removed blast files generated by chimera.slayer, altered makefile to allow for 64bit...

diff --git a/blastdb.cpp b/blastdb.cpp
index 760824dbb23f9b2a9d680ace769ccc1c6ffab96c..d8a04da762b65406af2d43062460de9324d41f61 100644 (file)
--- a/blastdb.cpp
+++ b/blastdb.cpp
@@ -29,23 +29,38 @@ gapOpen(gO), gapExtend(gE), match(m), misMatch(mM) {
 /**************************************************************************************************/
 
 BlastDB::BlastDB() : Database() {
-       
-       globaldata = GlobalData::getInstance();
-       count = 0;
-
-       int randNumber = rand();
-       dbFileName = toString(randNumber) + ".template.unaligned.fasta";
-       queryFileName = toString(randNumber) + ".candidate.unaligned.fasta";
-       blastFileName = toString(randNumber) + ".blast";
+       try {
+               globaldata = GlobalData::getInstance();
+               count = 0;
 
+               int randNumber = rand();
+               dbFileName = toString(randNumber) + ".template.unaligned.fasta";
+               queryFileName = toString(randNumber) + ".candidate.unaligned.fasta";
+               blastFileName = toString(randNumber) + ".blast";
+       }
+       catch(exception& e) {
+               m->errorOut(e, "BlastDB", "BlastDB");
+               exit(1);
+       }
 }
 
 /**************************************************************************************************/
 
 BlastDB::~BlastDB(){
-       remove(queryFileName.c_str());                          //      let's clean stuff up and remove the temp files
-       remove(dbFileName.c_str());                                     //      let's clean stuff up and remove the temp files
-       remove(blastFileName.c_str());                          //      let's clean stuff up and remove the temp files
+       try{
+               remove(queryFileName.c_str());                          //      let's clean stuff up and remove the temp files
+               remove(dbFileName.c_str());                                     //      let's clean stuff up and remove the temp files
+               remove((dbFileName+".nsq").c_str());                                    //      let's clean stuff up and remove the temp files
+               remove((dbFileName+".nsi").c_str());                                    //      let's clean stuff up and remove the temp files
+               remove((dbFileName+".nsd").c_str());                                    //      let's clean stuff up and remove the temp files
+               remove((dbFileName+".nin").c_str());                                    //      let's clean stuff up and remove the temp files
+               remove((dbFileName+".nhr").c_str());                                    //      let's clean stuff up and remove the temp files
+               remove(blastFileName.c_str());                          //      let's clean stuff up and remove the temp files
+       }
+       catch(exception& e) {
+               m->errorOut(e, "BlastDB", "~BlastDB");
+               exit(1);
+       }
 }
 /**************************************************************************************************/
 //assumes you have added all the template sequences using the addSequence function and run generateDB.

diff --git a/cluster.cpp b/cluster.cpp
index 40537fe7b51eb759cf7be438bdd61978835a192c..d0a83cfd0f4a7ccd5c73c8ea8966a8e3d49fc03c 100644 (file)
--- a/cluster.cpp
+++ b/cluster.cpp
@@ -17,6 +17,7 @@
 Cluster::Cluster(RAbundVector* rav, ListVector* lv, SparseMatrix* dm, float c, string f) :
 rabund(rav), list(lv), dMatrix(dm), method(f)
 {
+       try {
 /*
        cout << "sizeof(MatData): " << sizeof(MatData) << endl;
        cout << "sizeof(PCell*): " << sizeof(PCell*) << endl;
@@ -66,6 +67,12 @@ rabund(rav), list(lv), dMatrix(dm), method(f)
        //save so you can modify as it changes in average neighbor
        cutoff = c;
        m = MothurOut::getInstance();
+       
+       }
+       catch(exception& e) {
+               m->errorOut(e, "Cluster", "Cluster");
+               exit(1);
+       }
 }
 
 /***********************************************************************/

diff --git a/makefile b/makefile
index 3e831124a7cc7a026dcad63df44da4a0674d186b..999664fcaf5787333d98d44bafcc04d465715fc3 100644 (file)
--- a/makefile
+++ b/makefile
@@ -1,1715 +1,1722 @@
-###################################################\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
-               ./weightedlinkage.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
-               ./classifyotucommand.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
-               ./weightedlinkage.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
-               ./classifyotucommand.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
-               ./weightedlinkage.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
-               ./classifyotucommand.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.cpp\r
-       $(CC) $(CC_OPTIONS) splitmatrix.cpp -c $(INCLUDE) -o ./splitmatrix.o\r
-       \r
-# Item # 207 -- clustersplit --\r
-./clustersplitcommand.o : clustersplitcommand.cpp\r
-       $(CC) $(CC_OPTIONS) clustersplitcommand.cpp -c $(INCLUDE) -o ./clustersplitcommand.o\r
-       \r
-# Item # 208 -- classifyotu --\r
-./classifyotucommand.o : classifyotucommand.cpp\r
-       $(CC) $(CC_OPTIONS) classifyotucommand.cpp -c $(INCLUDE) -o ./classifyotucommand.o\r
-\r
-# Item # 209 -- weightedlinkage --\r
-./weightedlinkage.o : weightedlinkage.cpp\r
-       $(CC) $(CC_OPTIONS) weightedlinkage.cpp -c $(INCLUDE) -o ./weightedlinkage.o\r
-\r
-##### END RUN ####\r
+###################################################
+#
+# Makefile for mothur
+# Creator [Xcode -> Makefile Ver: Feb 14 2007 09:18:41]
+# Created: April 16, 2010
+#
+###################################################
+
+#
+# Macros
+#
+
+CC = g++ 
+CC_OPTIONS = -O3 
+
+# if you do not want to use the readline library set to no, default yes.
+# make sure you have the library installed
+
+64BIT_VERSION ?= yes
+
+ifeq  ($(strip $(64BIT_VERSION)),yes)
+    CC_OPTIONS += -arch x86_64
+       LNK_OPTIONS += -arch x86_64
+endif
+
+USEREADLINE ?= yes
+
+ifeq  ($(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\
+               ./weightedlinkage.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\
+               ./classifyotucommand.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\
+               ./weightedlinkage.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\
+               ./classifyotucommand.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 ../Release/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\
+               ./weightedlinkage.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\
+               ./classifyotucommand.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.o : splitabundcommand.cpp
+       $(CC) $(CC_OPTIONS) splitabundcommand.cpp -c $(INCLUDE) -o ./splitabundcommand.o
+       
+# Item # 206 -- splitmatrix --
+./splitmatrix.o : splitmatrix.cpp
+       $(CC) $(CC_OPTIONS) splitmatrix.cpp -c $(INCLUDE) -o ./splitmatrix.o
+       
+# Item # 207 -- clustersplit --
+./clustersplitcommand.o : clustersplitcommand.cpp
+       $(CC) $(CC_OPTIONS) clustersplitcommand.cpp -c $(INCLUDE) -o ./clustersplitcommand.o
+       
+# Item # 208 -- classifyotu --
+./classifyotucommand.o : classifyotucommand.cpp
+       $(CC) $(CC_OPTIONS) classifyotucommand.cpp -c $(INCLUDE) -o ./classifyotucommand.o
+
+# Item # 209 -- weightedlinkage --
+./weightedlinkage.o : weightedlinkage.cpp
+       $(CC) $(CC_OPTIONS) weightedlinkage.cpp -c $(INCLUDE) -o ./weightedlinkage.o
+
+##### END RUN ####

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 4947b38ec8acb49ac0925f8b277133cc18196519..dcd95cb94344063333d8f1c1c2abac6408dd314d 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -591,7 +591,7 @@ void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec){ //vector<ofstream*
                                                outputNames.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + toString(index) + "." + group + ".fasta"));
                                                outFASTAVec.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + toString(index) + "." + group + ".fasta"));
                                        }
-                               }
+                               }else{  m->mothurOut(type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine();  }
                        }
                }