From: westcott <westcott>
Date: Fri, 18 Jun 2010 18:47:51 +0000 (+0000)
Subject: removed blast files generated by chimera.slayer, altered makefile to allow for 64bit... 
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=14bf280629e8e52ff1ea3c9da6f7aae1e28f9acb

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

diff --git a/blastdb.cpp b/blastdb.cpp
index 760824d..d8a04da 100644
--- 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 40537fe..d0a83cf 100644
--- 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 3e83112..999664f 100644
--- a/makefile
+++ b/makefile
@@ -1,1715 +1,1722 @@
-###################################################
-#
-# Makefile for mothur
-# Creator [Xcode -> Makefile Ver: Feb 14 2007 09:18:41]
-# Created: April 16, 2010
-#
-###################################################
-
-#
-# Macros
-#
-
-CC = g++ 
-CC_OPTIONS = -O3
-
-# if you do not want to use the readline library set to no, default yes.
-# make sure you have the library installed
-
-USEREADLINE ?= yes
-
-ifeq  ($(strip $(USEREADLINE)),yes)
-    CC_OPTIONS += -DUSE_READLINE
-	LNK_OPTIONS += \
-      -lreadline\
-      -lncurses\
-      -L../readline-6.0
-endif
-
-USEMPI ?= no
-
-ifeq  ($(strip $(USEMPI)),yes)
-	CC = mpic++
-    CC_OPTIONS += -DUSE_MPI
-endif
-
-#
-# INCLUDE directories for mothur
-#
-
-     INCLUDE = -I.
-
-#
-# Build mothur
-#
-
-mothur : \
-		./sharedutilities.o\
-		./treegroupscommand.o\
-		./bootstrapsharedcommand.o\
-		./matrixoutputcommand.o\
-		./getoturepcommand.o\
-		./screenseqscommand.o\
-		./chimera.o\
-		./decalc.o\
-		./readotucommand.o\
-		./readdistcommand.o\
-		./commandfactory.o\
-		./alignment.o\
-		./alignmentcell.o\
-		./gotohoverlap.o\
-		./overlap.o\
-		./needlemanoverlap.o\
-		./blastalign.o\
-		./noalign.o\
-		./suffixdb.o\
-		./suffixnodes.o\
-		./suffixtree.o\
-		./blastdb.o\
-		./nast.o\
-		./nastreport.o\
-		./boneh.o\
-		./efron.o\
-		./solow.o\
-		./unifracweightedcommand.o\
-		./weighted.o\
-		./unweighted.o\
-		./unifracunweightedcommand.o\
-		./getsabundcommand.o\
-		./getrabundcommand.o\
-		./bellerophon.o\
-		./pintail.o\
-		./sharedanderbergs.o\
-		./venncommand.o\
-		./venn.o\
-		./fullmatrix.o\
-		./heatmap.o\
-		./heatmapcommand.o\
-		./libshuffcommand.o\
-		./nocommands.o\
-		./sharedbraycurtis.o\
-		./sharedkulczynski.o\
-		./sharedlennon.o\
-		./sharedkulczynskicody.o\
-		./sharedmorisitahorn.o\
-		./sharedochiai.o\
-		./readcolumn.o\
-		./readotu.o\
-		./readphylip.o\
-		./consensuscommand.o\
-		./heatmapsimcommand.o\
-		./heatmapsim.o\
-		./optionparser.o\
-		./filterseqscommand.o\
-		./goodscoverage.o\
-		./sequencedb.o\
-		./sharedjackknife.o\
-		./sharedmarczewski.o\
-		./aligncommand.o\
-		./treemap.o\
-		./parsimonycommand.o\
-		./parsimony.o\
-		./seqsummarycommand.o\
-		./chimeraccodecommand.o\
-		./chimerabellerophoncommand.o\
-		./chimeracheckcommand.o\
-		./chimeraslayercommand.o\
-		./chimerapintailcommand.o\
-		./chimeraseqscommand.o\
-		./sharedlistvector.o\
-		./tree.o\
-		./readtree.o\
-		./sharedsobscollectsummary.o\
-		./deconvolutecommand.o\
-		./listseqscommand.o\
-		./getseqscommand.o\
-		./removeseqscommand.o\
-		./systemcommand.o\
-		./binsequencecommand.o\
-		./distancecommand.o\
-		./ace.o\
-		./averagelinkage.o\
-		./bootstrap.o\
-		./calculator.o\
-		./chao1.o\
-		./cluster.o\
-		./clustercommand.o\
-		./collect.o\
-		./collectcommand.o\
-		./collectsharedcommand.o\
-		./commandoptionparser.o\
-		./completelinkage.o\
-		./database.o\
-		./engine.o\
-		./fastamap.o\
-		./fileoutput.o\
-		./globaldata.o\
-		./groupmap.o\
-		./helpcommand.o\
-		./makegroupcommand.o\
-		./chopseqscommand.o\
-		./clearcutcommand.o\
-		./catchallcommand.o\
-		./splitabundcommand.o\
-		./splitmatrix.o\
-		./clustersplitcommand.o\
-		./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 $(INCLUDE) -o ./weightedlinkage.o
-
-##### END RUN ####
+###################################################
+#
+# Makefile for mothur
+# Creator [Xcode -> Makefile Ver: Feb 14 2007 09:18:41]
+# Created: April 16, 2010
+#
+###################################################
+
+#
+# Macros
+#
+
+CC = g++ 
+CC_OPTIONS = -O3 
+
+# if you do not want to use the readline library set to no, default yes.
+# make sure you have the library installed
+
+64BIT_VERSION ?= yes
+
+ifeq  ($(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 4947b38..dcd95cb 100644
--- 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();  }
 			}
 		}