
-
-# Item # 18 -- noalign --
-./noalign.o : noalign.cpp
-       $(CC) $(CC_OPTIONS) noalign.cpp -c $(INCLUDE) -o ./noalign.o
-
-
-# Item # 19 -- suffixdb --
-./suffixdb.o : suffixdb.cpp
-       $(CC) $(CC_OPTIONS) suffixdb.cpp -c $(INCLUDE) -o ./suffixdb.o
-
-
-# Item # 20 -- suffixnodes --
-./suffixnodes.o : suffixnodes.cpp
-       $(CC) $(CC_OPTIONS) suffixnodes.cpp -c $(INCLUDE) -o ./suffixnodes.o
-
-
-# Item # 21 -- suffixtree --
-./suffixtree.o : suffixtree.cpp
-       $(CC) $(CC_OPTIONS) suffixtree.cpp -c $(INCLUDE) -o ./suffixtree.o
-
-
-# Item # 22 -- blastdb --
-./blastdb.o : blastdb.cpp
-       $(CC) $(CC_OPTIONS) blastdb.cpp -c $(INCLUDE) -o ./blastdb.o
-
-
-# Item # 23 -- nast --
-./nast.o : nast.cpp
-       $(CC) $(CC_OPTIONS) nast.cpp -c $(INCLUDE) -o ./nast.o
-
-
-# Item # 24 -- nastreport --
-./nastreport.o : nastreport.cpp
-       $(CC) $(CC_OPTIONS) nastreport.cpp -c $(INCLUDE) -o ./nastreport.o
-
-
-# Item # 25 -- boneh --
-./boneh.o : boneh.cpp
-       $(CC) $(CC_OPTIONS) boneh.cpp -c $(INCLUDE) -o ./boneh.o
-
-
-# Item # 26 -- efron --
-./efron.o : efron.cpp
-       $(CC) $(CC_OPTIONS) efron.cpp -c $(INCLUDE) -o ./efron.o
-
-
-# Item # 27 -- solow --
-./solow.o : solow.cpp
-       $(CC) $(CC_OPTIONS) solow.cpp -c $(INCLUDE) -o ./solow.o
-
-
-# Item # 28 -- unifracweightedcommand --
-./unifracweightedcommand.o : unifracweightedcommand.cpp
-       $(CC) $(CC_OPTIONS) unifracweightedcommand.cpp -c $(INCLUDE) -o ./unifracweightedcommand.o
-
-
-# Item # 29 -- weighted --
-./weighted.o : weighted.cpp
-       $(CC) $(CC_OPTIONS) weighted.cpp -c $(INCLUDE) -o ./weighted.o
-
-
-# Item # 30 -- unweighted --
-./unweighted.o : unweighted.cpp
-       $(CC) $(CC_OPTIONS) unweighted.cpp -c $(INCLUDE) -o ./unweighted.o
-
-
-# Item # 31 -- unifracunweightedcommand --
-./unifracunweightedcommand.o : unifracunweightedcommand.cpp
-       $(CC) $(CC_OPTIONS) unifracunweightedcommand.cpp -c $(INCLUDE) -o ./unifracunweightedcommand.o
-
-
-# Item # 32 -- getsabundcommand --
-./getsabundcommand.o : getsabundcommand.cpp
-       $(CC) $(CC_OPTIONS) getsabundcommand.cpp -c $(INCLUDE) -o ./getsabundcommand.o
-
-
-# Item # 33 -- getrabundcommand --
-./getrabundcommand.o : getrabundcommand.cpp
-       $(CC) $(CC_OPTIONS) getrabundcommand.cpp -c $(INCLUDE) -o ./getrabundcommand.o
-
-
-# Item # 34 -- bellerophon --
-./bellerophon.o : bellerophon.cpp
-       $(CC) $(CC_OPTIONS) bellerophon.cpp -c $(INCLUDE) -o ./bellerophon.o
-
-
-# Item # 35 -- pintail --
-./pintail.o : pintail.cpp
-       $(CC) $(CC_OPTIONS) pintail.cpp -c $(INCLUDE) -o ./pintail.o
-
-
-# Item # 36 -- sharedanderbergs --
-./sharedanderbergs.o : sharedanderbergs.cpp
-       $(CC) $(CC_OPTIONS) sharedanderbergs.cpp -c $(INCLUDE) -o ./sharedanderbergs.o
-
-
-# Item # 37 -- venncommand --
-./venncommand.o : venncommand.cpp
-       $(CC) $(CC_OPTIONS) venncommand.cpp -c $(INCLUDE) -o ./venncommand.o
-
-
-# Item # 38 -- venn --
-./venn.o : venn.cpp
-       $(CC) $(CC_OPTIONS) venn.cpp -c $(INCLUDE) -o ./venn.o
-
-
-# Item # 39 -- fullmatrix --
-./fullmatrix.o : fullmatrix.cpp
-       $(CC) $(CC_OPTIONS) fullmatrix.cpp -c $(INCLUDE) -o ./fullmatrix.o
-
-
-# Item # 40 -- heatmap --
-./heatmap.o : heatmap.cpp
-       $(CC) $(CC_OPTIONS) heatmap.cpp -c $(INCLUDE) -o ./heatmap.o
-
-
-# Item # 41 -- heatmapcommand --
-./heatmapcommand.o : heatmapcommand.cpp
-       $(CC) $(CC_OPTIONS) heatmapcommand.cpp -c $(INCLUDE) -o ./heatmapcommand.o
-
-
-# Item # 42 -- libshuffcommand --
-./libshuffcommand.o : libshuffcommand.cpp
-       $(CC) $(CC_OPTIONS) libshuffcommand.cpp -c $(INCLUDE) -o ./libshuffcommand.o
-
-
-# Item # 43 -- nocommands --
-./nocommands.o : nocommands.cpp
-       $(CC) $(CC_OPTIONS) nocommands.cpp -c $(INCLUDE) -o ./nocommands.o
-
-
-# Item # 44 -- sharedbraycurtis --
-./sharedbraycurtis.o : sharedbraycurtis.cpp
-       $(CC) $(CC_OPTIONS) sharedbraycurtis.cpp -c $(INCLUDE) -o ./sharedbraycurtis.o
-
-
-# Item # 45 -- sharedkulczynski --
-./sharedkulczynski.o : sharedkulczynski.cpp
-       $(CC) $(CC_OPTIONS) sharedkulczynski.cpp -c $(INCLUDE) -o ./sharedkulczynski.o
-
-
-# Item # 46 -- sharedlennon --
-./sharedlennon.o : sharedlennon.cpp
-       $(CC) $(CC_OPTIONS) sharedlennon.cpp -c $(INCLUDE) -o ./sharedlennon.o
-
-
-# Item # 47 -- sharedkulczynskicody --
-./sharedkulczynskicody.o : sharedkulczynskicody.cpp
-       $(CC) $(CC_OPTIONS) sharedkulczynskicody.cpp -c $(INCLUDE) -o ./sharedkulczynskicody.o
-
-
-# Item # 48 -- sharedmorisitahorn --
-./sharedmorisitahorn.o : sharedmorisitahorn.cpp
-       $(CC) $(CC_OPTIONS) sharedmorisitahorn.cpp -c $(INCLUDE) -o ./sharedmorisitahorn.o
-
-
-# Item # 49 -- sharedochiai --
-./sharedochiai.o : sharedochiai.cpp
-       $(CC) $(CC_OPTIONS) sharedochiai.cpp -c $(INCLUDE) -o ./sharedochiai.o
-
-
-# Item # 50 -- readcolumn --
-./readcolumn.o : readcolumn.cpp
-       $(CC) $(CC_OPTIONS) readcolumn.cpp -c $(INCLUDE) -o ./readcolumn.o
-
-
-# Item # 51 -- readotu --
-./readotu.o : readotu.cpp
-       $(CC) $(CC_OPTIONS) readotu.cpp -c $(INCLUDE) -o ./readotu.o
-
-
-# Item # 52 -- readphylip --
-./readphylip.o : readphylip.cpp
-       $(CC) $(CC_OPTIONS) readphylip.cpp -c $(INCLUDE) -o ./readphylip.o
-
-
-# Item # 53 -- consensuscommand --
-./consensuscommand.o : consensuscommand.cpp
-       $(CC) $(CC_OPTIONS) consensuscommand.cpp -c $(INCLUDE) -o ./consensuscommand.o
-
-
-# Item # 54 -- heatmapsimcommand --
-./heatmapsimcommand.o : heatmapsimcommand.cpp
-       $(CC) $(CC_OPTIONS) heatmapsimcommand.cpp -c $(INCLUDE) -o ./heatmapsimcommand.o
-
-
-# Item # 55 -- heatmapsim --
-./heatmapsim.o : heatmapsim.cpp
-       $(CC) $(CC_OPTIONS) heatmapsim.cpp -c $(INCLUDE) -o ./heatmapsim.o
-
-
-# Item # 56 -- optionparser --
-./optionparser.o : optionparser.cpp
-       $(CC) $(CC_OPTIONS) optionparser.cpp -c $(INCLUDE) -o ./optionparser.o
-
-
-# Item # 57 -- filterseqscommand --
-./filterseqscommand.o : filterseqscommand.cpp
-       $(CC) $(CC_OPTIONS) filterseqscommand.cpp -c $(INCLUDE) -o ./filterseqscommand.o
-
-
-# Item # 58 -- goodscoverage --
-./goodscoverage.o : goodscoverage.cpp
-       $(CC) $(CC_OPTIONS) goodscoverage.cpp -c $(INCLUDE) -o ./goodscoverage.o
-
-
-# Item # 59 -- sequencedb --
-./sequencedb.o : sequencedb.cpp
-       $(CC) $(CC_OPTIONS) sequencedb.cpp -c $(INCLUDE) -o ./sequencedb.o
-
-
-# Item # 60 -- sharedjackknife --
-./sharedjackknife.o : sharedjackknife.cpp
-       $(CC) $(CC_OPTIONS) sharedjackknife.cpp -c $(INCLUDE) -o ./sharedjackknife.o
-
-
-# Item # 61 -- sharedmarczewski --
-./sharedmarczewski.o : sharedmarczewski.cpp
-       $(CC) $(CC_OPTIONS) sharedmarczewski.cpp -c $(INCLUDE) -o ./sharedmarczewski.o
-
-
-# Item # 62 -- aligncommand --
-./aligncommand.o : aligncommand.cpp
-       $(CC) $(CC_OPTIONS) aligncommand.cpp -c $(INCLUDE) -o ./aligncommand.o
-
-
-# Item # 63 -- treemap --
-./treemap.o : treemap.cpp
-       $(CC) $(CC_OPTIONS) treemap.cpp -c $(INCLUDE) -o ./treemap.o
-
-
-# Item # 64 -- parsimonycommand --
-./parsimonycommand.o : parsimonycommand.cpp
-       $(CC) $(CC_OPTIONS) parsimonycommand.cpp -c $(INCLUDE) -o ./parsimonycommand.o
-
-
-# Item # 65 -- parsimony --
-./parsimony.o : parsimony.cpp
-       $(CC) $(CC_OPTIONS) parsimony.cpp -c $(INCLUDE) -o ./parsimony.o
-
-
-# Item # 66 -- seqsummarycommand --
-./seqsummarycommand.o : seqsummarycommand.cpp
-       $(CC) $(CC_OPTIONS) seqsummarycommand.cpp -c $(INCLUDE) -o ./seqsummarycommand.o
-
-
-# Item # 67 -- chimeraseqscommand --
-./chimeraseqscommand.o : chimeraseqscommand.cpp
-       $(CC) $(CC_OPTIONS) chimeraseqscommand.cpp -c $(INCLUDE) -o ./chimeraseqscommand.o
-
-
-# Item # 68 -- sharedlistvector --
-./sharedlistvector.o : sharedlistvector.cpp
-       $(CC) $(CC_OPTIONS) sharedlistvector.cpp -c $(INCLUDE) -o ./sharedlistvector.o
-
-
-# Item # 69 -- tree --
-./tree.o : tree.cpp
-       $(CC) $(CC_OPTIONS) tree.cpp -c $(INCLUDE) -o ./tree.o
-
-
-# Item # 70 -- readtree --
-./readtree.o : readtree.cpp
-       $(CC) $(CC_OPTIONS) readtree.cpp -c $(INCLUDE) -o ./readtree.o
-
-
-# Item # 71 -- sharedsobscollectsummary --
-./sharedsobscollectsummary.o : sharedsobscollectsummary.cpp
-       $(CC) $(CC_OPTIONS) sharedsobscollectsummary.cpp -c $(INCLUDE) -o ./sharedsobscollectsummary.o
-
-
-# Item # 72 -- deconvolutecommand --
-./deconvolutecommand.o : deconvolutecommand.cpp
-       $(CC) $(CC_OPTIONS) deconvolutecommand.cpp -c $(INCLUDE) -o ./deconvolutecommand.o
-
-
-# Item # 73 -- listseqscommand --
-./listseqscommand.o : listseqscommand.cpp
-       $(CC) $(CC_OPTIONS) listseqscommand.cpp -c $(INCLUDE) -o ./listseqscommand.o
-
-
-# Item # 74 -- getseqscommand --
-./getseqscommand.o : getseqscommand.cpp
-       $(CC) $(CC_OPTIONS) getseqscommand.cpp -c $(INCLUDE) -o ./getseqscommand.o
-
-
-# Item # 75 -- removeseqscommand --
-./removeseqscommand.o : removeseqscommand.cpp
-       $(CC) $(CC_OPTIONS) removeseqscommand.cpp -c $(INCLUDE) -o ./removeseqscommand.o
-
-
-# Item # 76 -- systemcommand --
-./systemcommand.o : systemcommand.cpp
-       $(CC) $(CC_OPTIONS) systemcommand.cpp -c $(INCLUDE) -o ./systemcommand.o
-
-
-# Item # 77 -- binsequencecommand --
-./binsequencecommand.o : binsequencecommand.cpp
-       $(CC) $(CC_OPTIONS) binsequencecommand.cpp -c $(INCLUDE) -o ./binsequencecommand.o
-
-
-# Item # 78 -- distancecommand --
-./distancecommand.o : distancecommand.cpp
-       $(CC) $(CC_OPTIONS) distancecommand.cpp -c $(INCLUDE) -o ./distancecommand.o
-
-
-# Item # 79 -- ace --
-./ace.o : ace.cpp
-       $(CC) $(CC_OPTIONS) ace.cpp -c $(INCLUDE) -o ./ace.o
-
-
-# Item # 80 -- averagelinkage --
-./averagelinkage.o : averagelinkage.cpp
-       $(CC) $(CC_OPTIONS) averagelinkage.cpp -c $(INCLUDE) -o ./averagelinkage.o
-
-
-# Item # 81 -- bootstrap --
-./bootstrap.o : bootstrap.cpp
-       $(CC) $(CC_OPTIONS) bootstrap.cpp -c $(INCLUDE) -o ./bootstrap.o
-
-
-# Item # 82 -- calculator --
-./calculator.o : calculator.cpp
-       $(CC) $(CC_OPTIONS) calculator.cpp -c $(INCLUDE) -o ./calculator.o
-
-
-# Item # 83 -- chao1 --
-./chao1.o : chao1.cpp
-       $(CC) $(CC_OPTIONS) chao1.cpp -c $(INCLUDE) -o ./chao1.o
-
-
-# Item # 84 -- cluster --
-./cluster.o : cluster.cpp
-       $(CC) $(CC_OPTIONS) cluster.cpp -c $(INCLUDE) -o ./cluster.o
-
-
-# Item # 85 -- clustercommand --
-./clustercommand.o : clustercommand.cpp
-       $(CC) $(CC_OPTIONS) clustercommand.cpp -c $(INCLUDE) -o ./clustercommand.o
-
-
-# Item # 86 -- collect --
-./collect.o : collect.cpp
-       $(CC) $(CC_OPTIONS) collect.cpp -c $(INCLUDE) -o ./collect.o
-
-
-# Item # 87 -- collectcommand --
-./collectcommand.o : collectcommand.cpp
-       $(CC) $(CC_OPTIONS) collectcommand.cpp -c $(INCLUDE) -o ./collectcommand.o
-
-
-# Item # 88 -- collectsharedcommand --
-./collectsharedcommand.o : collectsharedcommand.cpp
-       $(CC) $(CC_OPTIONS) collectsharedcommand.cpp -c $(INCLUDE) -o ./collectsharedcommand.o
-
-
-# Item # 89 -- commandoptionparser --
-./commandoptionparser.o : commandoptionparser.cpp
-       $(CC) $(CC_OPTIONS) commandoptionparser.cpp -c $(INCLUDE) -o ./commandoptionparser.o
-
-
-# Item # 90 -- completelinkage --
-./completelinkage.o : completelinkage.cpp
-       $(CC) $(CC_OPTIONS) completelinkage.cpp -c $(INCLUDE) -o ./completelinkage.o
-
-
-# Item # 91 -- database --
-./database.o : database.cpp
-       $(CC) $(CC_OPTIONS) database.cpp -c $(INCLUDE) -o ./database.o
-
-
-# Item # 92 -- engine --
-./engine.o : engine.cpp
-       $(CC) $(CC_OPTIONS) engine.cpp -c $(INCLUDE) -o ./engine.o
-
-
-# Item # 93 -- fastamap --
-./fastamap.o : fastamap.cpp
-       $(CC) $(CC_OPTIONS) fastamap.cpp -c $(INCLUDE) -o ./fastamap.o
-
-
-# Item # 94 -- fileoutput --
-./fileoutput.o : fileoutput.cpp
-       $(CC) $(CC_OPTIONS) fileoutput.cpp -c $(INCLUDE) -o ./fileoutput.o
-
-
-# Item # 95 -- globaldata --
-./globaldata.o : globaldata.cpp
-       $(CC) $(CC_OPTIONS) globaldata.cpp -c $(INCLUDE) -o ./globaldata.o
-
-
-# Item # 96 -- groupmap --
-./groupmap.o : groupmap.cpp
-       $(CC) $(CC_OPTIONS) groupmap.cpp -c $(INCLUDE) -o ./groupmap.o
-
-
-# Item # 97 -- helpcommand --
-./helpcommand.o : helpcommand.cpp
-       $(CC) $(CC_OPTIONS) helpcommand.cpp -c $(INCLUDE) -o ./helpcommand.o
-
-
-# Item # 98 -- inputdata --
-./inputdata.o : inputdata.cpp
-       $(CC) $(CC_OPTIONS) inputdata.cpp -c $(INCLUDE) -o ./inputdata.o
-
-
-# Item # 99 -- jackknife --
-./jackknife.o : jackknife.cpp
-       $(CC) $(CC_OPTIONS) jackknife.cpp -c $(INCLUDE) -o ./jackknife.o
-
-
-# Item # 100 -- kmer --
-./kmer.o : kmer.cpp
-       $(CC) $(CC_OPTIONS) kmer.cpp -c $(INCLUDE) -o ./kmer.o
-
-
-# Item # 101 -- kmerdb --
-./kmerdb.o : kmerdb.cpp
-       $(CC) $(CC_OPTIONS) kmerdb.cpp -c $(INCLUDE) -o ./kmerdb.o
-
-
-# Item # 102 -- listvector --
-./listvector.o : listvector.cpp
-       $(CC) $(CC_OPTIONS) listvector.cpp -c $(INCLUDE) -o ./listvector.o
-
-
-# Item # 103 -- mothur --
-./mothur.o : mothur.cpp
-       $(CC) $(CC_OPTIONS) mothur.cpp -c $(INCLUDE) -o ./mothur.o
-
-
-# Item # 104 -- nameassignment --
-./nameassignment.o : nameassignment.cpp
-       $(CC) $(CC_OPTIONS) nameassignment.cpp -c $(INCLUDE) -o ./nameassignment.o
-
-
-# Item # 105 -- npshannon --
-./npshannon.o : npshannon.cpp
-       $(CC) $(CC_OPTIONS) npshannon.cpp -c $(INCLUDE) -o ./npshannon.o
-
-
-# Item # 106 -- ordervector --
-./ordervector.o : ordervector.cpp
-       $(CC) $(CC_OPTIONS) ordervector.cpp -c $(INCLUDE) -o ./ordervector.o
-
-
-# Item # 107 -- progress --
-./progress.o : progress.cpp
-       $(CC) $(CC_OPTIONS) progress.cpp -c $(INCLUDE) -o ./progress.o
-
-
-# Item # 108 -- quitcommand --
-./quitcommand.o : quitcommand.cpp
-       $(CC) $(CC_OPTIONS) quitcommand.cpp -c $(INCLUDE) -o ./quitcommand.o
-
-
-# Item # 109 -- rabundvector --
-./rabundvector.o : rabundvector.cpp
-       $(CC) $(CC_OPTIONS) rabundvector.cpp -c $(INCLUDE) -o ./rabundvector.o
-
-
-# Item # 110 -- rarecalc --
-./rarecalc.o : rarecalc.cpp
-       $(CC) $(CC_OPTIONS) rarecalc.cpp -c $(INCLUDE) -o ./rarecalc.o
-
-
-# Item # 111 -- raredisplay --
-./raredisplay.o : raredisplay.cpp
-       $(CC) $(CC_OPTIONS) raredisplay.cpp -c $(INCLUDE) -o ./raredisplay.o
-
-
-# Item # 112 -- rarefact --
-./rarefact.o : rarefact.cpp
-       $(CC) $(CC_OPTIONS) rarefact.cpp -c $(INCLUDE) -o ./rarefact.o
-
-
-# Item # 113 -- rarefactcommand --
-./rarefactcommand.o : rarefactcommand.cpp
-       $(CC) $(CC_OPTIONS) rarefactcommand.cpp -c $(INCLUDE) -o ./rarefactcommand.o
-
-
-# Item # 114 -- rarefactsharedcommand --
-./rarefactsharedcommand.o : rarefactsharedcommand.cpp
-       $(CC) $(CC_OPTIONS) rarefactsharedcommand.cpp -c $(INCLUDE) -o ./rarefactsharedcommand.o
-
-
-# Item # 115 -- sabundvector --
-./sabundvector.o : sabundvector.cpp
-       $(CC) $(CC_OPTIONS) sabundvector.cpp -c $(INCLUDE) -o ./sabundvector.o
-
-
-# Item # 116 -- sequence --
-./sequence.o : sequence.cpp
-       $(CC) $(CC_OPTIONS) sequence.cpp -c $(INCLUDE) -o ./sequence.o
-
-
-# Item # 117 -- shannon --
-./shannon.o : shannon.cpp
-       $(CC) $(CC_OPTIONS) shannon.cpp -c $(INCLUDE) -o ./shannon.o
-
-
-# Item # 118 -- sharedace --
-./sharedace.o : sharedace.cpp
-       $(CC) $(CC_OPTIONS) sharedace.cpp -c $(INCLUDE) -o ./sharedace.o
-
-
-# Item # 119 -- sharedchao1 --
-./sharedchao1.o : sharedchao1.cpp
-       $(CC) $(CC_OPTIONS) sharedchao1.cpp -c $(INCLUDE) -o ./sharedchao1.o
-
-
-# Item # 120 -- sharedcommand --
-./sharedcommand.o : sharedcommand.cpp
-       $(CC) $(CC_OPTIONS) sharedcommand.cpp -c $(INCLUDE) -o ./sharedcommand.o
-
-
-# Item # 121 -- sharedjabund --
-./sharedjabund.o : sharedjabund.cpp
-       $(CC) $(CC_OPTIONS) sharedjabund.cpp -c $(INCLUDE) -o ./sharedjabund.o
-
-
-# Item # 122 -- sharedjclass --
-./sharedjclass.o : sharedjclass.cpp
-       $(CC) $(CC_OPTIONS) sharedjclass.cpp -c $(INCLUDE) -o ./sharedjclass.o
-
-
-# Item # 123 -- sharedjest --
-./sharedjest.o : sharedjest.cpp
-       $(CC) $(CC_OPTIONS) sharedjest.cpp -c $(INCLUDE) -o ./sharedjest.o
-
-
-# Item # 124 -- sharedordervector --
-./sharedordervector.o : sharedordervector.cpp
-       $(CC) $(CC_OPTIONS) sharedordervector.cpp -c $(INCLUDE) -o ./sharedordervector.o
-
-
-# Item # 125 -- sharedrabundvector --
-./sharedrabundvector.o : sharedrabundvector.cpp
-       $(CC) $(CC_OPTIONS) sharedrabundvector.cpp -c $(INCLUDE) -o ./sharedrabundvector.o
-
-
-# Item # 126 -- sharedsabundvector --
-./sharedsabundvector.o : sharedsabundvector.cpp
-       $(CC) $(CC_OPTIONS) sharedsabundvector.cpp -c $(INCLUDE) -o ./sharedsabundvector.o
-
-
-# Item # 127 -- sharedsobs --
-./sharedsobs.o : sharedsobs.cpp
-       $(CC) $(CC_OPTIONS) sharedsobs.cpp -c $(INCLUDE) -o ./sharedsobs.o
-
-
-# Item # 128 -- sharedsorabund --
-./sharedsorabund.o : sharedsorabund.cpp
-       $(CC) $(CC_OPTIONS) sharedsorabund.cpp -c $(INCLUDE) -o ./sharedsorabund.o
-
-
-# Item # 129 -- sharedsorclass --
-./sharedsorclass.o : sharedsorclass.cpp
-       $(CC) $(CC_OPTIONS) sharedsorclass.cpp -c $(INCLUDE) -o ./sharedsorclass.o
-
-
-# Item # 130 -- sharedsorest --
-./sharedsorest.o : sharedsorest.cpp
-       $(CC) $(CC_OPTIONS) sharedsorest.cpp -c $(INCLUDE) -o ./sharedsorest.o
-
-
-# Item # 131 -- sharedthetan --
-./sharedthetan.o : sharedthetan.cpp
-       $(CC) $(CC_OPTIONS) sharedthetan.cpp -c $(INCLUDE) -o ./sharedthetan.o
-
-
-# Item # 132 -- sharedthetayc --
-./sharedthetayc.o : sharedthetayc.cpp
-       $(CC) $(CC_OPTIONS) sharedthetayc.cpp -c $(INCLUDE) -o ./sharedthetayc.o
-
-
-# Item # 133 -- simpson --
-./simpson.o : simpson.cpp
-       $(CC) $(CC_OPTIONS) simpson.cpp -c $(INCLUDE) -o ./simpson.o
-
-
-# Item # 134 -- singlelinkage --
-./singlelinkage.o : singlelinkage.cpp
-       $(CC) $(CC_OPTIONS) singlelinkage.cpp -c $(INCLUDE) -o ./singlelinkage.o
-
-
-# Item # 135 -- sparsematrix --
-./sparsematrix.o : sparsematrix.cpp
-       $(CC) $(CC_OPTIONS) sparsematrix.cpp -c $(INCLUDE) -o ./sparsematrix.o
-
-
-# Item # 136 -- summarycommand --
-./summarycommand.o : summarycommand.cpp
-       $(CC) $(CC_OPTIONS) summarycommand.cpp -c $(INCLUDE) -o ./summarycommand.o
-
-
-# Item # 137 -- summarysharedcommand --
-./summarysharedcommand.o : summarysharedcommand.cpp
-       $(CC) $(CC_OPTIONS) summarysharedcommand.cpp -c $(INCLUDE) -o ./summarysharedcommand.o
-
-
-# Item # 138 -- uvest --
-./uvest.o : uvest.cpp
-       $(CC) $(CC_OPTIONS) uvest.cpp -c $(INCLUDE) -o ./uvest.o
-
-
-# Item # 139 -- validcalculator --
-./validcalculator.o : validcalculator.cpp
-       $(CC) $(CC_OPTIONS) validcalculator.cpp -c $(INCLUDE) -o ./validcalculator.o
-
-
-# Item # 140 -- validparameter --
-./validparameter.o : validparameter.cpp
-       $(CC) $(CC_OPTIONS) validparameter.cpp -c $(INCLUDE) -o ./validparameter.o
-
-
-# Item # 141 -- treenode --
-./treenode.o : treenode.cpp
-       $(CC) $(CC_OPTIONS) treenode.cpp -c $(INCLUDE) -o ./treenode.o
-
-
-# Item # 142 -- readtreecommand --
-./readtreecommand.o : readtreecommand.cpp
-       $(CC) $(CC_OPTIONS) readtreecommand.cpp -c $(INCLUDE) -o ./readtreecommand.o
-
-
-# Item # 143 -- reversecommand --
-./reversecommand.o : reversecommand.cpp
-       $(CC) $(CC_OPTIONS) reversecommand.cpp -c $(INCLUDE) -o ./reversecommand.o
-
-
-# Item # 144 -- trimseqscommand --
-./trimseqscommand.o : trimseqscommand.cpp
-       $(CC) $(CC_OPTIONS) trimseqscommand.cpp -c $(INCLUDE) -o ./trimseqscommand.o
-
-
-# Item # 145 -- slibshuff --
-./slibshuff.o : slibshuff.cpp
-       $(CC) $(CC_OPTIONS) slibshuff.cpp -c $(INCLUDE) -o ./slibshuff.o
-
-
-# Item # 146 -- libshuff --
-./libshuff.o : libshuff.cpp
-       $(CC) $(CC_OPTIONS) libshuff.cpp -c $(INCLUDE) -o ./libshuff.o
-
-
-# Item # 147 -- dlibshuff --
-./dlibshuff.o : dlibshuff.cpp
-       $(CC) $(CC_OPTIONS) dlibshuff.cpp -c $(INCLUDE) -o ./dlibshuff.o
-
-
-# Item # 148 -- mergefilecommand --
-./mergefilecommand.o : mergefilecommand.cpp
-       $(CC) $(CC_OPTIONS) mergefilecommand.cpp -c $(INCLUDE) -o ./mergefilecommand.o
-
-
-# Item # 149 -- coverage --
-./coverage.o : coverage.cpp
-       $(CC) $(CC_OPTIONS) coverage.cpp -c $(INCLUDE) -o ./coverage.o
-
-
-# Item # 150 -- whittaker --
-./whittaker.o : whittaker.cpp
-       $(CC) $(CC_OPTIONS) whittaker.cpp -c $(INCLUDE) -o ./whittaker.o
-
-
-# Item # 151 -- preclustercommand --
-./preclustercommand.o : preclustercommand.cpp
-       $(CC) $(CC_OPTIONS) preclustercommand.cpp -c $(INCLUDE) -o ./preclustercommand.o
-
-
-# Item # 152 -- otuhierarchycommand --
-./otuhierarchycommand.o : otuhierarchycommand.cpp
-       $(CC) $(CC_OPTIONS) otuhierarchycommand.cpp -c $(INCLUDE) -o ./otuhierarchycommand.o
-
-
-# Item # 153 -- setdircommand --
-./setdircommand.o : setdircommand.cpp
-       $(CC) $(CC_OPTIONS) setdircommand.cpp -c $(INCLUDE) -o ./setdircommand.o
-
-
-# Item # 154 -- getgroupcommand --
-./getgroupcommand.o : getgroupcommand.cpp
-       $(CC) $(CC_OPTIONS) getgroupcommand.cpp -c $(INCLUDE) -o ./getgroupcommand.o
-
-
-# Item # 155 -- getlabelcommand --
-./getlabelcommand.o : getlabelcommand.cpp
-       $(CC) $(CC_OPTIONS) getlabelcommand.cpp -c $(INCLUDE) -o ./getlabelcommand.o
-
-
-# Item # 156 -- secondarystructurecommand --
-./secondarystructurecommand.o : secondarystructurecommand.cpp
-       $(CC) $(CC_OPTIONS) secondarystructurecommand.cpp -c $(INCLUDE) -o ./secondarystructurecommand.o
-
-
-# Item # 157 -- mothurout --
-./mothurout.o : mothurout.cpp
-       $(CC) $(CC_OPTIONS) mothurout.cpp -c $(INCLUDE) -o ./mothurout.o
-
-
-# Item # 158 -- parselistscommand --
-./parselistscommand.o : parselistscommand.cpp
-       $(CC) $(CC_OPTIONS) parselistscommand.cpp -c $(INCLUDE) -o ./parselistscommand.o
-
-
-# Item # 159 -- readblast --
-./readblast.o : readblast.cpp
-       $(CC) $(CC_OPTIONS) readblast.cpp -c $(INCLUDE) -o ./readblast.o
-
-
-# Item # 160 -- chimeracheckrdp --
-./chimeracheckrdp.o : chimeracheckrdp.cpp
-       $(CC) $(CC_OPTIONS) chimeracheckrdp.cpp -c $(INCLUDE) -o ./chimeracheckrdp.o
-
-
-# Item # 161 -- hclustercommand --
-./hclustercommand.o : hclustercommand.cpp
-       $(CC) $(CC_OPTIONS) hclustercommand.cpp -c $(INCLUDE) -o ./hclustercommand.o
-
-
-# Item # 162 -- hcluster --
-./hcluster.o : hcluster.cpp
-       $(CC) $(CC_OPTIONS) hcluster.cpp -c $(INCLUDE) -o ./hcluster.o
-
-
-# Item # 163 -- getlistcountcommand --
-./getlistcountcommand.o : getlistcountcommand.cpp
-       $(CC) $(CC_OPTIONS) getlistcountcommand.cpp -c $(INCLUDE) -o ./getlistcountcommand.o
-
-
-# Item # 164 -- readcluster --
-./readcluster.o : readcluster.cpp
-       $(CC) $(CC_OPTIONS) readcluster.cpp -c $(INCLUDE) -o ./readcluster.o
-
-
-# Item # 165 -- ccode --
-./ccode.o : ccode.cpp
-       $(CC) $(CC_OPTIONS) ccode.cpp -c $(INCLUDE) -o ./ccode.o
-
-
-# Item # 166 -- taxonomyequalizer --
-./taxonomyequalizer.o : taxonomyequalizer.cpp
-       $(CC) $(CC_OPTIONS) taxonomyequalizer.cpp -c $(INCLUDE) -o ./taxonomyequalizer.o
-
-
-# Item # 167 -- phylotypecommand --
-./phylotypecommand.o : phylotypecommand.cpp
-       $(CC) $(CC_OPTIONS) phylotypecommand.cpp -c $(INCLUDE) -o ./phylotypecommand.o
-
-
-# Item # 168 -- classifyseqscommand --
-./classifyseqscommand.o : classifyseqscommand.cpp
-       $(CC) $(CC_OPTIONS) classifyseqscommand.cpp -c $(INCLUDE) -o ./classifyseqscommand.o
-
-
-# Item # 169 -- classify --
-./classify.o : classify.cpp
-       $(CC) $(CC_OPTIONS) classify.cpp -c $(INCLUDE) -o ./classify.o
-
-
-# Item # 170 -- phylotree --
-./phylotree.o : phylotree.cpp
-       $(CC) $(CC_OPTIONS) phylotree.cpp -c $(INCLUDE) -o ./phylotree.o
-
-
-# Item # 171 -- bayesian --
-./bayesian.o : bayesian.cpp
-       $(CC) $(CC_OPTIONS) bayesian.cpp -c $(INCLUDE) -o ./bayesian.o
-
-
-# Item # 172 -- alignmentdb --
-./alignmentdb.o : alignmentdb.cpp
-       $(CC) $(CC_OPTIONS) alignmentdb.cpp -c $(INCLUDE) -o ./alignmentdb.o
-
-
-# Item # 173 -- knn --
-./knn.o : knn.cpp
-       $(CC) $(CC_OPTIONS) knn.cpp -c $(INCLUDE) -o ./knn.o
-
-
-# Item # 174 -- distancedb --
-./distancedb.o : distancedb.cpp
-       $(CC) $(CC_OPTIONS) distancedb.cpp -c $(INCLUDE) -o ./distancedb.o
-
-
-# Item # 175 -- chimeraslayer --
-./chimeraslayer.o : chimeraslayer.cpp
-       $(CC) $(CC_OPTIONS) chimeraslayer.cpp -c $(INCLUDE) -o ./chimeraslayer.o
-
-
-# Item # 176 -- slayer --
-./slayer.o : slayer.cpp
-       $(CC) $(CC_OPTIONS) slayer.cpp -c $(INCLUDE) -o ./slayer.o
-
-
-# Item # 177 -- pcacommand --
-./pcacommand.o : pcacommand.cpp
-       $(CC) $(CC_OPTIONS) pcacommand.cpp -c $(INCLUDE) -o ./pcacommand.o
-
-
-# Item # 178 -- formatcolumn --
-./formatcolumn.o : formatcolumn.cpp
-       $(CC) $(CC_OPTIONS) formatcolumn.cpp -c $(INCLUDE) -o ./formatcolumn.o
-
-
-# Item # 179 -- formatphylip --
-./formatphylip.o : formatphylip.cpp
-       $(CC) $(CC_OPTIONS) formatphylip.cpp -c $(INCLUDE) -o ./formatphylip.o
-
-
-# Item # 180 -- mgclustercommand --
-./mgclustercommand.o : mgclustercommand.cpp
-       $(CC) $(CC_OPTIONS) mgclustercommand.cpp -c $(INCLUDE) -o ./mgclustercommand.o
-
-
-# Item # 181 -- getsharedotucommand --
-./getsharedotucommand.o : getsharedotucommand.cpp
-       $(CC) $(CC_OPTIONS) getsharedotucommand.cpp -c $(INCLUDE) -o ./getsharedotucommand.o
-
-
-# Item # 182 -- maligner --
-./maligner.o : maligner.cpp
-       $(CC) $(CC_OPTIONS) maligner.cpp -c $(INCLUDE) -o ./maligner.o
-
-
-# Item # 183 -- chimerarealigner --
-./chimerarealigner.o : chimerarealigner.cpp
-       $(CC) $(CC_OPTIONS) chimerarealigner.cpp -c $(INCLUDE) -o ./chimerarealigner.o
-
-
-# Item # 184 -- bergerparker --
-./bergerparker.o : bergerparker.cpp
-       $(CC) $(CC_OPTIONS) bergerparker.cpp -c $(INCLUDE) -o ./bergerparker.o
-
-
-# Item # 185 -- bstick --
-./bstick.o : bstick.cpp
-       $(CC) $(CC_OPTIONS) bstick.cpp -c $(INCLUDE) -o ./bstick.o
-
-
-# Item # 186 -- sharedkstest --
-./sharedkstest.o : sharedkstest.cpp
-       $(CC) $(CC_OPTIONS) sharedkstest.cpp -c $(INCLUDE) -o ./sharedkstest.o
-
-
-# Item # 187 -- qstat --
-./qstat.o : qstat.cpp
-       $(CC) $(CC_OPTIONS) qstat.cpp -c $(INCLUDE) -o ./qstat.o
-
-
-# Item # 188 -- shen --
-./shen.o : shen.cpp
-       $(CC) $(CC_OPTIONS) shen.cpp -c $(INCLUDE) -o ./shen.o
-
-
-# Item # 189 -- logsd --
-./logsd.o : logsd.cpp
-       $(CC) $(CC_OPTIONS) logsd.cpp -c $(INCLUDE) -o ./logsd.o
-
-
-# Item # 190 -- geom --
-./geom.o : geom.cpp
-       $(CC) $(CC_OPTIONS) geom.cpp -c $(INCLUDE) -o ./geom.o
-
-# Item # 191 -- parsesffcommand --
-./parsesffcommand.o : parsesffcommand.cpp
-       $(CC) $(CC_OPTIONS) parsesffcommand.cpp -c $(INCLUDE) -o ./parsesffcommand.o
-
-# Item # 192 -- chimeraccodecommand --
-./chimeraccodecommand.o : chimeraccodecommand.cpp
-       $(CC) $(CC_OPTIONS) chimeraccodecommand.cpp -c $(INCLUDE) -o ./chimeraccodecommand.o
-
-# Item # 193 -- chimeracheckcommand --
-./chimeracheckcommand.o : chimeracheckcommand.cpp
-       $(CC) $(CC_OPTIONS) chimeracheckcommand.cpp -c $(INCLUDE) -o ./chimeracheckcommand.o
-
-
-# Item # 194 -- chimeraslayercommand --
-./chimeraslayercommand.o : chimeraslayercommand.cpp
-       $(CC) $(CC_OPTIONS) chimeraslayercommand.cpp -c $(INCLUDE) -o ./chimeraslayercommand.o
-
-# Item # 195 -- chimerapintailcommand --
-./chimerapintailcommand.o : chimerapintailcommand.cpp
-       $(CC) $(CC_OPTIONS) chimerapintailcommand.cpp -c $(INCLUDE) -o ./chimerapintailcommand.o
-
-# Item # 196 -- chimerabellerophoncommand --
-./chimerabellerophoncommand.o : chimerabellerophoncommand.cpp
-       $(CC) $(CC_OPTIONS) chimerabellerophoncommand.cpp -c $(INCLUDE) -o ./chimerabellerophoncommand.o
-
-# Item # 197 -- phylosummary --
-./phylosummary.o : phylosummary.cpp
-       $(CC) $(CC_OPTIONS) phylosummary.cpp -c $(INCLUDE) -o ./phylosummary.o
-
-# Item # 198 -- setlogfilecommand --
-./setlogfilecommand.o : setlogfilecommand.cpp
-       $(CC) $(CC_OPTIONS) setlogfilecommand.cpp -c $(INCLUDE) -o ./setlogfilecommand.o
-
-# Item # 199 -- phylodiversity --
-./phylodiversity.o : phylodiversity.cpp
-       $(CC) $(CC_OPTIONS) phylodiversity.cpp -c $(INCLUDE) -o ./phylodiversity.o
-
-# Item # 200 -- phylodiversitycommand --
-./phylodiversitycommand.o : phylodiversitycommand.cpp
-       $(CC) $(CC_OPTIONS) phylodiversitycommand.cpp -c $(INCLUDE) -o ./phylodiversitycommand.o
-
-# Item # 201 -- makegroupcommand --
-./makegroupcommand.o : makegroupcommand.cpp
-       $(CC) $(CC_OPTIONS) makegroupcommand.cpp -c $(INCLUDE) -o ./makegroupcommand.o
-
-# Item # 202 -- chopseqscommand --
-./chopseqscommand.o : chopseqscommand.cpp
-       $(CC) $(CC_OPTIONS) chopseqscommand.cpp -c $(INCLUDE) -o ./chopseqscommand.o
-
-# Item # 203 -- clearcutcommand --
-./clearcutcommand.o : clearcutcommand.cpp
-       $(CC) $(CC_OPTIONS) clearcutcommand.cpp -c $(INCLUDE) -o ./clearcutcommand.o
-
-# Item # 204 -- catchallcommand --
-./catchallcommand.o : catchallcommand.cpp
-       $(CC) $(CC_OPTIONS) catchallcommand.cpp -c $(INCLUDE) -o ./catchallcommand.o
-
-# Item # 205 -- splitabundcommand --
-./splitabundcommand : splitabundcommand
-       $(CC) $(CC_OPTIONS) splitabundcommand -c $(INCLUDE) -o ./splitabundcommand
-       
-# Item # 206 -- splitmatrix --
-./splitmatrix : splitmatrix
-       $(CC) $(CC_OPTIONS) splitmatrix -c $(INCLUDE) -o ./splitmatrix
-       
-# Item # 207 -- splitmatrix --
-./clustersplitcommand : clustersplitcommand
-       $(CC) $(CC_OPTIONS) clustersplitcommand -c $(INCLUDE) -o ./clustersplitcommand
-
-##### END RUN ####
+###################################################\r
+#\r
+# Makefile for mothur\r
+# Creator [Xcode -> Makefile Ver: Feb 14 2007 09:18:41]\r
+# Created: April 16, 2010\r
+#\r
+###################################################\r
+\r
+#\r
+# Macros\r
+#\r
+\r
+CC = g++ \r
+CC_OPTIONS = -O3\r
+\r
+# if you do not want to use the readline library set to no, default yes.\r
+# make sure you have the library installed\r
+\r
+USEREADLINE ?= yes\r
+\r
+ifeq  ($(strip $(USEREADLINE)),yes)\r
+    CC_OPTIONS += -DUSE_READLINE\r
+       LNK_OPTIONS += \\r
+      -lreadline\\r
+      -lncurses\\r
+      -L../readline-6.0\r
+endif\r
+\r
+USEMPI ?= no\r
+\r
+ifeq  ($(strip $(USEMPI)),yes)\r
+       CC = mpic++\r
+    CC_OPTIONS += -DUSE_MPI\r
+endif\r
+\r
+#\r
+# INCLUDE directories for mothur\r
+#\r
+\r
+     INCLUDE = -I.\r
+\r
+#\r
+# Build mothur\r
+#\r
+\r
+mothur : \\r
+               ./sharedutilities.o\\r
+               ./treegroupscommand.o\\r
+               ./bootstrapsharedcommand.o\\r
+               ./matrixoutputcommand.o\\r
+               ./getoturepcommand.o\\r
+               ./screenseqscommand.o\\r
+               ./chimera.o\\r
+               ./decalc.o\\r
+               ./readotucommand.o\\r
+               ./readdistcommand.o\\r
+               ./commandfactory.o\\r
+               ./alignment.o\\r
+               ./alignmentcell.o\\r
+               ./gotohoverlap.o\\r
+               ./overlap.o\\r
+               ./needlemanoverlap.o\\r
+               ./blastalign.o\\r
+               ./noalign.o\\r
+               ./suffixdb.o\\r
+               ./suffixnodes.o\\r
+               ./suffixtree.o\\r
+               ./blastdb.o\\r
+               ./nast.o\\r
+               ./nastreport.o\\r
+               ./boneh.o\\r
+               ./efron.o\\r
+               ./solow.o\\r
+               ./unifracweightedcommand.o\\r
+               ./weighted.o\\r
+               ./unweighted.o\\r
+               ./unifracunweightedcommand.o\\r
+               ./getsabundcommand.o\\r
+               ./getrabundcommand.o\\r
+               ./bellerophon.o\\r
+               ./pintail.o\\r
+               ./sharedanderbergs.o\\r
+               ./venncommand.o\\r
+               ./venn.o\\r
+               ./fullmatrix.o\\r
+               ./heatmap.o\\r
+               ./heatmapcommand.o\\r
+               ./libshuffcommand.o\\r
+               ./nocommands.o\\r
+               ./sharedbraycurtis.o\\r
+               ./sharedkulczynski.o\\r
+               ./sharedlennon.o\\r
+               ./sharedkulczynskicody.o\\r
+               ./sharedmorisitahorn.o\\r
+               ./sharedochiai.o\\r
+               ./readcolumn.o\\r
+               ./readotu.o\\r
+               ./readphylip.o\\r
+               ./consensuscommand.o\\r
+               ./heatmapsimcommand.o\\r
+               ./heatmapsim.o\\r
+               ./optionparser.o\\r
+               ./filterseqscommand.o\\r
+               ./goodscoverage.o\\r
+               ./sequencedb.o\\r
+               ./sharedjackknife.o\\r
+               ./sharedmarczewski.o\\r
+               ./aligncommand.o\\r
+               ./treemap.o\\r
+               ./parsimonycommand.o\\r
+               ./parsimony.o\\r
+               ./seqsummarycommand.o\\r
+               ./chimeraccodecommand.o\\r
+               ./chimerabellerophoncommand.o\\r
+               ./chimeracheckcommand.o\\r
+               ./chimeraslayercommand.o\\r
+               ./chimerapintailcommand.o\\r
+               ./chimeraseqscommand.o\\r
+               ./sharedlistvector.o\\r
+               ./tree.o\\r
+               ./readtree.o\\r
+               ./sharedsobscollectsummary.o\\r
+               ./deconvolutecommand.o\\r
+               ./listseqscommand.o\\r
+               ./getseqscommand.o\\r
+               ./removeseqscommand.o\\r
+               ./systemcommand.o\\r
+               ./binsequencecommand.o\\r
+               ./distancecommand.o\\r
+               ./ace.o\\r
+               ./averagelinkage.o\\r
+               ./bootstrap.o\\r
+               ./calculator.o\\r
+               ./chao1.o\\r
+               ./cluster.o\\r
+               ./clustercommand.o\\r
+               ./collect.o\\r
+               ./collectcommand.o\\r
+               ./collectsharedcommand.o\\r
+               ./commandoptionparser.o\\r
+               ./completelinkage.o\\r
+               ./database.o\\r
+               ./engine.o\\r
+               ./fastamap.o\\r
+               ./fileoutput.o\\r
+               ./globaldata.o\\r
+               ./groupmap.o\\r
+               ./helpcommand.o\\r
+               ./makegroupcommand.o\\r
+               ./chopseqscommand.o\\r
+               ./clearcutcommand.o\\r
+               ./catchallcommand.o\\r
+               ./splitabundcommand.o\\r
+               ./splitmatrix.o\\r
+               ./clustersplitcommand.o\\r
+               ./inputdata.o\\r
+               ./jackknife.o\\r
+               ./kmer.o\\r
+               ./kmerdb.o\\r
+               ./listvector.o\\r
+               ./mothur.o\\r
+               ./nameassignment.o\\r
+               ./npshannon.o\\r
+               ./ordervector.o\\r
+               ./progress.o\\r
+               ./quitcommand.o\\r
+               ./rabundvector.o\\r
+               ./rarecalc.o\\r
+               ./raredisplay.o\\r
+               ./rarefact.o\\r
+               ./rarefactcommand.o\\r
+               ./rarefactsharedcommand.o\\r
+               ./sabundvector.o\\r
+               ./sequence.o\\r
+               ./shannon.o\\r
+               ./sharedace.o\\r
+               ./sharedchao1.o\\r
+               ./sharedcommand.o\\r
+               ./sharedjabund.o\\r
+               ./sharedjclass.o\\r
+               ./sharedjest.o\\r
+               ./sharedordervector.o\\r
+               ./sharedrabundvector.o\\r
+               ./sharedsabundvector.o\\r
+               ./sharedsobs.o\\r
+               ./sharedsorabund.o\\r
+               ./sharedsorclass.o\\r
+               ./sharedsorest.o\\r
+               ./sharedthetan.o\\r
+               ./sharedthetayc.o\\r
+               ./simpson.o\\r
+               ./singlelinkage.o\\r
+               ./sparsematrix.o\\r
+               ./summarycommand.o\\r
+               ./summarysharedcommand.o\\r
+               ./uvest.o\\r
+               ./validcalculator.o\\r
+               ./validparameter.o\\r
+               ./treenode.o\\r
+               ./readtreecommand.o\\r
+               ./reversecommand.o\\r
+               ./trimseqscommand.o\\r
+               ./slibshuff.o\\r
+               ./libshuff.o\\r
+               ./dlibshuff.o\\r
+               ./mergefilecommand.o\\r
+               ./coverage.o\\r
+               ./whittaker.o\\r
+               ./preclustercommand.o\\r
+               ./otuhierarchycommand.o\\r
+               ./setdircommand.o\\r
+               ./getgroupcommand.o\\r
+               ./getlabelcommand.o\\r
+               ./secondarystructurecommand.o\\r
+               ./mothurout.o\\r
+               ./parselistscommand.o\\r
+               ./readblast.o\\r
+               ./chimeracheckrdp.o\\r
+               ./hclustercommand.o\\r
+               ./hcluster.o\\r
+               ./getlistcountcommand.o\\r
+               ./readcluster.o\\r
+               ./ccode.o\\r
+               ./taxonomyequalizer.o\\r
+               ./phylotypecommand.o\\r
+               ./classifyseqscommand.o\\r
+               ./parsesffcommand.o\\r
+               ./classify.o\\r
+               ./phylotree.o\\r
+               ./phylodiversity.o\\r
+               ./phylodiversitycommand.o\\r
+               ./bayesian.o\\r
+               ./phylosummary.o\\r
+               ./alignmentdb.o\\r
+               ./knn.o\\r
+               ./distancedb.o\\r
+               ./chimeraslayer.o\\r
+               ./slayer.o\\r
+               ./pcacommand.o\\r
+               ./formatcolumn.o\\r
+               ./formatphylip.o\\r
+               ./mgclustercommand.o\\r
+               ./getsharedotucommand.o\\r
+               ./maligner.o\\r
+               ./chimerarealigner.o\\r
+               ./bergerparker.o\\r
+               ./bstick.o\\r
+               ./sharedkstest.o\\r
+               ./qstat.o\\r
+               ./shen.o\\r
+               ./logsd.o\\r
+               ./geom.o\\r
+               ./setlogfilecommand.o\r
+       $(CC) $(LNK_OPTIONS) \\r
+               ./sharedutilities.o\\r
+               ./treegroupscommand.o\\r
+               ./bootstrapsharedcommand.o\\r
+               ./matrixoutputcommand.o\\r
+               ./getoturepcommand.o\\r
+               ./screenseqscommand.o\\r
+               ./chimera.o\\r
+               ./decalc.o\\r
+               ./readotucommand.o\\r
+               ./readdistcommand.o\\r
+               ./commandfactory.o\\r
+               ./alignment.o\\r
+               ./alignmentcell.o\\r
+               ./gotohoverlap.o\\r
+               ./overlap.o\\r
+               ./needlemanoverlap.o\\r
+               ./blastalign.o\\r
+               ./noalign.o\\r
+               ./suffixdb.o\\r
+               ./suffixnodes.o\\r
+               ./suffixtree.o\\r
+               ./blastdb.o\\r
+               ./nast.o\\r
+               ./nastreport.o\\r
+               ./boneh.o\\r
+               ./efron.o\\r
+               ./solow.o\\r
+               ./unifracweightedcommand.o\\r
+               ./weighted.o\\r
+               ./unweighted.o\\r
+               ./unifracunweightedcommand.o\\r
+               ./getsabundcommand.o\\r
+               ./getrabundcommand.o\\r
+               ./bellerophon.o\\r
+               ./pintail.o\\r
+               ./sharedanderbergs.o\\r
+               ./venncommand.o\\r
+               ./venn.o\\r
+               ./fullmatrix.o\\r
+               ./heatmap.o\\r
+               ./heatmapcommand.o\\r
+               ./libshuffcommand.o\\r
+               ./nocommands.o\\r
+               ./sharedbraycurtis.o\\r
+               ./sharedkulczynski.o\\r
+               ./sharedlennon.o\\r
+               ./sharedkulczynskicody.o\\r
+               ./sharedmorisitahorn.o\\r
+               ./sharedochiai.o\\r
+               ./readcolumn.o\\r
+               ./readotu.o\\r
+               ./readphylip.o\\r
+               ./consensuscommand.o\\r
+               ./heatmapsimcommand.o\\r
+               ./heatmapsim.o\\r
+               ./optionparser.o\\r
+               ./filterseqscommand.o\\r
+               ./goodscoverage.o\\r
+               ./sequencedb.o\\r
+               ./sharedjackknife.o\\r
+               ./sharedmarczewski.o\\r
+               ./aligncommand.o\\r
+               ./treemap.o\\r
+               ./parsimonycommand.o\\r
+               ./parsimony.o\\r
+               ./seqsummarycommand.o\\r
+               ./chimeraccodecommand.o\\r
+               ./chimerabellerophoncommand.o\\r
+               ./chimeracheckcommand.o\\r
+               ./chimeraslayercommand.o\\r
+               ./chimerapintailcommand.o\\r
+               ./chimeraseqscommand.o\\r
+               ./sharedlistvector.o\\r
+               ./tree.o\\r
+               ./readtree.o\\r
+               ./sharedsobscollectsummary.o\\r
+               ./deconvolutecommand.o\\r
+               ./listseqscommand.o\\r
+               ./getseqscommand.o\\r
+               ./removeseqscommand.o\\r
+               ./systemcommand.o\\r
+               ./binsequencecommand.o\\r
+               ./distancecommand.o\\r
+               ./ace.o\\r
+               ./averagelinkage.o\\r
+               ./bootstrap.o\\r
+               ./calculator.o\\r
+               ./chao1.o\\r
+               ./cluster.o\\r
+               ./clustercommand.o\\r
+               ./collect.o\\r
+               ./collectcommand.o\\r
+               ./collectsharedcommand.o\\r
+               ./commandoptionparser.o\\r
+               ./completelinkage.o\\r
+               ./database.o\\r
+               ./engine.o\\r
+               ./fastamap.o\\r
+               ./fileoutput.o\\r
+               ./globaldata.o\\r
+               ./groupmap.o\\r
+               ./helpcommand.o\\r
+               ./makegroupcommand.o\\r
+               ./chopseqscommand.o\\r
+               ./clearcutcommand.o\\r
+               ./catchallcommand.o\\r
+               ./splitabundcommand.o\\r
+               ./splitmatrix.o\\r
+               ./clustersplitcommand.o\\r
+               ./inputdata.o\\r
+               ./jackknife.o\\r
+               ./kmer.o\\r
+               ./kmerdb.o\\r
+               ./listvector.o\\r
+               ./mothur.o\\r
+               ./nameassignment.o\\r
+               ./npshannon.o\\r
+               ./ordervector.o\\r
+               ./progress.o\\r
+               ./quitcommand.o\\r
+               ./rabundvector.o\\r
+               ./rarecalc.o\\r
+               ./raredisplay.o\\r
+               ./rarefact.o\\r
+               ./rarefactcommand.o\\r
+               ./rarefactsharedcommand.o\\r
+               ./sabundvector.o\\r
+               ./sequence.o\\r
+               ./shannon.o\\r
+               ./sharedace.o\\r
+               ./sharedchao1.o\\r
+               ./sharedcommand.o\\r
+               ./sharedjabund.o\\r
+               ./sharedjclass.o\\r
+               ./sharedjest.o\\r
+               ./sharedordervector.o\\r
+               ./sharedrabundvector.o\\r
+               ./sharedsabundvector.o\\r
+               ./sharedsobs.o\\r
+               ./sharedsorabund.o\\r
+               ./sharedsorclass.o\\r
+               ./sharedsorest.o\\r
+               ./sharedthetan.o\\r
+               ./sharedthetayc.o\\r
+               ./simpson.o\\r
+               ./singlelinkage.o\\r
+               ./sparsematrix.o\\r
+               ./summarycommand.o\\r
+               ./summarysharedcommand.o\\r
+               ./uvest.o\\r
+               ./validcalculator.o\\r
+               ./validparameter.o\\r
+               ./treenode.o\\r
+               ./readtreecommand.o\\r
+               ./reversecommand.o\\r
+               ./trimseqscommand.o\\r
+               ./slibshuff.o\\r
+               ./libshuff.o\\r
+               ./dlibshuff.o\\r
+               ./mergefilecommand.o\\r
+               ./coverage.o\\r
+               ./whittaker.o\\r
+               ./preclustercommand.o\\r
+               ./otuhierarchycommand.o\\r
+               ./setdircommand.o\\r
+               ./getgroupcommand.o\\r
+               ./getlabelcommand.o\\r
+               ./secondarystructurecommand.o\\r
+               ./mothurout.o\\r
+               ./parselistscommand.o\\r
+               ./readblast.o\\r
+               ./chimeracheckrdp.o\\r
+               ./hclustercommand.o\\r
+               ./hcluster.o\\r
+               ./getlistcountcommand.o\\r
+               ./readcluster.o\\r
+               ./ccode.o\\r
+               ./taxonomyequalizer.o\\r
+               ./phylotypecommand.o\\r
+               ./classifyseqscommand.o\\r
+               ./parsesffcommand.o\\r
+               ./classify.o\\r
+               ./phylotree.o\\r
+               ./phylodiversity.o\\r
+               ./phylodiversitycommand.o\\r
+               ./bayesian.o\\r
+               ./phylosummary.o\\r
+               ./alignmentdb.o\\r
+               ./knn.o\\r
+               ./distancedb.o\\r
+               ./chimeraslayer.o\\r
+               ./slayer.o\\r
+               ./pcacommand.o\\r
+               ./formatcolumn.o\\r
+               ./formatphylip.o\\r
+               ./mgclustercommand.o\\r
+               ./getsharedotucommand.o\\r
+               ./maligner.o\\r
+               ./chimerarealigner.o\\r
+               ./bergerparker.o\\r
+               ./bstick.o\\r
+               ./sharedkstest.o\\r
+               ./qstat.o\\r
+               ./shen.o\\r
+               ./logsd.o\\r
+               ./geom.o\\r
+               ./setlogfilecommand.o\\r
+               -o ../Release/mothur\r
+\r
+clean : \r
+               rm \\r
+               ./sharedutilities.o\\r
+               ./treegroupscommand.o\\r
+               ./bootstrapsharedcommand.o\\r
+               ./matrixoutputcommand.o\\r
+               ./getoturepcommand.o\\r
+               ./screenseqscommand.o\\r
+               ./chimera.o\\r
+               ./decalc.o\\r
+               ./readotucommand.o\\r
+               ./readdistcommand.o\\r
+               ./commandfactory.o\\r
+               ./alignment.o\\r
+               ./alignmentcell.o\\r
+               ./gotohoverlap.o\\r
+               ./overlap.o\\r
+               ./needlemanoverlap.o\\r
+               ./blastalign.o\\r
+               ./noalign.o\\r
+               ./suffixdb.o\\r
+               ./suffixnodes.o\\r
+               ./suffixtree.o\\r
+               ./blastdb.o\\r
+               ./nast.o\\r
+               ./nastreport.o\\r
+               ./boneh.o\\r
+               ./efron.o\\r
+               ./solow.o\\r
+               ./unifracweightedcommand.o\\r
+               ./weighted.o\\r
+               ./unweighted.o\\r
+               ./unifracunweightedcommand.o\\r
+               ./getsabundcommand.o\\r
+               ./getrabundcommand.o\\r
+               ./bellerophon.o\\r
+               ./pintail.o\\r
+               ./sharedanderbergs.o\\r
+               ./venncommand.o\\r
+               ./venn.o\\r
+               ./fullmatrix.o\\r
+               ./heatmap.o\\r
+               ./heatmapcommand.o\\r
+               ./libshuffcommand.o\\r
+               ./nocommands.o\\r
+               ./sharedbraycurtis.o\\r
+               ./sharedkulczynski.o\\r
+               ./sharedlennon.o\\r
+               ./sharedkulczynskicody.o\\r
+               ./sharedmorisitahorn.o\\r
+               ./sharedochiai.o\\r
+               ./readcolumn.o\\r
+               ./readotu.o\\r
+               ./readphylip.o\\r
+               ./consensuscommand.o\\r
+               ./heatmapsimcommand.o\\r
+               ./heatmapsim.o\\r
+               ./optionparser.o\\r
+               ./filterseqscommand.o\\r
+               ./goodscoverage.o\\r
+               ./sequencedb.o\\r
+               ./sharedjackknife.o\\r
+               ./sharedmarczewski.o\\r
+               ./aligncommand.o\\r
+               ./treemap.o\\r
+               ./parsimonycommand.o\\r
+               ./parsimony.o\\r
+               ./seqsummarycommand.o\\r
+               ./chimeraccodecommand.o\\r
+               ./chimerabellerophoncommand.o\\r
+               ./chimeracheckcommand.o\\r
+               ./chimeraslayercommand.o\\r
+               ./chimerapintailcommand.o\\r
+               ./chimeraseqscommand.o\\r
+               ./sharedlistvector.o\\r
+               ./tree.o\\r
+               ./readtree.o\\r
+               ./sharedsobscollectsummary.o\\r
+               ./deconvolutecommand.o\\r
+               ./listseqscommand.o\\r
+               ./getseqscommand.o\\r
+               ./removeseqscommand.o\\r
+               ./systemcommand.o\\r
+               ./binsequencecommand.o\\r
+               ./distancecommand.o\\r
+               ./ace.o\\r
+               ./averagelinkage.o\\r
+               ./bootstrap.o\\r
+               ./calculator.o\\r
+               ./chao1.o\\r
+               ./cluster.o\\r
+               ./clustercommand.o\\r
+               ./collect.o\\r
+               ./collectcommand.o\\r
+               ./collectsharedcommand.o\\r
+               ./commandoptionparser.o\\r
+               ./completelinkage.o\\r
+               ./database.o\\r
+               ./engine.o\\r
+               ./fastamap.o\\r
+               ./fileoutput.o\\r
+               ./globaldata.o\\r
+               ./groupmap.o\\r
+               ./helpcommand.o\\r
+               ./makegroupcommand.o\\r
+               ./chopseqscommand.o\\r
+               ./clearcutcommand.o\\r
+               ./catchallcommand.o\\r
+               ./splitabundcommand.o\\r
+               ./splitmatrix.o\\r
+               ./clustersplitcommand.o\\r
+               ./inputdata.o\\r
+               ./jackknife.o\\r
+               ./kmer.o\\r
+               ./kmerdb.o\\r
+               ./listvector.o\\r
+               ./mothur.o\\r
+               ./nameassignment.o\\r
+               ./npshannon.o\\r
+               ./ordervector.o\\r
+               ./progress.o\\r
+               ./quitcommand.o\\r
+               ./rabundvector.o\\r
+               ./rarecalc.o\\r
+               ./raredisplay.o\\r
+               ./rarefact.o\\r
+               ./rarefactcommand.o\\r
+               ./rarefactsharedcommand.o\\r
+               ./sabundvector.o\\r
+               ./sequence.o\\r
+               ./shannon.o\\r
+               ./sharedace.o\\r
+               ./sharedchao1.o\\r
+               ./sharedcommand.o\\r
+               ./sharedjabund.o\\r
+               ./sharedjclass.o\\r
+               ./sharedjest.o\\r
+               ./sharedordervector.o\\r
+               ./sharedrabundvector.o\\r
+               ./sharedsabundvector.o\\r
+               ./sharedsobs.o\\r
+               ./sharedsorabund.o\\r
+               ./sharedsorclass.o\\r
+               ./sharedsorest.o\\r
+               ./sharedthetan.o\\r
+               ./sharedthetayc.o\\r
+               ./simpson.o\\r
+               ./singlelinkage.o\\r
+               ./sparsematrix.o\\r
+               ./summarycommand.o\\r
+               ./summarysharedcommand.o\\r
+               ./uvest.o\\r
+               ./validcalculator.o\\r
+               ./validparameter.o\\r
+               ./treenode.o\\r
+               ./readtreecommand.o\\r
+               ./reversecommand.o\\r
+               ./trimseqscommand.o\\r
+               ./slibshuff.o\\r
+               ./libshuff.o\\r
+               ./dlibshuff.o\\r
+               ./mergefilecommand.o\\r
+               ./coverage.o\\r
+               ./whittaker.o\\r
+               ./preclustercommand.o\\r
+               ./otuhierarchycommand.o\\r
+               ./setdircommand.o\\r
+               ./getgroupcommand.o\\r
+               ./getlabelcommand.o\\r
+               ./secondarystructurecommand.o\\r
+               ./mothurout.o\\r
+               ./parselistscommand.o\\r
+               ./readblast.o\\r
+               ./chimeracheckrdp.o\\r
+               ./hclustercommand.o\\r
+               ./hcluster.o\\r
+               ./getlistcountcommand.o\\r
+               ./readcluster.o\\r
+               ./ccode.o\\r
+               ./taxonomyequalizer.o\\r
+               ./phylotypecommand.o\\r
+               ./classifyseqscommand.o\\r
+               ./parsesffcommand.o\\r
+               ./classify.o\\r
+               ./phylotree.o\\r
+               ./phylodiversity.o\\r
+               ./phylodiversitycommand.o\\r
+               ./bayesian.o\\r
+               ./phylosummary.o\\r
+               ./alignmentdb.o\\r
+               ./knn.o\\r
+               ./distancedb.o\\r
+               ./chimeraslayer.o\\r
+               ./slayer.o\\r
+               ./pcacommand.o\\r
+               ./formatcolumn.o\\r
+               ./formatphylip.o\\r
+               ./mgclustercommand.o\\r
+               ./getsharedotucommand.o\\r
+               ./maligner.o\\r
+               ./chimerarealigner.o\\r
+               ./bergerparker.o\\r
+               ./bstick.o\\r
+               ./sharedkstest.o\\r
+               ./qstat.o\\r
+               ./shen.o\\r
+               ./logsd.o\\r
+               ./geom.o\\r
+               ./setlogfilecommand.o\\r
+               mothur\r
+\r
+install : mothur\r
+               #cp mothur ../Release/mothur\r
+\r
+#\r
+# Build the parts of mothur\r
+#\r
+\r
+\r
+# Item # 1 -- sharedutilities --\r
+./sharedutilities.o : sharedutilities.cpp\r
+       $(CC) $(CC_OPTIONS) sharedutilities.cpp -c $(INCLUDE) -o ./sharedutilities.o\r
+\r
+\r
+# Item # 2 -- treegroupscommand --\r
+./treegroupscommand.o : treegroupscommand.cpp\r
+       $(CC) $(CC_OPTIONS) treegroupscommand.cpp -c $(INCLUDE) -o ./treegroupscommand.o\r
+\r
+\r
+# Item # 3 -- bootstrapsharedcommand --\r
+./bootstrapsharedcommand.o : bootstrapsharedcommand.cpp\r
+       $(CC) $(CC_OPTIONS) bootstrapsharedcommand.cpp -c $(INCLUDE) -o ./bootstrapsharedcommand.o\r
+\r
+\r
+# Item # 4 -- matrixoutputcommand --\r
+./matrixoutputcommand.o : matrixoutputcommand.cpp\r
+       $(CC) $(CC_OPTIONS) matrixoutputcommand.cpp -c $(INCLUDE) -o ./matrixoutputcommand.o\r
+\r
+\r
+# Item # 5 -- getoturepcommand --\r
+./getoturepcommand.o : getoturepcommand.cpp\r
+       $(CC) $(CC_OPTIONS) getoturepcommand.cpp -c $(INCLUDE) -o ./getoturepcommand.o\r
+\r
+\r
+# Item # 6 -- screenseqscommand --\r
+./screenseqscommand.o : screenseqscommand.cpp\r
+       $(CC) $(CC_OPTIONS) screenseqscommand.cpp -c $(INCLUDE) -o ./screenseqscommand.o\r
+\r
+\r
+# Item # 7 -- chimera --\r
+./chimera.o : chimera.cpp\r
+       $(CC) $(CC_OPTIONS) chimera.cpp -c $(INCLUDE) -o ./chimera.o\r
+\r
+\r
+# Item # 8 -- decalc --\r
+./decalc.o : decalc.cpp\r
+       $(CC) $(CC_OPTIONS) decalc.cpp -c $(INCLUDE) -o ./decalc.o\r
+\r
+\r
+# Item # 9 -- readotucommand --\r
+./readotucommand.o : readotucommand.cpp\r
+       $(CC) $(CC_OPTIONS) readotucommand.cpp -c $(INCLUDE) -o ./readotucommand.o\r
+\r
+\r
+# Item # 10 -- readdistcommand --\r
+./readdistcommand.o : readdistcommand.cpp\r
+       $(CC) $(CC_OPTIONS) readdistcommand.cpp -c $(INCLUDE) -o ./readdistcommand.o\r
+\r
+\r
+# Item # 11 -- commandfactory --\r
+./commandfactory.o : commandfactory.cpp\r
+       $(CC) $(CC_OPTIONS) commandfactory.cpp -c $(INCLUDE) -o ./commandfactory.o\r
+\r
+\r
+# Item # 12 -- alignment --\r
+./alignment.o : alignment.cpp\r
+       $(CC) $(CC_OPTIONS) alignment.cpp -c $(INCLUDE) -o ./alignment.o\r
+\r
+\r
+# Item # 13 -- alignmentcell --\r
+./alignmentcell.o : alignmentcell.cpp\r
+       $(CC) $(CC_OPTIONS) alignmentcell.cpp -c $(INCLUDE) -o ./alignmentcell.o\r
+\r
+\r
+# Item # 14 -- gotohoverlap --\r
+./gotohoverlap.o : gotohoverlap.cpp\r
+       $(CC) $(CC_OPTIONS) gotohoverlap.cpp -c $(INCLUDE) -o ./gotohoverlap.o\r
+\r
+\r
+# Item # 15 -- overlap --\r
+./overlap.o : overlap.cpp\r
+       $(CC) $(CC_OPTIONS) overlap.cpp -c $(INCLUDE) -o ./overlap.o\r
+\r
+\r
+# Item # 16 -- needlemanoverlap --\r
+./needlemanoverlap.o : needlemanoverlap.cpp\r
+       $(CC) $(CC_OPTIONS) needlemanoverlap.cpp -c $(INCLUDE) -o ./needlemanoverlap.o\r
+\r
+\r
+# Item # 17 -- blastalign --\r
+./blastalign.o : blastalign.cpp\r
+       $(CC) $(CC_OPTIONS) blastalign.cpp -c $(INCLUDE) -o ./blastalign.o\r
+\r
+\r
+# Item # 18 -- noalign --\r
+./noalign.o : noalign.cpp\r
+       $(CC) $(CC_OPTIONS) noalign.cpp -c $(INCLUDE) -o ./noalign.o\r
+\r
+\r
+# Item # 19 -- suffixdb --\r
+./suffixdb.o : suffixdb.cpp\r
+       $(CC) $(CC_OPTIONS) suffixdb.cpp -c $(INCLUDE) -o ./suffixdb.o\r
+\r
+\r
+# Item # 20 -- suffixnodes --\r
+./suffixnodes.o : suffixnodes.cpp\r
+       $(CC) $(CC_OPTIONS) suffixnodes.cpp -c $(INCLUDE) -o ./suffixnodes.o\r
+\r
+\r
+# Item # 21 -- suffixtree --\r
+./suffixtree.o : suffixtree.cpp\r
+       $(CC) $(CC_OPTIONS) suffixtree.cpp -c $(INCLUDE) -o ./suffixtree.o\r
+\r
+\r
+# Item # 22 -- blastdb --\r
+./blastdb.o : blastdb.cpp\r
+       $(CC) $(CC_OPTIONS) blastdb.cpp -c $(INCLUDE) -o ./blastdb.o\r
+\r
+\r
+# Item # 23 -- nast --\r
+./nast.o : nast.cpp\r
+       $(CC) $(CC_OPTIONS) nast.cpp -c $(INCLUDE) -o ./nast.o\r
+\r
+\r
+# Item # 24 -- nastreport --\r
+./nastreport.o : nastreport.cpp\r
+       $(CC) $(CC_OPTIONS) nastreport.cpp -c $(INCLUDE) -o ./nastreport.o\r
+\r
+\r
+# Item # 25 -- boneh --\r
+./boneh.o : boneh.cpp\r
+       $(CC) $(CC_OPTIONS) boneh.cpp -c $(INCLUDE) -o ./boneh.o\r
+\r
+\r
+# Item # 26 -- efron --\r
+./efron.o : efron.cpp\r
+       $(CC) $(CC_OPTIONS) efron.cpp -c $(INCLUDE) -o ./efron.o\r
+\r
+\r
+# Item # 27 -- solow --\r
+./solow.o : solow.cpp\r
+       $(CC) $(CC_OPTIONS) solow.cpp -c $(INCLUDE) -o ./solow.o\r
+\r
+\r
+# Item # 28 -- unifracweightedcommand --\r
+./unifracweightedcommand.o : unifracweightedcommand.cpp\r
+       $(CC) $(CC_OPTIONS) unifracweightedcommand.cpp -c $(INCLUDE) -o ./unifracweightedcommand.o\r
+\r
+\r
+# Item # 29 -- weighted --\r
+./weighted.o : weighted.cpp\r
+       $(CC) $(CC_OPTIONS) weighted.cpp -c $(INCLUDE) -o ./weighted.o\r
+\r
+\r
+# Item # 30 -- unweighted --\r
+./unweighted.o : unweighted.cpp\r
+       $(CC) $(CC_OPTIONS) unweighted.cpp -c $(INCLUDE) -o ./unweighted.o\r
+\r
+\r
+# Item # 31 -- unifracunweightedcommand --\r
+./unifracunweightedcommand.o : unifracunweightedcommand.cpp\r
+       $(CC) $(CC_OPTIONS) unifracunweightedcommand.cpp -c $(INCLUDE) -o ./unifracunweightedcommand.o\r
+\r
+\r
+# Item # 32 -- getsabundcommand --\r
+./getsabundcommand.o : getsabundcommand.cpp\r
+       $(CC) $(CC_OPTIONS) getsabundcommand.cpp -c $(INCLUDE) -o ./getsabundcommand.o\r
+\r
+\r
+# Item # 33 -- getrabundcommand --\r
+./getrabundcommand.o : getrabundcommand.cpp\r
+       $(CC) $(CC_OPTIONS) getrabundcommand.cpp -c $(INCLUDE) -o ./getrabundcommand.o\r
+\r
+\r
+# Item # 34 -- bellerophon --\r
+./bellerophon.o : bellerophon.cpp\r
+       $(CC) $(CC_OPTIONS) bellerophon.cpp -c $(INCLUDE) -o ./bellerophon.o\r
+\r
+\r
+# Item # 35 -- pintail --\r
+./pintail.o : pintail.cpp\r
+       $(CC) $(CC_OPTIONS) pintail.cpp -c $(INCLUDE) -o ./pintail.o\r
+\r
+\r
+# Item # 36 -- sharedanderbergs --\r
+./sharedanderbergs.o : sharedanderbergs.cpp\r
+       $(CC) $(CC_OPTIONS) sharedanderbergs.cpp -c $(INCLUDE) -o ./sharedanderbergs.o\r
+\r
+\r
+# Item # 37 -- venncommand --\r
+./venncommand.o : venncommand.cpp\r
+       $(CC) $(CC_OPTIONS) venncommand.cpp -c $(INCLUDE) -o ./venncommand.o\r
+\r
+\r
+# Item # 38 -- venn --\r
+./venn.o : venn.cpp\r
+       $(CC) $(CC_OPTIONS) venn.cpp -c $(INCLUDE) -o ./venn.o\r
+\r
+\r
+# Item # 39 -- fullmatrix --\r
+./fullmatrix.o : fullmatrix.cpp\r
+       $(CC) $(CC_OPTIONS) fullmatrix.cpp -c $(INCLUDE) -o ./fullmatrix.o\r
+\r
+\r
+# Item # 40 -- heatmap --\r
+./heatmap.o : heatmap.cpp\r
+       $(CC) $(CC_OPTIONS) heatmap.cpp -c $(INCLUDE) -o ./heatmap.o\r
+\r
+\r
+# Item # 41 -- heatmapcommand --\r
+./heatmapcommand.o : heatmapcommand.cpp\r
+       $(CC) $(CC_OPTIONS) heatmapcommand.cpp -c $(INCLUDE) -o ./heatmapcommand.o\r
+\r
+\r
+# Item # 42 -- libshuffcommand --\r
+./libshuffcommand.o : libshuffcommand.cpp\r
+       $(CC) $(CC_OPTIONS) libshuffcommand.cpp -c $(INCLUDE) -o ./libshuffcommand.o\r
+\r
+\r
+# Item # 43 -- nocommands --\r
+./nocommands.o : nocommands.cpp\r
+       $(CC) $(CC_OPTIONS) nocommands.cpp -c $(INCLUDE) -o ./nocommands.o\r
+\r
+\r
+# Item # 44 -- sharedbraycurtis --\r
+./sharedbraycurtis.o : sharedbraycurtis.cpp\r
+       $(CC) $(CC_OPTIONS) sharedbraycurtis.cpp -c $(INCLUDE) -o ./sharedbraycurtis.o\r
+\r
+\r
+# Item # 45 -- sharedkulczynski --\r
+./sharedkulczynski.o : sharedkulczynski.cpp\r
+       $(CC) $(CC_OPTIONS) sharedkulczynski.cpp -c $(INCLUDE) -o ./sharedkulczynski.o\r
+\r
+\r
+# Item # 46 -- sharedlennon --\r
+./sharedlennon.o : sharedlennon.cpp\r
+       $(CC) $(CC_OPTIONS) sharedlennon.cpp -c $(INCLUDE) -o ./sharedlennon.o\r
+\r
+\r
+# Item # 47 -- sharedkulczynskicody --\r
+./sharedkulczynskicody.o : sharedkulczynskicody.cpp\r
+       $(CC) $(CC_OPTIONS) sharedkulczynskicody.cpp -c $(INCLUDE) -o ./sharedkulczynskicody.o\r
+\r
+\r
+# Item # 48 -- sharedmorisitahorn --\r
+./sharedmorisitahorn.o : sharedmorisitahorn.cpp\r
+       $(CC) $(CC_OPTIONS) sharedmorisitahorn.cpp -c $(INCLUDE) -o ./sharedmorisitahorn.o\r
+\r
+\r
+# Item # 49 -- sharedochiai --\r
+./sharedochiai.o : sharedochiai.cpp\r
+       $(CC) $(CC_OPTIONS) sharedochiai.cpp -c $(INCLUDE) -o ./sharedochiai.o\r
+\r
+\r
+# Item # 50 -- readcolumn --\r
+./readcolumn.o : readcolumn.cpp\r
+       $(CC) $(CC_OPTIONS) readcolumn.cpp -c $(INCLUDE) -o ./readcolumn.o\r
+\r
+\r
+# Item # 51 -- readotu --\r
+./readotu.o : readotu.cpp\r
+       $(CC) $(CC_OPTIONS) readotu.cpp -c $(INCLUDE) -o ./readotu.o\r
+\r
+\r
+# Item # 52 -- readphylip --\r
+./readphylip.o : readphylip.cpp\r
+       $(CC) $(CC_OPTIONS) readphylip.cpp -c $(INCLUDE) -o ./readphylip.o\r
+\r
+\r
+# Item # 53 -- consensuscommand --\r
+./consensuscommand.o : consensuscommand.cpp\r
+       $(CC) $(CC_OPTIONS) consensuscommand.cpp -c $(INCLUDE) -o ./consensuscommand.o\r
+\r
+\r
+# Item # 54 -- heatmapsimcommand --\r
+./heatmapsimcommand.o : heatmapsimcommand.cpp\r
+       $(CC) $(CC_OPTIONS) heatmapsimcommand.cpp -c $(INCLUDE) -o ./heatmapsimcommand.o\r
+\r
+\r
+# Item # 55 -- heatmapsim --\r
+./heatmapsim.o : heatmapsim.cpp\r
+       $(CC) $(CC_OPTIONS) heatmapsim.cpp -c $(INCLUDE) -o ./heatmapsim.o\r
+\r
+\r
+# Item # 56 -- optionparser --\r
+./optionparser.o : optionparser.cpp\r
+       $(CC) $(CC_OPTIONS) optionparser.cpp -c $(INCLUDE) -o ./optionparser.o\r
+\r
+\r
+# Item # 57 -- filterseqscommand --\r
+./filterseqscommand.o : filterseqscommand.cpp\r
+       $(CC) $(CC_OPTIONS) filterseqscommand.cpp -c $(INCLUDE) -o ./filterseqscommand.o\r
+\r
+\r
+# Item # 58 -- goodscoverage --\r
+./goodscoverage.o : goodscoverage.cpp\r
+       $(CC) $(CC_OPTIONS) goodscoverage.cpp -c $(INCLUDE) -o ./goodscoverage.o\r
+\r
+\r
+# Item # 59 -- sequencedb --\r
+./sequencedb.o : sequencedb.cpp\r
+       $(CC) $(CC_OPTIONS) sequencedb.cpp -c $(INCLUDE) -o ./sequencedb.o\r
+\r
+\r
+# Item # 60 -- sharedjackknife --\r
+./sharedjackknife.o : sharedjackknife.cpp\r
+       $(CC) $(CC_OPTIONS) sharedjackknife.cpp -c $(INCLUDE) -o ./sharedjackknife.o\r
+\r
+\r
+# Item # 61 -- sharedmarczewski --\r
+./sharedmarczewski.o : sharedmarczewski.cpp\r
+       $(CC) $(CC_OPTIONS) sharedmarczewski.cpp -c $(INCLUDE) -o ./sharedmarczewski.o\r
+\r
+\r
+# Item # 62 -- aligncommand --\r
+./aligncommand.o : aligncommand.cpp\r
+       $(CC) $(CC_OPTIONS) aligncommand.cpp -c $(INCLUDE) -o ./aligncommand.o\r
+\r
+\r
+# Item # 63 -- treemap --\r
+./treemap.o : treemap.cpp\r
+       $(CC) $(CC_OPTIONS) treemap.cpp -c $(INCLUDE) -o ./treemap.o\r
+\r
+\r
+# Item # 64 -- parsimonycommand --\r
+./parsimonycommand.o : parsimonycommand.cpp\r
+       $(CC) $(CC_OPTIONS) parsimonycommand.cpp -c $(INCLUDE) -o ./parsimonycommand.o\r
+\r
+\r
+# Item # 65 -- parsimony --\r
+./parsimony.o : parsimony.cpp\r
+       $(CC) $(CC_OPTIONS) parsimony.cpp -c $(INCLUDE) -o ./parsimony.o\r
+\r
+\r
+# Item # 66 -- seqsummarycommand --\r
+./seqsummarycommand.o : seqsummarycommand.cpp\r
+       $(CC) $(CC_OPTIONS) seqsummarycommand.cpp -c $(INCLUDE) -o ./seqsummarycommand.o\r
+\r
+\r
+# Item # 67 -- chimeraseqscommand --\r
+./chimeraseqscommand.o : chimeraseqscommand.cpp\r
+       $(CC) $(CC_OPTIONS) chimeraseqscommand.cpp -c $(INCLUDE) -o ./chimeraseqscommand.o\r
+\r
+\r
+# Item # 68 -- sharedlistvector --\r
+./sharedlistvector.o : sharedlistvector.cpp\r
+       $(CC) $(CC_OPTIONS) sharedlistvector.cpp -c $(INCLUDE) -o ./sharedlistvector.o\r
+\r
+\r
+# Item # 69 -- tree --\r
+./tree.o : tree.cpp\r
+       $(CC) $(CC_OPTIONS) tree.cpp -c $(INCLUDE) -o ./tree.o\r
+\r
+\r
+# Item # 70 -- readtree --\r
+./readtree.o : readtree.cpp\r
+       $(CC) $(CC_OPTIONS) readtree.cpp -c $(INCLUDE) -o ./readtree.o\r
+\r
+\r
+# Item # 71 -- sharedsobscollectsummary --\r
+./sharedsobscollectsummary.o : sharedsobscollectsummary.cpp\r
+       $(CC) $(CC_OPTIONS) sharedsobscollectsummary.cpp -c $(INCLUDE) -o ./sharedsobscollectsummary.o\r
+\r
+\r
+# Item # 72 -- deconvolutecommand --\r
+./deconvolutecommand.o : deconvolutecommand.cpp\r
+       $(CC) $(CC_OPTIONS) deconvolutecommand.cpp -c $(INCLUDE) -o ./deconvolutecommand.o\r
+\r
+\r
+# Item # 73 -- listseqscommand --\r
+./listseqscommand.o : listseqscommand.cpp\r
+       $(CC) $(CC_OPTIONS) listseqscommand.cpp -c $(INCLUDE) -o ./listseqscommand.o\r
+\r
+\r
+# Item # 74 -- getseqscommand --\r
+./getseqscommand.o : getseqscommand.cpp\r
+       $(CC) $(CC_OPTIONS) getseqscommand.cpp -c $(INCLUDE) -o ./getseqscommand.o\r
+\r
+\r
+# Item # 75 -- removeseqscommand --\r
+./removeseqscommand.o : removeseqscommand.cpp\r
+       $(CC) $(CC_OPTIONS) removeseqscommand.cpp -c $(INCLUDE) -o ./removeseqscommand.o\r
+\r
+\r
+# Item # 76 -- systemcommand --\r
+./systemcommand.o : systemcommand.cpp\r
+       $(CC) $(CC_OPTIONS) systemcommand.cpp -c $(INCLUDE) -o ./systemcommand.o\r
+\r
+\r
+# Item # 77 -- binsequencecommand --\r
+./binsequencecommand.o : binsequencecommand.cpp\r
+       $(CC) $(CC_OPTIONS) binsequencecommand.cpp -c $(INCLUDE) -o ./binsequencecommand.o\r
+\r
+\r
+# Item # 78 -- distancecommand --\r
+./distancecommand.o : distancecommand.cpp\r
+       $(CC) $(CC_OPTIONS) distancecommand.cpp -c $(INCLUDE) -o ./distancecommand.o\r
+\r
+\r
+# Item # 79 -- ace --\r
+./ace.o : ace.cpp\r
+       $(CC) $(CC_OPTIONS) ace.cpp -c $(INCLUDE) -o ./ace.o\r
+\r
+\r
+# Item # 80 -- averagelinkage --\r
+./averagelinkage.o : averagelinkage.cpp\r
+       $(CC) $(CC_OPTIONS) averagelinkage.cpp -c $(INCLUDE) -o ./averagelinkage.o\r
+\r
+\r
+# Item # 81 -- bootstrap --\r
+./bootstrap.o : bootstrap.cpp\r
+       $(CC) $(CC_OPTIONS) bootstrap.cpp -c $(INCLUDE) -o ./bootstrap.o\r
+\r
+\r
+# Item # 82 -- calculator --\r
+./calculator.o : calculator.cpp\r
+       $(CC) $(CC_OPTIONS) calculator.cpp -c $(INCLUDE) -o ./calculator.o\r
+\r
+\r
+# Item # 83 -- chao1 --\r
+./chao1.o : chao1.cpp\r
+       $(CC) $(CC_OPTIONS) chao1.cpp -c $(INCLUDE) -o ./chao1.o\r
+\r
+\r
+# Item # 84 -- cluster --\r
+./cluster.o : cluster.cpp\r
+       $(CC) $(CC_OPTIONS) cluster.cpp -c $(INCLUDE) -o ./cluster.o\r
+\r
+\r
+# Item # 85 -- clustercommand --\r
+./clustercommand.o : clustercommand.cpp\r
+       $(CC) $(CC_OPTIONS) clustercommand.cpp -c $(INCLUDE) -o ./clustercommand.o\r
+\r
+\r
+# Item # 86 -- collect --\r
+./collect.o : collect.cpp\r
+       $(CC) $(CC_OPTIONS) collect.cpp -c $(INCLUDE) -o ./collect.o\r
+\r
+\r
+# Item # 87 -- collectcommand --\r
+./collectcommand.o : collectcommand.cpp\r
+       $(CC) $(CC_OPTIONS) collectcommand.cpp -c $(INCLUDE) -o ./collectcommand.o\r
+\r
+\r
+# Item # 88 -- collectsharedcommand --\r
+./collectsharedcommand.o : collectsharedcommand.cpp\r
+       $(CC) $(CC_OPTIONS) collectsharedcommand.cpp -c $(INCLUDE) -o ./collectsharedcommand.o\r
+\r
+\r
+# Item # 89 -- commandoptionparser --\r
+./commandoptionparser.o : commandoptionparser.cpp\r
+       $(CC) $(CC_OPTIONS) commandoptionparser.cpp -c $(INCLUDE) -o ./commandoptionparser.o\r
+\r
+\r
+# Item # 90 -- completelinkage --\r
+./completelinkage.o : completelinkage.cpp\r
+       $(CC) $(CC_OPTIONS) completelinkage.cpp -c $(INCLUDE) -o ./completelinkage.o\r
+\r
+\r
+# Item # 91 -- database --\r
+./database.o : database.cpp\r
+       $(CC) $(CC_OPTIONS) database.cpp -c $(INCLUDE) -o ./database.o\r
+\r
+\r
+# Item # 92 -- engine --\r
+./engine.o : engine.cpp\r
+       $(CC) $(CC_OPTIONS) engine.cpp -c $(INCLUDE) -o ./engine.o\r
+\r
+\r
+# Item # 93 -- fastamap --\r
+./fastamap.o : fastamap.cpp\r
+       $(CC) $(CC_OPTIONS) fastamap.cpp -c $(INCLUDE) -o ./fastamap.o\r
+\r
+\r
+# Item # 94 -- fileoutput --\r
+./fileoutput.o : fileoutput.cpp\r
+       $(CC) $(CC_OPTIONS) fileoutput.cpp -c $(INCLUDE) -o ./fileoutput.o\r
+\r
+\r
+# Item # 95 -- globaldata --\r
+./globaldata.o : globaldata.cpp\r
+       $(CC) $(CC_OPTIONS) globaldata.cpp -c $(INCLUDE) -o ./globaldata.o\r
+\r
+\r
+# Item # 96 -- groupmap --\r
+./groupmap.o : groupmap.cpp\r
+       $(CC) $(CC_OPTIONS) groupmap.cpp -c $(INCLUDE) -o ./groupmap.o\r
+\r
+\r
+# Item # 97 -- helpcommand --\r
+./helpcommand.o : helpcommand.cpp\r
+       $(CC) $(CC_OPTIONS) helpcommand.cpp -c $(INCLUDE) -o ./helpcommand.o\r
+\r
+\r
+# Item # 98 -- inputdata --\r
+./inputdata.o : inputdata.cpp\r
+       $(CC) $(CC_OPTIONS) inputdata.cpp -c $(INCLUDE) -o ./inputdata.o\r
+\r
+\r
+# Item # 99 -- jackknife --\r
+./jackknife.o : jackknife.cpp\r
+       $(CC) $(CC_OPTIONS) jackknife.cpp -c $(INCLUDE) -o ./jackknife.o\r
+\r
+\r
+# Item # 100 -- kmer --\r
+./kmer.o : kmer.cpp\r
+       $(CC) $(CC_OPTIONS) kmer.cpp -c $(INCLUDE) -o ./kmer.o\r
+\r
+\r
+# Item # 101 -- kmerdb --\r
+./kmerdb.o : kmerdb.cpp\r
+       $(CC) $(CC_OPTIONS) kmerdb.cpp -c $(INCLUDE) -o ./kmerdb.o\r
+\r
+\r
+# Item # 102 -- listvector --\r
+./listvector.o : listvector.cpp\r
+       $(CC) $(CC_OPTIONS) listvector.cpp -c $(INCLUDE) -o ./listvector.o\r
+\r
+\r
+# Item # 103 -- mothur --\r
+./mothur.o : mothur.cpp\r
+       $(CC) $(CC_OPTIONS) mothur.cpp -c $(INCLUDE) -o ./mothur.o\r
+\r
+\r
+# Item # 104 -- nameassignment --\r
+./nameassignment.o : nameassignment.cpp\r
+       $(CC) $(CC_OPTIONS) nameassignment.cpp -c $(INCLUDE) -o ./nameassignment.o\r
+\r
+\r
+# Item # 105 -- npshannon --\r
+./npshannon.o : npshannon.cpp\r
+       $(CC) $(CC_OPTIONS) npshannon.cpp -c $(INCLUDE) -o ./npshannon.o\r
+\r
+\r
+# Item # 106 -- ordervector --\r
+./ordervector.o : ordervector.cpp\r
+       $(CC) $(CC_OPTIONS) ordervector.cpp -c $(INCLUDE) -o ./ordervector.o\r
+\r
+\r
+# Item # 107 -- progress --\r
+./progress.o : progress.cpp\r
+       $(CC) $(CC_OPTIONS) progress.cpp -c $(INCLUDE) -o ./progress.o\r
+\r
+\r
+# Item # 108 -- quitcommand --\r
+./quitcommand.o : quitcommand.cpp\r
+       $(CC) $(CC_OPTIONS) quitcommand.cpp -c $(INCLUDE) -o ./quitcommand.o\r
+\r
+\r
+# Item # 109 -- rabundvector --\r
+./rabundvector.o : rabundvector.cpp\r
+       $(CC) $(CC_OPTIONS) rabundvector.cpp -c $(INCLUDE) -o ./rabundvector.o\r
+\r
+\r
+# Item # 110 -- rarecalc --\r
+./rarecalc.o : rarecalc.cpp\r
+       $(CC) $(CC_OPTIONS) rarecalc.cpp -c $(INCLUDE) -o ./rarecalc.o\r
+\r
+\r
+# Item # 111 -- raredisplay --\r
+./raredisplay.o : raredisplay.cpp\r
+       $(CC) $(CC_OPTIONS) raredisplay.cpp -c $(INCLUDE) -o ./raredisplay.o\r
+\r
+\r
+# Item # 112 -- rarefact --\r
+./rarefact.o : rarefact.cpp\r
+       $(CC) $(CC_OPTIONS) rarefact.cpp -c $(INCLUDE) -o ./rarefact.o\r
+\r
+\r
+# Item # 113 -- rarefactcommand --\r
+./rarefactcommand.o : rarefactcommand.cpp\r
+       $(CC) $(CC_OPTIONS) rarefactcommand.cpp -c $(INCLUDE) -o ./rarefactcommand.o\r
+\r
+\r
+# Item # 114 -- rarefactsharedcommand --\r
+./rarefactsharedcommand.o : rarefactsharedcommand.cpp\r
+       $(CC) $(CC_OPTIONS) rarefactsharedcommand.cpp -c $(INCLUDE) -o ./rarefactsharedcommand.o\r
+\r
+\r
+# Item # 115 -- sabundvector --\r
+./sabundvector.o : sabundvector.cpp\r
+       $(CC) $(CC_OPTIONS) sabundvector.cpp -c $(INCLUDE) -o ./sabundvector.o\r
+\r
+\r
+# Item # 116 -- sequence --\r
+./sequence.o : sequence.cpp\r
+       $(CC) $(CC_OPTIONS) sequence.cpp -c $(INCLUDE) -o ./sequence.o\r
+\r
+\r
+# Item # 117 -- shannon --\r
+./shannon.o : shannon.cpp\r
+       $(CC) $(CC_OPTIONS) shannon.cpp -c $(INCLUDE) -o ./shannon.o\r
+\r
+\r
+# Item # 118 -- sharedace --\r
+./sharedace.o : sharedace.cpp\r
+       $(CC) $(CC_OPTIONS) sharedace.cpp -c $(INCLUDE) -o ./sharedace.o\r
+\r
+\r
+# Item # 119 -- sharedchao1 --\r
+./sharedchao1.o : sharedchao1.cpp\r
+       $(CC) $(CC_OPTIONS) sharedchao1.cpp -c $(INCLUDE) -o ./sharedchao1.o\r
+\r
+\r
+# Item # 120 -- sharedcommand --\r
+./sharedcommand.o : sharedcommand.cpp\r
+       $(CC) $(CC_OPTIONS) sharedcommand.cpp -c $(INCLUDE) -o ./sharedcommand.o\r
+\r
+\r
+# Item # 121 -- sharedjabund --\r
+./sharedjabund.o : sharedjabund.cpp\r
+       $(CC) $(CC_OPTIONS) sharedjabund.cpp -c $(INCLUDE) -o ./sharedjabund.o\r
+\r
+\r
+# Item # 122 -- sharedjclass --\r
+./sharedjclass.o : sharedjclass.cpp\r
+       $(CC) $(CC_OPTIONS) sharedjclass.cpp -c $(INCLUDE) -o ./sharedjclass.o\r
+\r
+\r
+# Item # 123 -- sharedjest --\r
+./sharedjest.o : sharedjest.cpp\r
+       $(CC) $(CC_OPTIONS) sharedjest.cpp -c $(INCLUDE) -o ./sharedjest.o\r
+\r
+\r
+# Item # 124 -- sharedordervector --\r
+./sharedordervector.o : sharedordervector.cpp\r
+       $(CC) $(CC_OPTIONS) sharedordervector.cpp -c $(INCLUDE) -o ./sharedordervector.o\r
+\r
+\r
+# Item # 125 -- sharedrabundvector --\r
+./sharedrabundvector.o : sharedrabundvector.cpp\r
+       $(CC) $(CC_OPTIONS) sharedrabundvector.cpp -c $(INCLUDE) -o ./sharedrabundvector.o\r
+\r
+\r
+# Item # 126 -- sharedsabundvector --\r
+./sharedsabundvector.o : sharedsabundvector.cpp\r
+       $(CC) $(CC_OPTIONS) sharedsabundvector.cpp -c $(INCLUDE) -o ./sharedsabundvector.o\r
+\r
+\r
+# Item # 127 -- sharedsobs --\r
+./sharedsobs.o : sharedsobs.cpp\r
+       $(CC) $(CC_OPTIONS) sharedsobs.cpp -c $(INCLUDE) -o ./sharedsobs.o\r
+\r
+\r
+# Item # 128 -- sharedsorabund --\r
+./sharedsorabund.o : sharedsorabund.cpp\r
+       $(CC) $(CC_OPTIONS) sharedsorabund.cpp -c $(INCLUDE) -o ./sharedsorabund.o\r
+\r
+\r
+# Item # 129 -- sharedsorclass --\r
+./sharedsorclass.o : sharedsorclass.cpp\r
+       $(CC) $(CC_OPTIONS) sharedsorclass.cpp -c $(INCLUDE) -o ./sharedsorclass.o\r
+\r
+\r
+# Item # 130 -- sharedsorest --\r
+./sharedsorest.o : sharedsorest.cpp\r
+       $(CC) $(CC_OPTIONS) sharedsorest.cpp -c $(INCLUDE) -o ./sharedsorest.o\r
+\r
+\r
+# Item # 131 -- sharedthetan --\r
+./sharedthetan.o : sharedthetan.cpp\r
+       $(CC) $(CC_OPTIONS) sharedthetan.cpp -c $(INCLUDE) -o ./sharedthetan.o\r
+\r
+\r
+# Item # 132 -- sharedthetayc --\r
+./sharedthetayc.o : sharedthetayc.cpp\r
+       $(CC) $(CC_OPTIONS) sharedthetayc.cpp -c $(INCLUDE) -o ./sharedthetayc.o\r
+\r
+\r
+# Item # 133 -- simpson --\r
+./simpson.o : simpson.cpp\r
+       $(CC) $(CC_OPTIONS) simpson.cpp -c $(INCLUDE) -o ./simpson.o\r
+\r
+\r
+# Item # 134 -- singlelinkage --\r
+./singlelinkage.o : singlelinkage.cpp\r
+       $(CC) $(CC_OPTIONS) singlelinkage.cpp -c $(INCLUDE) -o ./singlelinkage.o\r
+\r
+\r
+# Item # 135 -- sparsematrix --\r
+./sparsematrix.o : sparsematrix.cpp\r
+       $(CC) $(CC_OPTIONS) sparsematrix.cpp -c $(INCLUDE) -o ./sparsematrix.o\r
+\r
+\r
+# Item # 136 -- summarycommand --\r
+./summarycommand.o : summarycommand.cpp\r
+       $(CC) $(CC_OPTIONS) summarycommand.cpp -c $(INCLUDE) -o ./summarycommand.o\r
+\r
+\r
+# Item # 137 -- summarysharedcommand --\r
+./summarysharedcommand.o : summarysharedcommand.cpp\r
+       $(CC) $(CC_OPTIONS) summarysharedcommand.cpp -c $(INCLUDE) -o ./summarysharedcommand.o\r
+\r
+\r
+# Item # 138 -- uvest --\r
+./uvest.o : uvest.cpp\r
+       $(CC) $(CC_OPTIONS) uvest.cpp -c $(INCLUDE) -o ./uvest.o\r
+\r
+\r
+# Item # 139 -- validcalculator --\r
+./validcalculator.o : validcalculator.cpp\r
+       $(CC) $(CC_OPTIONS) validcalculator.cpp -c $(INCLUDE) -o ./validcalculator.o\r
+\r
+\r
+# Item # 140 -- validparameter --\r
+./validparameter.o : validparameter.cpp\r
+       $(CC) $(CC_OPTIONS) validparameter.cpp -c $(INCLUDE) -o ./validparameter.o\r
+\r
+\r
+# Item # 141 -- treenode --\r
+./treenode.o : treenode.cpp\r
+       $(CC) $(CC_OPTIONS) treenode.cpp -c $(INCLUDE) -o ./treenode.o\r
+\r
+\r
+# Item # 142 -- readtreecommand --\r
+./readtreecommand.o : readtreecommand.cpp\r
+       $(CC) $(CC_OPTIONS) readtreecommand.cpp -c $(INCLUDE) -o ./readtreecommand.o\r
+\r
+\r
+# Item # 143 -- reversecommand --\r
+./reversecommand.o : reversecommand.cpp\r
+       $(CC) $(CC_OPTIONS) reversecommand.cpp -c $(INCLUDE) -o ./reversecommand.o\r
+\r
+\r
+# Item # 144 -- trimseqscommand --\r
+./trimseqscommand.o : trimseqscommand.cpp\r
+       $(CC) $(CC_OPTIONS) trimseqscommand.cpp -c $(INCLUDE) -o ./trimseqscommand.o\r
+\r
+\r
+# Item # 145 -- slibshuff --\r
+./slibshuff.o : slibshuff.cpp\r
+       $(CC) $(CC_OPTIONS) slibshuff.cpp -c $(INCLUDE) -o ./slibshuff.o\r
+\r
+\r
+# Item # 146 -- libshuff --\r
+./libshuff.o : libshuff.cpp\r
+       $(CC) $(CC_OPTIONS) libshuff.cpp -c $(INCLUDE) -o ./libshuff.o\r
+\r
+\r
+# Item # 147 -- dlibshuff --\r
+./dlibshuff.o : dlibshuff.cpp\r
+       $(CC) $(CC_OPTIONS) dlibshuff.cpp -c $(INCLUDE) -o ./dlibshuff.o\r
+\r
+\r
+# Item # 148 -- mergefilecommand --\r
+./mergefilecommand.o : mergefilecommand.cpp\r
+       $(CC) $(CC_OPTIONS) mergefilecommand.cpp -c $(INCLUDE) -o ./mergefilecommand.o\r
+\r
+\r
+# Item # 149 -- coverage --\r
+./coverage.o : coverage.cpp\r
+       $(CC) $(CC_OPTIONS) coverage.cpp -c $(INCLUDE) -o ./coverage.o\r
+\r
+\r
+# Item # 150 -- whittaker --\r
+./whittaker.o : whittaker.cpp\r
+       $(CC) $(CC_OPTIONS) whittaker.cpp -c $(INCLUDE) -o ./whittaker.o\r
+\r
+\r
+# Item # 151 -- preclustercommand --\r
+./preclustercommand.o : preclustercommand.cpp\r
+       $(CC) $(CC_OPTIONS) preclustercommand.cpp -c $(INCLUDE) -o ./preclustercommand.o\r
+\r
+\r
+# Item # 152 -- otuhierarchycommand --\r
+./otuhierarchycommand.o : otuhierarchycommand.cpp\r
+       $(CC) $(CC_OPTIONS) otuhierarchycommand.cpp -c $(INCLUDE) -o ./otuhierarchycommand.o\r
+\r
+\r
+# Item # 153 -- setdircommand --\r
+./setdircommand.o : setdircommand.cpp\r
+       $(CC) $(CC_OPTIONS) setdircommand.cpp -c $(INCLUDE) -o ./setdircommand.o\r
+\r
+\r
+# Item # 154 -- getgroupcommand --\r
+./getgroupcommand.o : getgroupcommand.cpp\r
+       $(CC) $(CC_OPTIONS) getgroupcommand.cpp -c $(INCLUDE) -o ./getgroupcommand.o\r
+\r
+\r
+# Item # 155 -- getlabelcommand --\r
+./getlabelcommand.o : getlabelcommand.cpp\r
+       $(CC) $(CC_OPTIONS) getlabelcommand.cpp -c $(INCLUDE) -o ./getlabelcommand.o\r
+\r
+\r
+# Item # 156 -- secondarystructurecommand --\r
+./secondarystructurecommand.o : secondarystructurecommand.cpp\r
+       $(CC) $(CC_OPTIONS) secondarystructurecommand.cpp -c $(INCLUDE) -o ./secondarystructurecommand.o\r
+\r
+\r
+# Item # 157 -- mothurout --\r
+./mothurout.o : mothurout.cpp\r
+       $(CC) $(CC_OPTIONS) mothurout.cpp -c $(INCLUDE) -o ./mothurout.o\r
+\r
+\r
+# Item # 158 -- parselistscommand --\r
+./parselistscommand.o : parselistscommand.cpp\r
+       $(CC) $(CC_OPTIONS) parselistscommand.cpp -c $(INCLUDE) -o ./parselistscommand.o\r
+\r
+\r
+# Item # 159 -- readblast --\r
+./readblast.o : readblast.cpp\r
+       $(CC) $(CC_OPTIONS) readblast.cpp -c $(INCLUDE) -o ./readblast.o\r
+\r
+\r
+# Item # 160 -- chimeracheckrdp --\r
+./chimeracheckrdp.o : chimeracheckrdp.cpp\r
+       $(CC) $(CC_OPTIONS) chimeracheckrdp.cpp -c $(INCLUDE) -o ./chimeracheckrdp.o\r
+\r
+\r
+# Item # 161 -- hclustercommand --\r
+./hclustercommand.o : hclustercommand.cpp\r
+       $(CC) $(CC_OPTIONS) hclustercommand.cpp -c $(INCLUDE) -o ./hclustercommand.o\r
+\r
+\r
+# Item # 162 -- hcluster --\r
+./hcluster.o : hcluster.cpp\r
+       $(CC) $(CC_OPTIONS) hcluster.cpp -c $(INCLUDE) -o ./hcluster.o\r
+\r
+\r
+# Item # 163 -- getlistcountcommand --\r
+./getlistcountcommand.o : getlistcountcommand.cpp\r
+       $(CC) $(CC_OPTIONS) getlistcountcommand.cpp -c $(INCLUDE) -o ./getlistcountcommand.o\r
+\r
+\r
+# Item # 164 -- readcluster --\r
+./readcluster.o : readcluster.cpp\r
+       $(CC) $(CC_OPTIONS) readcluster.cpp -c $(INCLUDE) -o ./readcluster.o\r
+\r
+\r
+# Item # 165 -- ccode --\r
+./ccode.o : ccode.cpp\r
+       $(CC) $(CC_OPTIONS) ccode.cpp -c $(INCLUDE) -o ./ccode.o\r
+\r
+\r
+# Item # 166 -- taxonomyequalizer --\r
+./taxonomyequalizer.o : taxonomyequalizer.cpp\r
+       $(CC) $(CC_OPTIONS) taxonomyequalizer.cpp -c $(INCLUDE) -o ./taxonomyequalizer.o\r
+\r
+\r
+# Item # 167 -- phylotypecommand --\r
+./phylotypecommand.o : phylotypecommand.cpp\r
+       $(CC) $(CC_OPTIONS) phylotypecommand.cpp -c $(INCLUDE) -o ./phylotypecommand.o\r
+\r
+\r
+# Item # 168 -- classifyseqscommand --\r
+./classifyseqscommand.o : classifyseqscommand.cpp\r
+       $(CC) $(CC_OPTIONS) classifyseqscommand.cpp -c $(INCLUDE) -o ./classifyseqscommand.o\r
+\r
+\r
+# Item # 169 -- classify --\r
+./classify.o : classify.cpp\r
+       $(CC) $(CC_OPTIONS) classify.cpp -c $(INCLUDE) -o ./classify.o\r
+\r
+\r
+# Item # 170 -- phylotree --\r
+./phylotree.o : phylotree.cpp\r
+       $(CC) $(CC_OPTIONS) phylotree.cpp -c $(INCLUDE) -o ./phylotree.o\r
+\r
+\r
+# Item # 171 -- bayesian --\r
+./bayesian.o : bayesian.cpp\r
+       $(CC) $(CC_OPTIONS) bayesian.cpp -c $(INCLUDE) -o ./bayesian.o\r
+\r
+\r
+# Item # 172 -- alignmentdb --\r
+./alignmentdb.o : alignmentdb.cpp\r
+       $(CC) $(CC_OPTIONS) alignmentdb.cpp -c $(INCLUDE) -o ./alignmentdb.o\r
+\r
+\r
+# Item # 173 -- knn --\r
+./knn.o : knn.cpp\r
+       $(CC) $(CC_OPTIONS) knn.cpp -c $(INCLUDE) -o ./knn.o\r
+\r
+\r
+# Item # 174 -- distancedb --\r
+./distancedb.o : distancedb.cpp\r
+       $(CC) $(CC_OPTIONS) distancedb.cpp -c $(INCLUDE) -o ./distancedb.o\r
+\r
+\r
+# Item # 175 -- chimeraslayer --\r
+./chimeraslayer.o : chimeraslayer.cpp\r
+       $(CC) $(CC_OPTIONS) chimeraslayer.cpp -c $(INCLUDE) -o ./chimeraslayer.o\r
+\r
+\r
+# Item # 176 -- slayer --\r
+./slayer.o : slayer.cpp\r
+       $(CC) $(CC_OPTIONS) slayer.cpp -c $(INCLUDE) -o ./slayer.o\r
+\r
+\r
+# Item # 177 -- pcacommand --\r
+./pcacommand.o : pcacommand.cpp\r
+       $(CC) $(CC_OPTIONS) pcacommand.cpp -c $(INCLUDE) -o ./pcacommand.o\r
+\r
+\r
+# Item # 178 -- formatcolumn --\r
+./formatcolumn.o : formatcolumn.cpp\r
+       $(CC) $(CC_OPTIONS) formatcolumn.cpp -c $(INCLUDE) -o ./formatcolumn.o\r
+\r
+\r
+# Item # 179 -- formatphylip --\r
+./formatphylip.o : formatphylip.cpp\r
+       $(CC) $(CC_OPTIONS) formatphylip.cpp -c $(INCLUDE) -o ./formatphylip.o\r
+\r
+\r
+# Item # 180 -- mgclustercommand --\r
+./mgclustercommand.o : mgclustercommand.cpp\r
+       $(CC) $(CC_OPTIONS) mgclustercommand.cpp -c $(INCLUDE) -o ./mgclustercommand.o\r
+\r
+\r
+# Item # 181 -- getsharedotucommand --\r
+./getsharedotucommand.o : getsharedotucommand.cpp\r
+       $(CC) $(CC_OPTIONS) getsharedotucommand.cpp -c $(INCLUDE) -o ./getsharedotucommand.o\r
+\r
+\r
+# Item # 182 -- maligner --\r
+./maligner.o : maligner.cpp\r
+       $(CC) $(CC_OPTIONS) maligner.cpp -c $(INCLUDE) -o ./maligner.o\r
+\r
+\r
+# Item # 183 -- chimerarealigner --\r
+./chimerarealigner.o : chimerarealigner.cpp\r
+       $(CC) $(CC_OPTIONS) chimerarealigner.cpp -c $(INCLUDE) -o ./chimerarealigner.o\r
+\r
+\r
+# Item # 184 -- bergerparker --\r
+./bergerparker.o : bergerparker.cpp\r
+       $(CC) $(CC_OPTIONS) bergerparker.cpp -c $(INCLUDE) -o ./bergerparker.o\r
+\r
+\r
+# Item # 185 -- bstick --\r
+./bstick.o : bstick.cpp\r
+       $(CC) $(CC_OPTIONS) bstick.cpp -c $(INCLUDE) -o ./bstick.o\r
+\r
+\r
+# Item # 186 -- sharedkstest --\r
+./sharedkstest.o : sharedkstest.cpp\r
+       $(CC) $(CC_OPTIONS) sharedkstest.cpp -c $(INCLUDE) -o ./sharedkstest.o\r
+\r
+\r
+# Item # 187 -- qstat --\r
+./qstat.o : qstat.cpp\r
+       $(CC) $(CC_OPTIONS) qstat.cpp -c $(INCLUDE) -o ./qstat.o\r
+\r
+\r
+# Item # 188 -- shen --\r
+./shen.o : shen.cpp\r
+       $(CC) $(CC_OPTIONS) shen.cpp -c $(INCLUDE) -o ./shen.o\r
+\r
+\r
+# Item # 189 -- logsd --\r
+./logsd.o : logsd.cpp\r
+       $(CC) $(CC_OPTIONS) logsd.cpp -c $(INCLUDE) -o ./logsd.o\r
+\r
+\r
+# Item # 190 -- geom --\r
+./geom.o : geom.cpp\r
+       $(CC) $(CC_OPTIONS) geom.cpp -c $(INCLUDE) -o ./geom.o\r
+\r
+# Item # 191 -- parsesffcommand --\r
+./parsesffcommand.o : parsesffcommand.cpp\r
+       $(CC) $(CC_OPTIONS) parsesffcommand.cpp -c $(INCLUDE) -o ./parsesffcommand.o\r
+\r
+# Item # 192 -- chimeraccodecommand --\r
+./chimeraccodecommand.o : chimeraccodecommand.cpp\r
+       $(CC) $(CC_OPTIONS) chimeraccodecommand.cpp -c $(INCLUDE) -o ./chimeraccodecommand.o\r
+\r
+# Item # 193 -- chimeracheckcommand --\r
+./chimeracheckcommand.o : chimeracheckcommand.cpp\r
+       $(CC) $(CC_OPTIONS) chimeracheckcommand.cpp -c $(INCLUDE) -o ./chimeracheckcommand.o\r
+\r
+\r
+# Item # 194 -- chimeraslayercommand --\r
+./chimeraslayercommand.o : chimeraslayercommand.cpp\r
+       $(CC) $(CC_OPTIONS) chimeraslayercommand.cpp -c $(INCLUDE) -o ./chimeraslayercommand.o\r
+\r
+# Item # 195 -- chimerapintailcommand --\r
+./chimerapintailcommand.o : chimerapintailcommand.cpp\r
+       $(CC) $(CC_OPTIONS) chimerapintailcommand.cpp -c $(INCLUDE) -o ./chimerapintailcommand.o\r
+\r
+# Item # 196 -- chimerabellerophoncommand --\r
+./chimerabellerophoncommand.o : chimerabellerophoncommand.cpp\r
+       $(CC) $(CC_OPTIONS) chimerabellerophoncommand.cpp -c $(INCLUDE) -o ./chimerabellerophoncommand.o\r
+\r
+# Item # 197 -- phylosummary --\r
+./phylosummary.o : phylosummary.cpp\r
+       $(CC) $(CC_OPTIONS) phylosummary.cpp -c $(INCLUDE) -o ./phylosummary.o\r
+\r
+# Item # 198 -- setlogfilecommand --\r
+./setlogfilecommand.o : setlogfilecommand.cpp\r
+       $(CC) $(CC_OPTIONS) setlogfilecommand.cpp -c $(INCLUDE) -o ./setlogfilecommand.o\r
+\r
+# Item # 199 -- phylodiversity --\r
+./phylodiversity.o : phylodiversity.cpp\r
+       $(CC) $(CC_OPTIONS) phylodiversity.cpp -c $(INCLUDE) -o ./phylodiversity.o\r
+\r
+# Item # 200 -- phylodiversitycommand --\r
+./phylodiversitycommand.o : phylodiversitycommand.cpp\r
+       $(CC) $(CC_OPTIONS) phylodiversitycommand.cpp -c $(INCLUDE) -o ./phylodiversitycommand.o\r
+\r
+# Item # 201 -- makegroupcommand --\r
+./makegroupcommand.o : makegroupcommand.cpp\r
+       $(CC) $(CC_OPTIONS) makegroupcommand.cpp -c $(INCLUDE) -o ./makegroupcommand.o\r
+\r
+# Item # 202 -- chopseqscommand --\r
+./chopseqscommand.o : chopseqscommand.cpp\r
+       $(CC) $(CC_OPTIONS) chopseqscommand.cpp -c $(INCLUDE) -o ./chopseqscommand.o\r
+\r
+# Item # 203 -- clearcutcommand --\r
+./clearcutcommand.o : clearcutcommand.cpp\r
+       $(CC) $(CC_OPTIONS) clearcutcommand.cpp -c $(INCLUDE) -o ./clearcutcommand.o\r
+\r
+# Item # 204 -- catchallcommand --\r
+./catchallcommand.o : catchallcommand.cpp\r
+       $(CC) $(CC_OPTIONS) catchallcommand.cpp -c $(INCLUDE) -o ./catchallcommand.o\r
+\r
+# Item # 205 -- splitabundcommand --\r
+./splitabundcommand.o : splitabundcommand.cpp\r
+       $(CC) $(CC_OPTIONS) splitabundcommand.cpp -c $(INCLUDE) -o ./splitabundcommand.o\r
+       \r
+# Item # 206 -- splitmatrix --\r
+./splitmatrix.o : splitmatrix.o\r
+       $(CC) $(CC_OPTIONS) splitmatrix.cpp -c $(INCLUDE) -o ./splitmatrix.o\r
+       \r
+# Item # 207 -- splitmatrix --\r
+./clustersplitcommand.o : clustersplitcommand.cpp\r
+       $(CC) $(CC_OPTIONS) clustersplitcommand.cpp -c $(INCLUDE) -o ./clustersplitcommand.o\r
+\r
+##### END RUN ####\r
diff --git a/mothur.cpp b/mothur.cpp

index 43b838c2d94bad311204d26a82603901238687e1..0249f6518cc08b7c902f598365739fc2bdeb032f 100644 (file)
--- a/mothur.cpp
+++ b/mothur.cpp
@@ -73,9 +73,9 @@ int main(int argc, char *argv[]){
                 #endif\r
                 \r
                 //header\r
-               m->mothurOut("mothur v.1.10.0");\r
+               m->mothurOut("mothur v.1.10.2");\r
                 m->mothurOutEndLine();          \r
-               m->mothurOut("Last updated: 5/14/2010");\r
+               m->mothurOut("Last updated: 5/26/2010");\r
                 m->mothurOutEndLine();  \r
                 m->mothurOutEndLine();          \r
                 m->mothurOut("by");\r
diff --git a/phylotree.cpp b/phylotree.cpp

index bfac59c5a694db4ec644ffedace6a02f920f2067..1c2deba8a303edd692470dd1deb8c4e60062ac15 100644 (file)
--- a/phylotree.cpp
+++ b/phylotree.cpp
@@ -32,6 +32,8 @@ PhyloTree::PhyloTree(ifstream& in, string filename){
         try {
                 m = MothurOut::getInstance();
                 calcTotals = false;
+               numNodes = 0;
+               numSeqs = 0;
                 
                 #ifdef USE_MPI
                         MPI_File inMPI;
@@ -216,6 +218,7 @@ string PhyloTree::getNextTaxon(string& heirarchy){
  
  int PhyloTree::addSeqToTree(string seqName, string seqTaxonomy){
         try {
+                       
                 numSeqs++;
                 
                 map<string, int>::iterator childPointer;
@@ -236,6 +239,8 @@ int PhyloTree::addSeqToTree(string seqName, string seqTaxonomy){
                         //use print to reassign the taxa id
                         taxon = getNextTaxon(seqTaxonomy);
                         
+                       if (taxon == "") {  m->mothurOut(seqName + " has an error in the taxonomy.  This may be due to a ;;"); m->mothurOutEndLine(); if (currentNode != 0) {  uniqueTaxonomies[currentNode] = currentNode; } break;  }
+                       
                         childPointer = tree[currentNode].children.find(taxon);
                         
                         if(childPointer != tree[currentNode].children.end()){   //if the node already exists, move on
@@ -260,7 +265,7 @@ int PhyloTree::addSeqToTree(string seqName, string seqTaxonomy){
                                 //                      tree[currentNode].childNumber = numChildren;
                                 //                      tree[currentNode].heirarchyID = heirarchyID + '.' + toString(tree[currentNode].childNumber);
                         }
-               
+       
                         if (seqTaxonomy == "") {   uniqueTaxonomies[currentNode] = currentNode; }
                 }
  
@@ -520,7 +525,6 @@ void PhyloTree::printTreeNodes(string treefilename) {
                         for (it2=uniqueTaxonomies.begin(); it2!=uniqueTaxonomies.end(); it2++) {  outTree << it2->first << '\t' << tree[it2->first].accessions.size() << endl;  }
                         outTree << endl;
                         
-                       
                         outTree.close();
                 
                 #ifdef USE_MPI
@@ -535,6 +539,93 @@ void PhyloTree::printTreeNodes(string treefilename) {
         }
  }
  /**************************************************************************************************/
+TaxNode PhyloTree::get(int i ){
+       try {
+               if (i < tree.size()) {  return tree[i];  }
+               else {  cout << i << '\t' << tree.size() << endl ; m->mothurOut("Mismatch with taxonomy and template files. Cannot continue."); m->mothurOutEndLine(); exit(1); }
+       }
+       catch(exception& e) {
+               m->errorOut(e, "PhyloTree", "get");
+               exit(1);
+       }
+}
+/**************************************************************************************************/
+TaxNode PhyloTree::get(string seqName){
+       try {
+               map<string, int>::iterator itFind = name2Taxonomy.find(seqName);
+       
+               if (itFind != name2Taxonomy.end()) {  return tree[name2Taxonomy[seqName]];  }
+               else { m->mothurOut("Cannot find " + seqName + ". Mismatch with taxonomy and template files. Cannot continue."); m->mothurOutEndLine(); exit(1);}
+       }
+       catch(exception& e) {
+               m->errorOut(e, "PhyloTree", "get");
+               exit(1);
+       }
+}
+/**************************************************************************************************/
+string PhyloTree::getName(int i ){
+       try {
+               if (i < tree.size()) {  return tree[i].name;     }
+               else { m->mothurOut("Mismatch with taxonomy and template files. Cannot continue."); m->mothurOutEndLine(); exit(1); }
+       }
+       catch(exception& e) {
+               m->errorOut(e, "PhyloTree", "get");
+               exit(1);
+       }
+}
+/**************************************************************************************************/
+int PhyloTree::getIndex(string seqName){
+       try {
+               map<string, int>::iterator itFind = name2Taxonomy.find(seqName);
+       
+               if (itFind != name2Taxonomy.end()) {  return name2Taxonomy[seqName];  }
+               else { m->mothurOut("Cannot find " + seqName + ". Mismatch with taxonomy and template files. Cannot continue."); m->mothurOutEndLine(); exit(1);}
+       }
+       catch(exception& e) {
+               m->errorOut(e, "PhyloTree", "get");
+               exit(1);
+       }
+}
+/**************************************************************************************************/
+bool PhyloTree::ErrorCheck(vector<string> templateFileNames){
+       try {
+       
+               bool okay = true;
+               
+               map<string, int>::iterator itFind;
+               map<string, int> taxonomyFileNames = name2Taxonomy;
+               
+               for (int i = 0; i < templateFileNames.size(); i++) {
+                       itFind = taxonomyFileNames.find(templateFileNames[i]);
+                       
+                       if (itFind != name2Taxonomy.end()) { //found it so erase it
+                               taxonomyFileNames.erase(itFind);
+                       }else {
+                               m->mothurOut(templateFileNames[i] + " is in your template file and is not in your taxonomy file. Please correct."); m->mothurOutEndLine();
+                               okay = false;
+                       }
+                       
+                       templateFileNames.erase(templateFileNames.begin()+i);
+                       i--;
+               }
+               
+               if (taxonomyFileNames.size() > 0) { //there are names in tax file that are not in template
+                       okay = false;
+                       
+                       for (itFind = taxonomyFileNames.begin(); itFind != taxonomyFileNames.end(); itFind++) {
+                               m->mothurOut(itFind->first + " is in your taxonomy file and is not in your template file. Please correct."); m->mothurOutEndLine();
+                       }
+               }
+               
+               return okay;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "PhyloTree", "ErrorCheck");
+               exit(1);
+       }
+}
+/**************************************************************************************************/
+       
  
  
         
diff --git a/phylotree.h b/phylotree.h

index 2f3745074e170210bfc0b8d6b000361b4a410687..a961721a77dad0f32624aa1ff7941651007fc757 100644 (file)
--- a/phylotree.h
+++ b/phylotree.h
@@ -41,13 +41,15 @@ public:
         vector<int> getGenusTotals();   
         void setUp(string);  //used to create file needed for summary file if you use () constructor and add seqs manually instead of passing taxonomyfile
                 
-       TaxNode get(int i)                              {       return tree[i];                                                 }
-       TaxNode get(string seqName)             {       return tree[name2Taxonomy[seqName]];    }
-       int getIndex(string seqName)    {       return name2Taxonomy[seqName];                  }
-       string getName(int i)                   {       return tree[i].name;                                    }
+       TaxNode get(int i);                             
+       TaxNode get(string seqName);
+       string getName(int i);                  
+       int getIndex(string seqName);   
+                       
         string getFullTaxonomy(string);  //pass a sequence name return taxonomy
         int getMaxLevel()                               {       return maxLevel;                                                }
         int getNumSeqs()  {  return numSeqs;  }
+       bool ErrorCheck(vector<string>);
         
  private:
         string getNextTaxon(string&);
author	westcott <westcott>
	Thu, 27 May 2010 12:47:59 +0000 (12:47 +0000)
committer	westcott <westcott>
	Thu, 27 May 2010 12:47:59 +0000 (12:47 +0000)
bayesian.cpp		patch \| blob \| history
chopseqscommand.cpp		patch \| blob \| history
chopseqscommand.h		patch \| blob \| history
classify.cpp		patch \| blob \| history
clustersplitcommand.cpp		patch \| blob \| history
commandfactory.cpp		patch \| blob \| history
makefile		patch \| blob \| history
mothur.cpp		patch \| blob \| history
phylotree.cpp		patch \| blob \| history
phylotree.h		patch \| blob \| history