+###################################################\r
+#\r
+# Makefile for mothur\r
+# Creator [Xcode -> Makefile Ver: Feb 14 2007 09:18:41]\r
+# Created: [Thu Mar 4 08:31:03 2010]\r
+#\r
+###################################################\r
+\r
+#\r
+# Macros\r
+#\r
+\r
+CC = mpic++\r
+CC_OPTIONS = -O3\r
+LNK_OPTIONS = \r
+\r
+# if you do not want to use the readline library set to no, default yes.\r
+# make sure you have the library installed\r
+\r
+USEREADLINE ?= yes\r
+\r
+ifeq ($(strip $(USEREADLINE)),yes)\r
+ CC_OPTIONS += -DUSE_READLINE\r
+ LNK_OPTIONS += \\r
+ -lreadline\\r
+ -lncurses\\r
+ -L../readline-6.0\r
+endif\r
+\r
+USEMPI ?= no\r
+\r
+ifeq ($(strip $(USEMPI)),yes)\r
+ CC_OPTIONS += -DUSE_MPI\r
+endif\r
+\r
+#\r
+# INCLUDE directories for mothur\r
+#\r
+
+ INCLUDE = -I.
+\r
+#\r
+# Build mothur\r
+#\r
+\r
+mothur : \\r
+ ./sharedutilities.o\\r
+ ./treegroupscommand.o\\r
+ ./bootstrapsharedcommand.o\\r
+ ./matrixoutputcommand.o\\r
+ ./getoturepcommand.o\\r
+ ./screenseqscommand.o\\r
+ ./chimera.o\\r
+ ./decalc.o\\r
+ ./readotucommand.o\\r
+ ./readdistcommand.o\\r
+ ./commandfactory.o\\r
+ ./alignment.o\\r
+ ./alignmentcell.o\\r
+ ./gotohoverlap.o\\r
+ ./overlap.o\\r
+ ./needlemanoverlap.o\\r
+ ./blastalign.o\\r
+ ./noalign.o\\r
+ ./suffixdb.o\\r
+ ./suffixnodes.o\\r
+ ./suffixtree.o\\r
+ ./blastdb.o\\r
+ ./nast.o\\r
+ ./nastreport.o\\r
+ ./boneh.o\\r
+ ./efron.o\\r
+ ./solow.o\\r
+ ./unifracweightedcommand.o\\r
+ ./weighted.o\\r
+ ./unweighted.o\\r
+ ./unifracunweightedcommand.o\\r
+ ./getsabundcommand.o\\r
+ ./getrabundcommand.o\\r
+ ./bellerophon.o\\r
+ ./pintail.o\\r
+ ./sharedanderbergs.o\\r
+ ./venncommand.o\\r
+ ./venn.o\\r
+ ./fullmatrix.o\\r
+ ./heatmap.o\\r
+ ./heatmapcommand.o\\r
+ ./libshuffcommand.o\\r
+ ./nocommands.o\\r
+ ./sharedbraycurtis.o\\r
+ ./sharedkulczynski.o\\r
+ ./sharedlennon.o\\r
+ ./sharedkulczynskicody.o\\r
+ ./sharedmorisitahorn.o\\r
+ ./sharedochiai.o\\r
+ ./readcolumn.o\\r
+ ./readotu.o\\r
+ ./readphylip.o\\r
+ ./consensuscommand.o\\r
+ ./heatmapsimcommand.o\\r
+ ./heatmapsim.o\\r
+ ./optionparser.o\\r
+ ./filterseqscommand.o\\r
+ ./goodscoverage.o\\r
+ ./sequencedb.o\\r
+ ./sharedjackknife.o\\r
+ ./sharedmarczewski.o\\r
+ ./aligncommand.o\\r
+ ./treemap.o\\r
+ ./parsimonycommand.o\\r
+ ./parsimony.o\\r
+ ./seqsummarycommand.o\\r
+ ./chimeraccodecommand.o\\r
+ ./chimerabellerophoncommand.o\\r
+ ./chimeracheckcommand.o\\r
+ ./chimeraslayercommand.o\\r
+ ./chimerapintailcommand.o\\r
+ ./chimeraseqscommand.o\\r
+ ./sharedlistvector.o\\r
+ ./tree.o\\r
+ ./readtree.o\\r
+ ./sharedsobscollectsummary.o\\r
+ ./deconvolutecommand.o\\r
+ ./listseqscommand.o\\r
+ ./getseqscommand.o\\r
+ ./removeseqscommand.o\\r
+ ./systemcommand.o\\r
+ ./binsequencecommand.o\\r
+ ./distancecommand.o\\r
+ ./ace.o\\r
+ ./averagelinkage.o\\r
+ ./bootstrap.o\\r
+ ./calculator.o\\r
+ ./chao1.o\\r
+ ./cluster.o\\r
+ ./clustercommand.o\\r
+ ./collect.o\\r
+ ./collectcommand.o\\r
+ ./collectsharedcommand.o\\r
+ ./commandoptionparser.o\\r
+ ./completelinkage.o\\r
+ ./database.o\\r
+ ./engine.o\\r
+ ./fastamap.o\\r
+ ./fileoutput.o\\r
+ ./globaldata.o\\r
+ ./groupmap.o\\r
+ ./helpcommand.o\\r
+ ./inputdata.o\\r
+ ./jackknife.o\\r
+ ./kmer.o\\r
+ ./kmerdb.o\\r
+ ./listvector.o\\r
+ ./mothur.o\\r
+ ./nameassignment.o\\r
+ ./npshannon.o\\r
+ ./ordervector.o\\r
+ ./progress.o\\r
+ ./quitcommand.o\\r
+ ./rabundvector.o\\r
+ ./rarecalc.o\\r
+ ./raredisplay.o\\r
+ ./rarefact.o\\r
+ ./rarefactcommand.o\\r
+ ./rarefactsharedcommand.o\\r
+ ./sabundvector.o\\r
+ ./sequence.o\\r
+ ./shannon.o\\r
+ ./sharedace.o\\r
+ ./sharedchao1.o\\r
+ ./sharedcommand.o\\r
+ ./sharedjabund.o\\r
+ ./sharedjclass.o\\r
+ ./sharedjest.o\\r
+ ./sharedordervector.o\\r
+ ./sharedrabundvector.o\\r
+ ./sharedsabundvector.o\\r
+ ./sharedsobs.o\\r
+ ./sharedsorabund.o\\r
+ ./sharedsorclass.o\\r
+ ./sharedsorest.o\\r
+ ./sharedthetan.o\\r
+ ./sharedthetayc.o\\r
+ ./simpson.o\\r
+ ./singlelinkage.o\\r
+ ./sparsematrix.o\\r
+ ./summarycommand.o\\r
+ ./summarysharedcommand.o\\r
+ ./uvest.o\\r
+ ./validcalculator.o\\r
+ ./validparameter.o\\r
+ ./treenode.o\\r
+ ./readtreecommand.o\\r
+ ./reversecommand.o\\r
+ ./trimseqscommand.o\\r
+ ./slibshuff.o\\r
+ ./libshuff.o\\r
+ ./dlibshuff.o\\r
+ ./mergefilecommand.o\\r
+ ./coverage.o\\r
+ ./whittaker.o\\r
+ ./preclustercommand.o\\r
+ ./otuhierarchycommand.o\\r
+ ./setdircommand.o\\r
+ ./getgroupcommand.o\\r
+ ./getlabelcommand.o\\r
+ ./secondarystructurecommand.o\\r
+ ./mothurout.o\\r
+ ./parselistscommand.o\\r
+ ./readblast.o\\r
+ ./chimeracheckrdp.o\\r
+ ./hclustercommand.o\\r
+ ./hcluster.o\\r
+ ./getlistcountcommand.o\\r
+ ./readcluster.o\\r
+ ./ccode.o\\r
+ ./taxonomyequalizer.o\\r
+ ./phylotypecommand.o\\r
+ ./classifyseqscommand.o\\r
+ ./parsesffcommand.o\\r
+ ./classify.o\\r
+ ./phylotree.o\\r
+ ./bayesian.o\\r
+ ./alignmentdb.o\\r
+ ./knn.o\\r
+ ./distancedb.o\\r
+ ./chimeraslayer.o\\r
+ ./slayer.o\\r
+ ./pcacommand.o\\r
+ ./formatcolumn.o\\r
+ ./formatphylip.o\\r
+ ./mgclustercommand.o\\r
+ ./getsharedotucommand.o\\r
+ ./maligner.o\\r
+ ./chimerarealigner.o\\r
+ ./bergerparker.o\\r
+ ./bstick.o\\r
+ ./sharedkstest.o\\r
+ ./qstat.o\\r
+ ./shen.o\\r
+ ./logsd.o\\r
+ ./geom.o\r
+ $(CC) $(LNK_OPTIONS) \\r
+ ./sharedutilities.o\\r
+ ./treegroupscommand.o\\r
+ ./bootstrapsharedcommand.o\\r
+ ./matrixoutputcommand.o\\r
+ ./getoturepcommand.o\\r
+ ./screenseqscommand.o\\r
+ ./chimera.o\\r
+ ./decalc.o\\r
+ ./readotucommand.o\\r
+ ./readdistcommand.o\\r
+ ./commandfactory.o\\r
+ ./alignment.o\\r
+ ./alignmentcell.o\\r
+ ./gotohoverlap.o\\r
+ ./overlap.o\\r
+ ./needlemanoverlap.o\\r
+ ./blastalign.o\\r
+ ./noalign.o\\r
+ ./suffixdb.o\\r
+ ./suffixnodes.o\\r
+ ./suffixtree.o\\r
+ ./blastdb.o\\r
+ ./nast.o\\r
+ ./nastreport.o\\r
+ ./boneh.o\\r
+ ./efron.o\\r
+ ./solow.o\\r
+ ./unifracweightedcommand.o\\r
+ ./weighted.o\\r
+ ./unweighted.o\\r
+ ./unifracunweightedcommand.o\\r
+ ./getsabundcommand.o\\r
+ ./getrabundcommand.o\\r
+ ./bellerophon.o\\r
+ ./pintail.o\\r
+ ./sharedanderbergs.o\\r
+ ./venncommand.o\\r
+ ./venn.o\\r
+ ./fullmatrix.o\\r
+ ./heatmap.o\\r
+ ./heatmapcommand.o\\r
+ ./libshuffcommand.o\\r
+ ./nocommands.o\\r
+ ./sharedbraycurtis.o\\r
+ ./sharedkulczynski.o\\r
+ ./sharedlennon.o\\r
+ ./sharedkulczynskicody.o\\r
+ ./sharedmorisitahorn.o\\r
+ ./sharedochiai.o\\r
+ ./readcolumn.o\\r
+ ./readotu.o\\r
+ ./readphylip.o\\r
+ ./consensuscommand.o\\r
+ ./heatmapsimcommand.o\\r
+ ./heatmapsim.o\\r
+ ./optionparser.o\\r
+ ./filterseqscommand.o\\r
+ ./goodscoverage.o\\r
+ ./sequencedb.o\\r
+ ./sharedjackknife.o\\r
+ ./sharedmarczewski.o\\r
+ ./aligncommand.o\\r
+ ./treemap.o\\r
+ ./parsimonycommand.o\\r
+ ./parsimony.o\\r
+ ./seqsummarycommand.o\\r
+ ./chimeraccodecommand.o\\r
+ ./chimerabellerophoncommand.o\\r
+ ./chimeracheckcommand.o\\r
+ ./chimeraslayercommand.o\\r
+ ./chimerapintailcommand.o\\r
+ ./chimeraseqscommand.o\\r
+ ./sharedlistvector.o\\r
+ ./tree.o\\r
+ ./readtree.o\\r
+ ./sharedsobscollectsummary.o\\r
+ ./deconvolutecommand.o\\r
+ ./listseqscommand.o\\r
+ ./getseqscommand.o\\r
+ ./removeseqscommand.o\\r
+ ./systemcommand.o\\r
+ ./binsequencecommand.o\\r
+ ./distancecommand.o\\r
+ ./ace.o\\r
+ ./averagelinkage.o\\r
+ ./bootstrap.o\\r
+ ./calculator.o\\r
+ ./chao1.o\\r
+ ./cluster.o\\r
+ ./clustercommand.o\\r
+ ./collect.o\\r
+ ./collectcommand.o\\r
+ ./collectsharedcommand.o\\r
+ ./commandoptionparser.o\\r
+ ./completelinkage.o\\r
+ ./database.o\\r
+ ./engine.o\\r
+ ./fastamap.o\\r
+ ./fileoutput.o\\r
+ ./globaldata.o\\r
+ ./groupmap.o\\r
+ ./helpcommand.o\\r
+ ./inputdata.o\\r
+ ./jackknife.o\\r
+ ./kmer.o\\r
+ ./kmerdb.o\\r
+ ./listvector.o\\r
+ ./mothur.o\\r
+ ./nameassignment.o\\r
+ ./npshannon.o\\r
+ ./ordervector.o\\r
+ ./progress.o\\r
+ ./quitcommand.o\\r
+ ./rabundvector.o\\r
+ ./rarecalc.o\\r
+ ./raredisplay.o\\r
+ ./rarefact.o\\r
+ ./rarefactcommand.o\\r
+ ./rarefactsharedcommand.o\\r
+ ./sabundvector.o\\r
+ ./sequence.o\\r
+ ./shannon.o\\r
+ ./sharedace.o\\r
+ ./sharedchao1.o\\r
+ ./sharedcommand.o\\r
+ ./sharedjabund.o\\r
+ ./sharedjclass.o\\r
+ ./sharedjest.o\\r
+ ./sharedordervector.o\\r
+ ./sharedrabundvector.o\\r
+ ./sharedsabundvector.o\\r
+ ./sharedsobs.o\\r
+ ./sharedsorabund.o\\r
+ ./sharedsorclass.o\\r
+ ./sharedsorest.o\\r
+ ./sharedthetan.o\\r
+ ./sharedthetayc.o\\r
+ ./simpson.o\\r
+ ./singlelinkage.o\\r
+ ./sparsematrix.o\\r
+ ./summarycommand.o\\r
+ ./summarysharedcommand.o\\r
+ ./uvest.o\\r
+ ./validcalculator.o\\r
+ ./validparameter.o\\r
+ ./treenode.o\\r
+ ./readtreecommand.o\\r
+ ./reversecommand.o\\r
+ ./trimseqscommand.o\\r
+ ./slibshuff.o\\r
+ ./libshuff.o\\r
+ ./dlibshuff.o\\r
+ ./mergefilecommand.o\\r
+ ./coverage.o\\r
+ ./whittaker.o\\r
+ ./preclustercommand.o\\r
+ ./otuhierarchycommand.o\\r
+ ./setdircommand.o\\r
+ ./getgroupcommand.o\\r
+ ./getlabelcommand.o\\r
+ ./secondarystructurecommand.o\\r
+ ./mothurout.o\\r
+ ./parselistscommand.o\\r
+ ./readblast.o\\r
+ ./chimeracheckrdp.o\\r
+ ./hclustercommand.o\\r
+ ./hcluster.o\\r
+ ./getlistcountcommand.o\\r
+ ./readcluster.o\\r
+ ./ccode.o\\r
+ ./taxonomyequalizer.o\\r
+ ./phylotypecommand.o\\r
+ ./classifyseqscommand.o\\r
+ ./parsesffcommand.o\\r
+ ./classify.o\\r
+ ./phylotree.o\\r
+ ./bayesian.o\\r
+ ./alignmentdb.o\\r
+ ./knn.o\\r
+ ./distancedb.o\\r
+ ./chimeraslayer.o\\r
+ ./slayer.o\\r
+ ./pcacommand.o\\r
+ ./formatcolumn.o\\r
+ ./formatphylip.o\\r
+ ./mgclustercommand.o\\r
+ ./getsharedotucommand.o\\r
+ ./maligner.o\\r
+ ./chimerarealigner.o\\r
+ ./bergerparker.o\\r
+ ./bstick.o\\r
+ ./sharedkstest.o\\r
+ ./qstat.o\\r
+ ./shen.o\\r
+ ./logsd.o\\r
+ ./geom.o\\r
+ -o ../Release/mothur\r
+\r
+clean : \r
+ rm \\r
+ ./sharedutilities.o\\r
+ ./treegroupscommand.o\\r
+ ./bootstrapsharedcommand.o\\r
+ ./matrixoutputcommand.o\\r
+ ./getoturepcommand.o\\r
+ ./screenseqscommand.o\\r
+ ./chimera.o\\r
+ ./decalc.o\\r
+ ./readotucommand.o\\r
+ ./readdistcommand.o\\r
+ ./commandfactory.o\\r
+ ./alignment.o\\r
+ ./alignmentcell.o\\r
+ ./gotohoverlap.o\\r
+ ./overlap.o\\r
+ ./needlemanoverlap.o\\r
+ ./blastalign.o\\r
+ ./noalign.o\\r
+ ./suffixdb.o\\r
+ ./suffixnodes.o\\r
+ ./suffixtree.o\\r
+ ./blastdb.o\\r
+ ./nast.o\\r
+ ./nastreport.o\\r
+ ./boneh.o\\r
+ ./efron.o\\r
+ ./solow.o\\r
+ ./unifracweightedcommand.o\\r
+ ./weighted.o\\r
+ ./unweighted.o\\r
+ ./unifracunweightedcommand.o\\r
+ ./getsabundcommand.o\\r
+ ./getrabundcommand.o\\r
+ ./bellerophon.o\\r
+ ./pintail.o\\r
+ ./sharedanderbergs.o\\r
+ ./venncommand.o\\r
+ ./venn.o\\r
+ ./fullmatrix.o\\r
+ ./heatmap.o\\r
+ ./heatmapcommand.o\\r
+ ./libshuffcommand.o\\r
+ ./nocommands.o\\r
+ ./sharedbraycurtis.o\\r
+ ./sharedkulczynski.o\\r
+ ./sharedlennon.o\\r
+ ./sharedkulczynskicody.o\\r
+ ./sharedmorisitahorn.o\\r
+ ./sharedochiai.o\\r
+ ./readcolumn.o\\r
+ ./readotu.o\\r
+ ./readphylip.o\\r
+ ./consensuscommand.o\\r
+ ./heatmapsimcommand.o\\r
+ ./heatmapsim.o\\r
+ ./optionparser.o\\r
+ ./filterseqscommand.o\\r
+ ./goodscoverage.o\\r
+ ./sequencedb.o\\r
+ ./sharedjackknife.o\\r
+ ./sharedmarczewski.o\\r
+ ./aligncommand.o\\r
+ ./treemap.o\\r
+ ./parsimonycommand.o\\r
+ ./parsimony.o\\r
+ ./seqsummarycommand.o\\r
+ ./chimeraccodecommand.o\\r
+ ./chimerabellerophoncommand.o\\r
+ ./chimeracheckcommand.o\\r
+ ./chimeraslayercommand.o\\r
+ ./chimerapintailcommand.o\\r
+ ./chimeraseqscommand.o\\r
+ ./sharedlistvector.o\\r
+ ./tree.o\\r
+ ./readtree.o\\r
+ ./sharedsobscollectsummary.o\\r
+ ./deconvolutecommand.o\\r
+ ./listseqscommand.o\\r
+ ./getseqscommand.o\\r
+ ./removeseqscommand.o\\r
+ ./systemcommand.o\\r
+ ./binsequencecommand.o\\r
+ ./distancecommand.o\\r
+ ./ace.o\\r
+ ./averagelinkage.o\\r
+ ./bootstrap.o\\r
+ ./calculator.o\\r
+ ./chao1.o\\r
+ ./cluster.o\\r
+ ./clustercommand.o\\r
+ ./collect.o\\r
+ ./collectcommand.o\\r
+ ./collectsharedcommand.o\\r
+ ./commandoptionparser.o\\r
+ ./completelinkage.o\\r
+ ./database.o\\r
+ ./engine.o\\r
+ ./fastamap.o\\r
+ ./fileoutput.o\\r
+ ./globaldata.o\\r
+ ./groupmap.o\\r
+ ./helpcommand.o\\r
+ ./inputdata.o\\r
+ ./jackknife.o\\r
+ ./kmer.o\\r
+ ./kmerdb.o\\r
+ ./listvector.o\\r
+ ./mothur.o\\r
+ ./nameassignment.o\\r
+ ./npshannon.o\\r
+ ./ordervector.o\\r
+ ./progress.o\\r
+ ./quitcommand.o\\r
+ ./rabundvector.o\\r
+ ./rarecalc.o\\r
+ ./raredisplay.o\\r
+ ./rarefact.o\\r
+ ./rarefactcommand.o\\r
+ ./rarefactsharedcommand.o\\r
+ ./sabundvector.o\\r
+ ./sequence.o\\r
+ ./shannon.o\\r
+ ./sharedace.o\\r
+ ./sharedchao1.o\\r
+ ./sharedcommand.o\\r
+ ./sharedjabund.o\\r
+ ./sharedjclass.o\\r
+ ./sharedjest.o\\r
+ ./sharedordervector.o\\r
+ ./sharedrabundvector.o\\r
+ ./sharedsabundvector.o\\r
+ ./sharedsobs.o\\r
+ ./sharedsorabund.o\\r
+ ./sharedsorclass.o\\r
+ ./sharedsorest.o\\r
+ ./sharedthetan.o\\r
+ ./sharedthetayc.o\\r
+ ./simpson.o\\r
+ ./singlelinkage.o\\r
+ ./sparsematrix.o\\r
+ ./summarycommand.o\\r
+ ./summarysharedcommand.o\\r
+ ./uvest.o\\r
+ ./validcalculator.o\\r
+ ./validparameter.o\\r
+ ./treenode.o\\r
+ ./readtreecommand.o\\r
+ ./reversecommand.o\\r
+ ./trimseqscommand.o\\r
+ ./slibshuff.o\\r
+ ./libshuff.o\\r
+ ./dlibshuff.o\\r
+ ./mergefilecommand.o\\r
+ ./coverage.o\\r
+ ./whittaker.o\\r
+ ./preclustercommand.o\\r
+ ./otuhierarchycommand.o\\r
+ ./setdircommand.o\\r
+ ./getgroupcommand.o\\r
+ ./getlabelcommand.o\\r
+ ./secondarystructurecommand.o\\r
+ ./mothurout.o\\r
+ ./parselistscommand.o\\r
+ ./readblast.o\\r
+ ./chimeracheckrdp.o\\r
+ ./hclustercommand.o\\r
+ ./hcluster.o\\r
+ ./getlistcountcommand.o\\r
+ ./readcluster.o\\r
+ ./ccode.o\\r
+ ./taxonomyequalizer.o\\r
+ ./phylotypecommand.o\\r
+ ./classifyseqscommand.o\\r
+ ./parsesffcommand.o\\r
+ ./classify.o\\r
+ ./phylotree.o\\r
+ ./bayesian.o\\r
+ ./alignmentdb.o\\r
+ ./knn.o\\r
+ ./distancedb.o\\r
+ ./chimeraslayer.o\\r
+ ./slayer.o\\r
+ ./pcacommand.o\\r
+ ./formatcolumn.o\\r
+ ./formatphylip.o\\r
+ ./mgclustercommand.o\\r
+ ./getsharedotucommand.o\\r
+ ./maligner.o\\r
+ ./chimerarealigner.o\\r
+ ./bergerparker.o\\r
+ ./bstick.o\\r
+ ./sharedkstest.o\\r
+ ./qstat.o\\r
+ ./shen.o\\r
+ ./logsd.o\\r
+ ./geom.o\\r
+ mothur\r
+\r
+install : mothur\r
+ #cp mothur ../Release/mothur\r
+\r
+#\r
+# Build the parts of mothur\r
+#\r
+\r
+\r
+# Item # 1 -- sharedutilities --\r
+./sharedutilities.o : sharedutilities.cpp\r
+ $(CC) $(CC_OPTIONS) sharedutilities.cpp -c $(INCLUDE) -o ./sharedutilities.o\r
+\r
+\r
+# Item # 2 -- treegroupscommand --\r
+./treegroupscommand.o : treegroupscommand.cpp\r
+ $(CC) $(CC_OPTIONS) treegroupscommand.cpp -c $(INCLUDE) -o ./treegroupscommand.o\r
+\r
+\r
+# Item # 3 -- bootstrapsharedcommand --\r
+./bootstrapsharedcommand.o : bootstrapsharedcommand.cpp\r
+ $(CC) $(CC_OPTIONS) bootstrapsharedcommand.cpp -c $(INCLUDE) -o ./bootstrapsharedcommand.o\r
+\r
+\r
+# Item # 4 -- matrixoutputcommand --\r
+./matrixoutputcommand.o : matrixoutputcommand.cpp\r
+ $(CC) $(CC_OPTIONS) matrixoutputcommand.cpp -c $(INCLUDE) -o ./matrixoutputcommand.o\r
+\r
+\r
+# Item # 5 -- getoturepcommand --\r
+./getoturepcommand.o : getoturepcommand.cpp\r
+ $(CC) $(CC_OPTIONS) getoturepcommand.cpp -c $(INCLUDE) -o ./getoturepcommand.o\r
+\r
+\r
+# Item # 6 -- screenseqscommand --\r
+./screenseqscommand.o : screenseqscommand.cpp\r
+ $(CC) $(CC_OPTIONS) screenseqscommand.cpp -c $(INCLUDE) -o ./screenseqscommand.o\r
+\r
+\r
+# Item # 7 -- chimera --\r
+./chimera.o : chimera.cpp\r
+ $(CC) $(CC_OPTIONS) chimera.cpp -c $(INCLUDE) -o ./chimera.o\r
+\r
+\r
+# Item # 8 -- decalc --\r
+./decalc.o : decalc.cpp\r
+ $(CC) $(CC_OPTIONS) decalc.cpp -c $(INCLUDE) -o ./decalc.o\r
+\r
+\r
+# Item # 9 -- readotucommand --\r
+./readotucommand.o : readotucommand.cpp\r
+ $(CC) $(CC_OPTIONS) readotucommand.cpp -c $(INCLUDE) -o ./readotucommand.o\r
+\r
+\r
+# Item # 10 -- readdistcommand --\r
+./readdistcommand.o : readdistcommand.cpp\r
+ $(CC) $(CC_OPTIONS) readdistcommand.cpp -c $(INCLUDE) -o ./readdistcommand.o\r
+\r
+\r
+# Item # 11 -- commandfactory --\r
+./commandfactory.o : commandfactory.cpp\r
+ $(CC) $(CC_OPTIONS) commandfactory.cpp -c $(INCLUDE) -o ./commandfactory.o\r
+\r
+\r
+# Item # 12 -- alignment --\r
+./alignment.o : alignment.cpp\r
+ $(CC) $(CC_OPTIONS) alignment.cpp -c $(INCLUDE) -o ./alignment.o\r
+\r
+\r
+# Item # 13 -- alignmentcell --\r
+./alignmentcell.o : alignmentcell.cpp\r
+ $(CC) $(CC_OPTIONS) alignmentcell.cpp -c $(INCLUDE) -o ./alignmentcell.o\r
+\r
+\r
+# Item # 14 -- gotohoverlap --\r
+./gotohoverlap.o : gotohoverlap.cpp\r
+ $(CC) $(CC_OPTIONS) gotohoverlap.cpp -c $(INCLUDE) -o ./gotohoverlap.o\r
+\r
+\r
+# Item # 15 -- overlap --\r
+./overlap.o : overlap.cpp\r
+ $(CC) $(CC_OPTIONS) overlap.cpp -c $(INCLUDE) -o ./overlap.o\r
+\r
+\r
+# Item # 16 -- needlemanoverlap --\r
+./needlemanoverlap.o : needlemanoverlap.cpp\r
+ $(CC) $(CC_OPTIONS) needlemanoverlap.cpp -c $(INCLUDE) -o ./needlemanoverlap.o\r
+\r
+\r
+# Item # 17 -- blastalign --\r
+./blastalign.o : blastalign.cpp\r
+ $(CC) $(CC_OPTIONS) blastalign.cpp -c $(INCLUDE) -o ./blastalign.o\r
+\r
+\r
+# Item # 18 -- noalign --\r
+./noalign.o : noalign.cpp\r
+ $(CC) $(CC_OPTIONS) noalign.cpp -c $(INCLUDE) -o ./noalign.o\r
+\r
+\r
+# Item # 19 -- suffixdb --\r
+./suffixdb.o : suffixdb.cpp\r
+ $(CC) $(CC_OPTIONS) suffixdb.cpp -c $(INCLUDE) -o ./suffixdb.o\r
+\r
+\r
+# Item # 20 -- suffixnodes --\r
+./suffixnodes.o : suffixnodes.cpp\r
+ $(CC) $(CC_OPTIONS) suffixnodes.cpp -c $(INCLUDE) -o ./suffixnodes.o\r
+\r
+\r
+# Item # 21 -- suffixtree --\r
+./suffixtree.o : suffixtree.cpp\r
+ $(CC) $(CC_OPTIONS) suffixtree.cpp -c $(INCLUDE) -o ./suffixtree.o\r
+\r
+\r
+# Item # 22 -- blastdb --\r
+./blastdb.o : blastdb.cpp\r
+ $(CC) $(CC_OPTIONS) blastdb.cpp -c $(INCLUDE) -o ./blastdb.o\r
+\r
+\r
+# Item # 23 -- nast --\r
+./nast.o : nast.cpp\r
+ $(CC) $(CC_OPTIONS) nast.cpp -c $(INCLUDE) -o ./nast.o\r
+\r
+\r
+# Item # 24 -- nastreport --\r
+./nastreport.o : nastreport.cpp\r
+ $(CC) $(CC_OPTIONS) nastreport.cpp -c $(INCLUDE) -o ./nastreport.o\r
+\r
+\r
+# Item # 25 -- boneh --\r
+./boneh.o : boneh.cpp\r
+ $(CC) $(CC_OPTIONS) boneh.cpp -c $(INCLUDE) -o ./boneh.o\r
+\r
+\r
+# Item # 26 -- efron --\r
+./efron.o : efron.cpp\r
+ $(CC) $(CC_OPTIONS) efron.cpp -c $(INCLUDE) -o ./efron.o\r
+\r
+\r
+# Item # 27 -- solow --\r
+./solow.o : solow.cpp\r
+ $(CC) $(CC_OPTIONS) solow.cpp -c $(INCLUDE) -o ./solow.o\r
+\r
+\r
+# Item # 28 -- unifracweightedcommand --\r
+./unifracweightedcommand.o : unifracweightedcommand.cpp\r
+ $(CC) $(CC_OPTIONS) unifracweightedcommand.cpp -c $(INCLUDE) -o ./unifracweightedcommand.o\r
+\r
+\r
+# Item # 29 -- weighted --\r
+./weighted.o : weighted.cpp\r
+ $(CC) $(CC_OPTIONS) weighted.cpp -c $(INCLUDE) -o ./weighted.o\r
+\r
+\r
+# Item # 30 -- unweighted --\r
+./unweighted.o : unweighted.cpp\r
+ $(CC) $(CC_OPTIONS) unweighted.cpp -c $(INCLUDE) -o ./unweighted.o\r
+\r
+\r
+# Item # 31 -- unifracunweightedcommand --\r
+./unifracunweightedcommand.o : unifracunweightedcommand.cpp\r
+ $(CC) $(CC_OPTIONS) unifracunweightedcommand.cpp -c $(INCLUDE) -o ./unifracunweightedcommand.o\r
+\r
+\r
+# Item # 32 -- getsabundcommand --\r
+./getsabundcommand.o : getsabundcommand.cpp\r
+ $(CC) $(CC_OPTIONS) getsabundcommand.cpp -c $(INCLUDE) -o ./getsabundcommand.o\r
+\r
+\r
+# Item # 33 -- getrabundcommand --\r
+./getrabundcommand.o : getrabundcommand.cpp\r
+ $(CC) $(CC_OPTIONS) getrabundcommand.cpp -c $(INCLUDE) -o ./getrabundcommand.o\r
+\r
+\r
+# Item # 34 -- bellerophon --\r
+./bellerophon.o : bellerophon.cpp\r
+ $(CC) $(CC_OPTIONS) bellerophon.cpp -c $(INCLUDE) -o ./bellerophon.o\r
+\r
+\r
+# Item # 35 -- pintail --\r
+./pintail.o : pintail.cpp\r
+ $(CC) $(CC_OPTIONS) pintail.cpp -c $(INCLUDE) -o ./pintail.o\r
+\r
+\r
+# Item # 36 -- sharedanderbergs --\r
+./sharedanderbergs.o : sharedanderbergs.cpp\r
+ $(CC) $(CC_OPTIONS) sharedanderbergs.cpp -c $(INCLUDE) -o ./sharedanderbergs.o\r
+\r
+\r
+# Item # 37 -- venncommand --\r
+./venncommand.o : venncommand.cpp\r
+ $(CC) $(CC_OPTIONS) venncommand.cpp -c $(INCLUDE) -o ./venncommand.o\r
+\r
+\r
+# Item # 38 -- venn --\r
+./venn.o : venn.cpp\r
+ $(CC) $(CC_OPTIONS) venn.cpp -c $(INCLUDE) -o ./venn.o\r
+\r
+\r
+# Item # 39 -- fullmatrix --\r
+./fullmatrix.o : fullmatrix.cpp\r
+ $(CC) $(CC_OPTIONS) fullmatrix.cpp -c $(INCLUDE) -o ./fullmatrix.o\r
+\r
+\r
+# Item # 40 -- heatmap --\r
+./heatmap.o : heatmap.cpp\r
+ $(CC) $(CC_OPTIONS) heatmap.cpp -c $(INCLUDE) -o ./heatmap.o\r
+\r
+\r
+# Item # 41 -- heatmapcommand --\r
+./heatmapcommand.o : heatmapcommand.cpp\r
+ $(CC) $(CC_OPTIONS) heatmapcommand.cpp -c $(INCLUDE) -o ./heatmapcommand.o\r
+\r
+\r
+# Item # 42 -- libshuffcommand --\r
+./libshuffcommand.o : libshuffcommand.cpp\r
+ $(CC) $(CC_OPTIONS) libshuffcommand.cpp -c $(INCLUDE) -o ./libshuffcommand.o\r
+\r
+\r
+# Item # 43 -- nocommands --\r
+./nocommands.o : nocommands.cpp\r
+ $(CC) $(CC_OPTIONS) nocommands.cpp -c $(INCLUDE) -o ./nocommands.o\r
+\r
+\r
+# Item # 44 -- sharedbraycurtis --\r
+./sharedbraycurtis.o : sharedbraycurtis.cpp\r
+ $(CC) $(CC_OPTIONS) sharedbraycurtis.cpp -c $(INCLUDE) -o ./sharedbraycurtis.o\r
+\r
+\r
+# Item # 45 -- sharedkulczynski --\r
+./sharedkulczynski.o : sharedkulczynski.cpp\r
+ $(CC) $(CC_OPTIONS) sharedkulczynski.cpp -c $(INCLUDE) -o ./sharedkulczynski.o\r
+\r
+\r
+# Item # 46 -- sharedlennon --\r
+./sharedlennon.o : sharedlennon.cpp\r
+ $(CC) $(CC_OPTIONS) sharedlennon.cpp -c $(INCLUDE) -o ./sharedlennon.o\r
+\r
+\r
+# Item # 47 -- sharedkulczynskicody --\r
+./sharedkulczynskicody.o : sharedkulczynskicody.cpp\r
+ $(CC) $(CC_OPTIONS) sharedkulczynskicody.cpp -c $(INCLUDE) -o ./sharedkulczynskicody.o\r
+\r
+\r
+# Item # 48 -- sharedmorisitahorn --\r
+./sharedmorisitahorn.o : sharedmorisitahorn.cpp\r
+ $(CC) $(CC_OPTIONS) sharedmorisitahorn.cpp -c $(INCLUDE) -o ./sharedmorisitahorn.o\r
+\r
+\r
+# Item # 49 -- sharedochiai --\r
+./sharedochiai.o : sharedochiai.cpp\r
+ $(CC) $(CC_OPTIONS) sharedochiai.cpp -c $(INCLUDE) -o ./sharedochiai.o\r
+\r
+\r
+# Item # 50 -- readcolumn --\r
+./readcolumn.o : readcolumn.cpp\r
+ $(CC) $(CC_OPTIONS) readcolumn.cpp -c $(INCLUDE) -o ./readcolumn.o\r
+\r
+\r
+# Item # 51 -- readotu --\r
+./readotu.o : readotu.cpp\r
+ $(CC) $(CC_OPTIONS) readotu.cpp -c $(INCLUDE) -o ./readotu.o\r
+\r
+\r
+# Item # 52 -- readphylip --\r
+./readphylip.o : readphylip.cpp\r
+ $(CC) $(CC_OPTIONS) readphylip.cpp -c $(INCLUDE) -o ./readphylip.o\r
+\r
+\r
+# Item # 53 -- consensuscommand --\r
+./consensuscommand.o : consensuscommand.cpp\r
+ $(CC) $(CC_OPTIONS) consensuscommand.cpp -c $(INCLUDE) -o ./consensuscommand.o\r
+\r
+\r
+# Item # 54 -- heatmapsimcommand --\r
+./heatmapsimcommand.o : heatmapsimcommand.cpp\r
+ $(CC) $(CC_OPTIONS) heatmapsimcommand.cpp -c $(INCLUDE) -o ./heatmapsimcommand.o\r
+\r
+\r
+# Item # 55 -- heatmapsim --\r
+./heatmapsim.o : heatmapsim.cpp\r
+ $(CC) $(CC_OPTIONS) heatmapsim.cpp -c $(INCLUDE) -o ./heatmapsim.o\r
+\r
+\r
+# Item # 56 -- optionparser --\r
+./optionparser.o : optionparser.cpp\r
+ $(CC) $(CC_OPTIONS) optionparser.cpp -c $(INCLUDE) -o ./optionparser.o\r
+\r
+\r
+# Item # 57 -- filterseqscommand --\r
+./filterseqscommand.o : filterseqscommand.cpp\r
+ $(CC) $(CC_OPTIONS) filterseqscommand.cpp -c $(INCLUDE) -o ./filterseqscommand.o\r
+\r
+\r
+# Item # 58 -- goodscoverage --\r
+./goodscoverage.o : goodscoverage.cpp\r
+ $(CC) $(CC_OPTIONS) goodscoverage.cpp -c $(INCLUDE) -o ./goodscoverage.o\r
+\r
+\r
+# Item # 59 -- sequencedb --\r
+./sequencedb.o : sequencedb.cpp\r
+ $(CC) $(CC_OPTIONS) sequencedb.cpp -c $(INCLUDE) -o ./sequencedb.o\r
+\r
+\r
+# Item # 60 -- sharedjackknife --\r
+./sharedjackknife.o : sharedjackknife.cpp\r
+ $(CC) $(CC_OPTIONS) sharedjackknife.cpp -c $(INCLUDE) -o ./sharedjackknife.o\r
+\r
+\r
+# Item # 61 -- sharedmarczewski --\r
+./sharedmarczewski.o : sharedmarczewski.cpp\r
+ $(CC) $(CC_OPTIONS) sharedmarczewski.cpp -c $(INCLUDE) -o ./sharedmarczewski.o\r
+\r
+\r
+# Item # 62 -- aligncommand --\r
+./aligncommand.o : aligncommand.cpp\r
+ $(CC) $(CC_OPTIONS) aligncommand.cpp -c $(INCLUDE) -o ./aligncommand.o\r
+\r
+\r
+# Item # 63 -- treemap --\r
+./treemap.o : treemap.cpp\r
+ $(CC) $(CC_OPTIONS) treemap.cpp -c $(INCLUDE) -o ./treemap.o\r
+\r
+\r
+# Item # 64 -- parsimonycommand --\r
+./parsimonycommand.o : parsimonycommand.cpp\r
+ $(CC) $(CC_OPTIONS) parsimonycommand.cpp -c $(INCLUDE) -o ./parsimonycommand.o\r
+\r
+\r
+# Item # 65 -- parsimony --\r
+./parsimony.o : parsimony.cpp\r
+ $(CC) $(CC_OPTIONS) parsimony.cpp -c $(INCLUDE) -o ./parsimony.o\r
+\r
+\r
+# Item # 66 -- seqsummarycommand --\r
+./seqsummarycommand.o : seqsummarycommand.cpp\r
+ $(CC) $(CC_OPTIONS) seqsummarycommand.cpp -c $(INCLUDE) -o ./seqsummarycommand.o\r
+\r
+\r
+# Item # 67 -- chimeraseqscommand --\r
+./chimeraseqscommand.o : chimeraseqscommand.cpp\r
+ $(CC) $(CC_OPTIONS) chimeraseqscommand.cpp -c $(INCLUDE) -o ./chimeraseqscommand.o\r
+\r
+\r
+# Item # 68 -- sharedlistvector --\r
+./sharedlistvector.o : sharedlistvector.cpp\r
+ $(CC) $(CC_OPTIONS) sharedlistvector.cpp -c $(INCLUDE) -o ./sharedlistvector.o\r
+\r
+\r
+# Item # 69 -- tree --\r
+./tree.o : tree.cpp\r
+ $(CC) $(CC_OPTIONS) tree.cpp -c $(INCLUDE) -o ./tree.o\r
+\r
+\r
+# Item # 70 -- readtree --\r
+./readtree.o : readtree.cpp\r
+ $(CC) $(CC_OPTIONS) readtree.cpp -c $(INCLUDE) -o ./readtree.o\r
+\r
+\r
+# Item # 71 -- sharedsobscollectsummary --\r
+./sharedsobscollectsummary.o : sharedsobscollectsummary.cpp\r
+ $(CC) $(CC_OPTIONS) sharedsobscollectsummary.cpp -c $(INCLUDE) -o ./sharedsobscollectsummary.o\r
+\r
+\r
+# Item # 72 -- deconvolutecommand --\r
+./deconvolutecommand.o : deconvolutecommand.cpp\r
+ $(CC) $(CC_OPTIONS) deconvolutecommand.cpp -c $(INCLUDE) -o ./deconvolutecommand.o\r
+\r
+\r
+# Item # 73 -- listseqscommand --\r
+./listseqscommand.o : listseqscommand.cpp\r
+ $(CC) $(CC_OPTIONS) listseqscommand.cpp -c $(INCLUDE) -o ./listseqscommand.o\r
+\r
+\r
+# Item # 74 -- getseqscommand --\r
+./getseqscommand.o : getseqscommand.cpp\r
+ $(CC) $(CC_OPTIONS) getseqscommand.cpp -c $(INCLUDE) -o ./getseqscommand.o\r
+\r
+\r
+# Item # 75 -- removeseqscommand --\r
+./removeseqscommand.o : removeseqscommand.cpp\r
+ $(CC) $(CC_OPTIONS) removeseqscommand.cpp -c $(INCLUDE) -o ./removeseqscommand.o\r
+\r
+\r
+# Item # 76 -- systemcommand --\r
+./systemcommand.o : systemcommand.cpp\r
+ $(CC) $(CC_OPTIONS) systemcommand.cpp -c $(INCLUDE) -o ./systemcommand.o\r
+\r
+\r
+# Item # 77 -- binsequencecommand --\r
+./binsequencecommand.o : binsequencecommand.cpp\r
+ $(CC) $(CC_OPTIONS) binsequencecommand.cpp -c $(INCLUDE) -o ./binsequencecommand.o\r
+\r
+\r
+# Item # 78 -- distancecommand --\r
+./distancecommand.o : distancecommand.cpp\r
+ $(CC) $(CC_OPTIONS) distancecommand.cpp -c $(INCLUDE) -o ./distancecommand.o\r
+\r
+\r
+# Item # 79 -- ace --\r
+./ace.o : ace.cpp\r
+ $(CC) $(CC_OPTIONS) ace.cpp -c $(INCLUDE) -o ./ace.o\r
+\r
+\r
+# Item # 80 -- averagelinkage --\r
+./averagelinkage.o : averagelinkage.cpp\r
+ $(CC) $(CC_OPTIONS) averagelinkage.cpp -c $(INCLUDE) -o ./averagelinkage.o\r
+\r
+\r
+# Item # 81 -- bootstrap --\r
+./bootstrap.o : bootstrap.cpp\r
+ $(CC) $(CC_OPTIONS) bootstrap.cpp -c $(INCLUDE) -o ./bootstrap.o\r
+\r
+\r
+# Item # 82 -- calculator --\r
+./calculator.o : calculator.cpp\r
+ $(CC) $(CC_OPTIONS) calculator.cpp -c $(INCLUDE) -o ./calculator.o\r
+\r
+\r
+# Item # 83 -- chao1 --\r
+./chao1.o : chao1.cpp\r
+ $(CC) $(CC_OPTIONS) chao1.cpp -c $(INCLUDE) -o ./chao1.o\r
+\r
+\r
+# Item # 84 -- cluster --\r
+./cluster.o : cluster.cpp\r
+ $(CC) $(CC_OPTIONS) cluster.cpp -c $(INCLUDE) -o ./cluster.o\r
+\r
+\r
+# Item # 85 -- clustercommand --\r
+./clustercommand.o : clustercommand.cpp\r
+ $(CC) $(CC_OPTIONS) clustercommand.cpp -c $(INCLUDE) -o ./clustercommand.o\r
+\r
+\r
+# Item # 86 -- collect --\r
+./collect.o : collect.cpp\r
+ $(CC) $(CC_OPTIONS) collect.cpp -c $(INCLUDE) -o ./collect.o\r
+\r
+\r
+# Item # 87 -- collectcommand --\r
+./collectcommand.o : collectcommand.cpp\r
+ $(CC) $(CC_OPTIONS) collectcommand.cpp -c $(INCLUDE) -o ./collectcommand.o\r
+\r
+\r
+# Item # 88 -- collectsharedcommand --\r
+./collectsharedcommand.o : collectsharedcommand.cpp\r
+ $(CC) $(CC_OPTIONS) collectsharedcommand.cpp -c $(INCLUDE) -o ./collectsharedcommand.o\r
+\r
+\r
+# Item # 89 -- commandoptionparser --\r
+./commandoptionparser.o : commandoptionparser.cpp\r
+ $(CC) $(CC_OPTIONS) commandoptionparser.cpp -c $(INCLUDE) -o ./commandoptionparser.o\r
+\r
+\r
+# Item # 90 -- completelinkage --\r
+./completelinkage.o : completelinkage.cpp\r
+ $(CC) $(CC_OPTIONS) completelinkage.cpp -c $(INCLUDE) -o ./completelinkage.o\r
+\r
+\r
+# Item # 91 -- database --\r
+./database.o : database.cpp\r
+ $(CC) $(CC_OPTIONS) database.cpp -c $(INCLUDE) -o ./database.o\r
+\r
+\r
+# Item # 92 -- engine --\r
+./engine.o : engine.cpp\r
+ $(CC) $(CC_OPTIONS) engine.cpp -c $(INCLUDE) -o ./engine.o\r
+\r
+\r
+# Item # 93 -- fastamap --\r
+./fastamap.o : fastamap.cpp\r
+ $(CC) $(CC_OPTIONS) fastamap.cpp -c $(INCLUDE) -o ./fastamap.o\r
+\r
+\r
+# Item # 94 -- fileoutput --\r
+./fileoutput.o : fileoutput.cpp\r
+ $(CC) $(CC_OPTIONS) fileoutput.cpp -c $(INCLUDE) -o ./fileoutput.o\r
+\r
+\r
+# Item # 95 -- globaldata --\r
+./globaldata.o : globaldata.cpp\r
+ $(CC) $(CC_OPTIONS) globaldata.cpp -c $(INCLUDE) -o ./globaldata.o\r
+\r
+\r
+# Item # 96 -- groupmap --\r
+./groupmap.o : groupmap.cpp\r
+ $(CC) $(CC_OPTIONS) groupmap.cpp -c $(INCLUDE) -o ./groupmap.o\r
+\r
+\r
+# Item # 97 -- helpcommand --\r
+./helpcommand.o : helpcommand.cpp\r
+ $(CC) $(CC_OPTIONS) helpcommand.cpp -c $(INCLUDE) -o ./helpcommand.o\r
+\r
+\r
+# Item # 98 -- inputdata --\r
+./inputdata.o : inputdata.cpp\r
+ $(CC) $(CC_OPTIONS) inputdata.cpp -c $(INCLUDE) -o ./inputdata.o\r
+\r
+\r
+# Item # 99 -- jackknife --\r
+./jackknife.o : jackknife.cpp\r
+ $(CC) $(CC_OPTIONS) jackknife.cpp -c $(INCLUDE) -o ./jackknife.o\r
+\r
+\r
+# Item # 100 -- kmer --\r
+./kmer.o : kmer.cpp\r
+ $(CC) $(CC_OPTIONS) kmer.cpp -c $(INCLUDE) -o ./kmer.o\r
+\r
+\r
+# Item # 101 -- kmerdb --\r
+./kmerdb.o : kmerdb.cpp\r
+ $(CC) $(CC_OPTIONS) kmerdb.cpp -c $(INCLUDE) -o ./kmerdb.o\r
+\r
+\r
+# Item # 102 -- listvector --\r
+./listvector.o : listvector.cpp\r
+ $(CC) $(CC_OPTIONS) listvector.cpp -c $(INCLUDE) -o ./listvector.o\r
+\r
+\r
+# Item # 103 -- mothur --\r
+./mothur.o : mothur.cpp\r
+ $(CC) $(CC_OPTIONS) mothur.cpp -c $(INCLUDE) -o ./mothur.o\r
+\r
+\r
+# Item # 104 -- nameassignment --\r
+./nameassignment.o : nameassignment.cpp\r
+ $(CC) $(CC_OPTIONS) nameassignment.cpp -c $(INCLUDE) -o ./nameassignment.o\r
+\r
+\r
+# Item # 105 -- npshannon --\r
+./npshannon.o : npshannon.cpp\r
+ $(CC) $(CC_OPTIONS) npshannon.cpp -c $(INCLUDE) -o ./npshannon.o\r
+\r
+\r
+# Item # 106 -- ordervector --\r
+./ordervector.o : ordervector.cpp\r
+ $(CC) $(CC_OPTIONS) ordervector.cpp -c $(INCLUDE) -o ./ordervector.o\r
+\r
+\r
+# Item # 107 -- progress --\r
+./progress.o : progress.cpp\r
+ $(CC) $(CC_OPTIONS) progress.cpp -c $(INCLUDE) -o ./progress.o\r
+\r
+\r
+# Item # 108 -- quitcommand --\r
+./quitcommand.o : quitcommand.cpp\r
+ $(CC) $(CC_OPTIONS) quitcommand.cpp -c $(INCLUDE) -o ./quitcommand.o\r
+\r
+\r
+# Item # 109 -- rabundvector --\r
+./rabundvector.o : rabundvector.cpp\r
+ $(CC) $(CC_OPTIONS) rabundvector.cpp -c $(INCLUDE) -o ./rabundvector.o\r
+\r
+\r
+# Item # 110 -- rarecalc --\r
+./rarecalc.o : rarecalc.cpp\r
+ $(CC) $(CC_OPTIONS) rarecalc.cpp -c $(INCLUDE) -o ./rarecalc.o\r
+\r
+\r
+# Item # 111 -- raredisplay --\r
+./raredisplay.o : raredisplay.cpp\r
+ $(CC) $(CC_OPTIONS) raredisplay.cpp -c $(INCLUDE) -o ./raredisplay.o\r
+\r
+\r
+# Item # 112 -- rarefact --\r
+./rarefact.o : rarefact.cpp\r
+ $(CC) $(CC_OPTIONS) rarefact.cpp -c $(INCLUDE) -o ./rarefact.o\r
+\r
+\r
+# Item # 113 -- rarefactcommand --\r
+./rarefactcommand.o : rarefactcommand.cpp\r
+ $(CC) $(CC_OPTIONS) rarefactcommand.cpp -c $(INCLUDE) -o ./rarefactcommand.o\r
+\r
+\r
+# Item # 114 -- rarefactsharedcommand --\r
+./rarefactsharedcommand.o : rarefactsharedcommand.cpp\r
+ $(CC) $(CC_OPTIONS) rarefactsharedcommand.cpp -c $(INCLUDE) -o ./rarefactsharedcommand.o\r
+\r
+\r
+# Item # 115 -- sabundvector --\r
+./sabundvector.o : sabundvector.cpp\r
+ $(CC) $(CC_OPTIONS) sabundvector.cpp -c $(INCLUDE) -o ./sabundvector.o\r
+\r
+\r
+# Item # 116 -- sequence --\r
+./sequence.o : sequence.cpp\r
+ $(CC) $(CC_OPTIONS) sequence.cpp -c $(INCLUDE) -o ./sequence.o\r
+\r
+\r
+# Item # 117 -- shannon --\r
+./shannon.o : shannon.cpp\r
+ $(CC) $(CC_OPTIONS) shannon.cpp -c $(INCLUDE) -o ./shannon.o\r
+\r
+\r
+# Item # 118 -- sharedace --\r
+./sharedace.o : sharedace.cpp\r
+ $(CC) $(CC_OPTIONS) sharedace.cpp -c $(INCLUDE) -o ./sharedace.o\r
+\r
+\r
+# Item # 119 -- sharedchao1 --\r
+./sharedchao1.o : sharedchao1.cpp\r
+ $(CC) $(CC_OPTIONS) sharedchao1.cpp -c $(INCLUDE) -o ./sharedchao1.o\r
+\r
+\r
+# Item # 120 -- sharedcommand --\r
+./sharedcommand.o : sharedcommand.cpp\r
+ $(CC) $(CC_OPTIONS) sharedcommand.cpp -c $(INCLUDE) -o ./sharedcommand.o\r
+\r
+\r
+# Item # 121 -- sharedjabund --\r
+./sharedjabund.o : sharedjabund.cpp\r
+ $(CC) $(CC_OPTIONS) sharedjabund.cpp -c $(INCLUDE) -o ./sharedjabund.o\r
+\r
+\r
+# Item # 122 -- sharedjclass --\r
+./sharedjclass.o : sharedjclass.cpp\r
+ $(CC) $(CC_OPTIONS) sharedjclass.cpp -c $(INCLUDE) -o ./sharedjclass.o\r
+\r
+\r
+# Item # 123 -- sharedjest --\r
+./sharedjest.o : sharedjest.cpp\r
+ $(CC) $(CC_OPTIONS) sharedjest.cpp -c $(INCLUDE) -o ./sharedjest.o\r
+\r
+\r
+# Item # 124 -- sharedordervector --\r
+./sharedordervector.o : sharedordervector.cpp\r
+ $(CC) $(CC_OPTIONS) sharedordervector.cpp -c $(INCLUDE) -o ./sharedordervector.o\r
+\r
+\r
+# Item # 125 -- sharedrabundvector --\r
+./sharedrabundvector.o : sharedrabundvector.cpp\r
+ $(CC) $(CC_OPTIONS) sharedrabundvector.cpp -c $(INCLUDE) -o ./sharedrabundvector.o\r
+\r
+\r
+# Item # 126 -- sharedsabundvector --\r
+./sharedsabundvector.o : sharedsabundvector.cpp\r
+ $(CC) $(CC_OPTIONS) sharedsabundvector.cpp -c $(INCLUDE) -o ./sharedsabundvector.o\r
+\r
+\r
+# Item # 127 -- sharedsobs --\r
+./sharedsobs.o : sharedsobs.cpp\r
+ $(CC) $(CC_OPTIONS) sharedsobs.cpp -c $(INCLUDE) -o ./sharedsobs.o\r
+\r
+\r
+# Item # 128 -- sharedsorabund --\r
+./sharedsorabund.o : sharedsorabund.cpp\r
+ $(CC) $(CC_OPTIONS) sharedsorabund.cpp -c $(INCLUDE) -o ./sharedsorabund.o\r
+\r
+\r
+# Item # 129 -- sharedsorclass --\r
+./sharedsorclass.o : sharedsorclass.cpp\r
+ $(CC) $(CC_OPTIONS) sharedsorclass.cpp -c $(INCLUDE) -o ./sharedsorclass.o\r
+\r
+\r
+# Item # 130 -- sharedsorest --\r
+./sharedsorest.o : sharedsorest.cpp\r
+ $(CC) $(CC_OPTIONS) sharedsorest.cpp -c $(INCLUDE) -o ./sharedsorest.o\r
+\r
+\r
+# Item # 131 -- sharedthetan --\r
+./sharedthetan.o : sharedthetan.cpp\r
+ $(CC) $(CC_OPTIONS) sharedthetan.cpp -c $(INCLUDE) -o ./sharedthetan.o\r
+\r
+\r
+# Item # 132 -- sharedthetayc --\r
+./sharedthetayc.o : sharedthetayc.cpp\r
+ $(CC) $(CC_OPTIONS) sharedthetayc.cpp -c $(INCLUDE) -o ./sharedthetayc.o\r
+\r
+\r
+# Item # 133 -- simpson --\r
+./simpson.o : simpson.cpp\r
+ $(CC) $(CC_OPTIONS) simpson.cpp -c $(INCLUDE) -o ./simpson.o\r
+\r
+\r
+# Item # 134 -- singlelinkage --\r
+./singlelinkage.o : singlelinkage.cpp\r
+ $(CC) $(CC_OPTIONS) singlelinkage.cpp -c $(INCLUDE) -o ./singlelinkage.o\r
+\r
+\r
+# Item # 135 -- sparsematrix --\r
+./sparsematrix.o : sparsematrix.cpp\r
+ $(CC) $(CC_OPTIONS) sparsematrix.cpp -c $(INCLUDE) -o ./sparsematrix.o\r
+\r
+\r
+# Item # 136 -- summarycommand --\r
+./summarycommand.o : summarycommand.cpp\r
+ $(CC) $(CC_OPTIONS) summarycommand.cpp -c $(INCLUDE) -o ./summarycommand.o\r
+\r
+\r
+# Item # 137 -- summarysharedcommand --\r
+./summarysharedcommand.o : summarysharedcommand.cpp\r
+ $(CC) $(CC_OPTIONS) summarysharedcommand.cpp -c $(INCLUDE) -o ./summarysharedcommand.o\r
+\r
+\r
+# Item # 138 -- uvest --\r
+./uvest.o : uvest.cpp\r
+ $(CC) $(CC_OPTIONS) uvest.cpp -c $(INCLUDE) -o ./uvest.o\r
+\r
+\r
+# Item # 139 -- validcalculator --\r
+./validcalculator.o : validcalculator.cpp\r
+ $(CC) $(CC_OPTIONS) validcalculator.cpp -c $(INCLUDE) -o ./validcalculator.o\r
+\r
+\r
+# Item # 140 -- validparameter --\r
+./validparameter.o : validparameter.cpp\r
+ $(CC) $(CC_OPTIONS) validparameter.cpp -c $(INCLUDE) -o ./validparameter.o\r
+\r
+\r
+# Item # 141 -- treenode --\r
+./treenode.o : treenode.cpp\r
+ $(CC) $(CC_OPTIONS) treenode.cpp -c $(INCLUDE) -o ./treenode.o\r
+\r
+\r
+# Item # 142 -- readtreecommand --\r
+./readtreecommand.o : readtreecommand.cpp\r
+ $(CC) $(CC_OPTIONS) readtreecommand.cpp -c $(INCLUDE) -o ./readtreecommand.o\r
+\r
+\r
+# Item # 143 -- reversecommand --\r
+./reversecommand.o : reversecommand.cpp\r
+ $(CC) $(CC_OPTIONS) reversecommand.cpp -c $(INCLUDE) -o ./reversecommand.o\r
+\r
+\r
+# Item # 144 -- trimseqscommand --\r
+./trimseqscommand.o : trimseqscommand.cpp\r
+ $(CC) $(CC_OPTIONS) trimseqscommand.cpp -c $(INCLUDE) -o ./trimseqscommand.o\r
+\r
+\r
+# Item # 145 -- slibshuff --\r
+./slibshuff.o : slibshuff.cpp\r
+ $(CC) $(CC_OPTIONS) slibshuff.cpp -c $(INCLUDE) -o ./slibshuff.o\r
+\r
+\r
+# Item # 146 -- libshuff --\r
+./libshuff.o : libshuff.cpp\r
+ $(CC) $(CC_OPTIONS) libshuff.cpp -c $(INCLUDE) -o ./libshuff.o\r
+\r
+\r
+# Item # 147 -- dlibshuff --\r
+./dlibshuff.o : dlibshuff.cpp\r
+ $(CC) $(CC_OPTIONS) dlibshuff.cpp -c $(INCLUDE) -o ./dlibshuff.o\r
+\r
+\r
+# Item # 148 -- mergefilecommand --\r
+./mergefilecommand.o : mergefilecommand.cpp\r
+ $(CC) $(CC_OPTIONS) mergefilecommand.cpp -c $(INCLUDE) -o ./mergefilecommand.o\r
+\r
+\r
+# Item # 149 -- coverage --\r
+./coverage.o : coverage.cpp\r
+ $(CC) $(CC_OPTIONS) coverage.cpp -c $(INCLUDE) -o ./coverage.o\r
+\r
+\r
+# Item # 150 -- whittaker --\r
+./whittaker.o : whittaker.cpp\r
+ $(CC) $(CC_OPTIONS) whittaker.cpp -c $(INCLUDE) -o ./whittaker.o\r
+\r
+\r
+# Item # 151 -- preclustercommand --\r
+./preclustercommand.o : preclustercommand.cpp\r
+ $(CC) $(CC_OPTIONS) preclustercommand.cpp -c $(INCLUDE) -o ./preclustercommand.o\r
+\r
+\r
+# Item # 152 -- otuhierarchycommand --\r
+./otuhierarchycommand.o : otuhierarchycommand.cpp\r
+ $(CC) $(CC_OPTIONS) otuhierarchycommand.cpp -c $(INCLUDE) -o ./otuhierarchycommand.o\r
+\r
+\r
+# Item # 153 -- setdircommand --\r
+./setdircommand.o : setdircommand.cpp\r
+ $(CC) $(CC_OPTIONS) setdircommand.cpp -c $(INCLUDE) -o ./setdircommand.o\r
+\r
+\r
+# Item # 154 -- getgroupcommand --\r
+./getgroupcommand.o : getgroupcommand.cpp\r
+ $(CC) $(CC_OPTIONS) getgroupcommand.cpp -c $(INCLUDE) -o ./getgroupcommand.o\r
+\r
+\r
+# Item # 155 -- getlabelcommand --\r
+./getlabelcommand.o : getlabelcommand.cpp\r
+ $(CC) $(CC_OPTIONS) getlabelcommand.cpp -c $(INCLUDE) -o ./getlabelcommand.o\r
+\r
+\r
+# Item # 156 -- secondarystructurecommand --\r
+./secondarystructurecommand.o : secondarystructurecommand.cpp\r
+ $(CC) $(CC_OPTIONS) secondarystructurecommand.cpp -c $(INCLUDE) -o ./secondarystructurecommand.o\r
+\r
+\r
+# Item # 157 -- mothurout --\r
+./mothurout.o : mothurout.cpp\r
+ $(CC) $(CC_OPTIONS) mothurout.cpp -c $(INCLUDE) -o ./mothurout.o\r
+\r
+\r
+# Item # 158 -- parselistscommand --\r
+./parselistscommand.o : parselistscommand.cpp\r
+ $(CC) $(CC_OPTIONS) parselistscommand.cpp -c $(INCLUDE) -o ./parselistscommand.o\r
+\r
+\r
+# Item # 159 -- readblast --\r
+./readblast.o : readblast.cpp\r
+ $(CC) $(CC_OPTIONS) readblast.cpp -c $(INCLUDE) -o ./readblast.o\r
+\r
+\r
+# Item # 160 -- chimeracheckrdp --\r
+./chimeracheckrdp.o : chimeracheckrdp.cpp\r
+ $(CC) $(CC_OPTIONS) chimeracheckrdp.cpp -c $(INCLUDE) -o ./chimeracheckrdp.o\r
+\r
+\r
+# Item # 161 -- hclustercommand --\r
+./hclustercommand.o : hclustercommand.cpp\r
+ $(CC) $(CC_OPTIONS) hclustercommand.cpp -c $(INCLUDE) -o ./hclustercommand.o\r
+\r
+\r
+# Item # 162 -- hcluster --\r
+./hcluster.o : hcluster.cpp\r
+ $(CC) $(CC_OPTIONS) hcluster.cpp -c $(INCLUDE) -o ./hcluster.o\r
+\r
+\r
+# Item # 163 -- getlistcountcommand --\r
+./getlistcountcommand.o : getlistcountcommand.cpp\r
+ $(CC) $(CC_OPTIONS) getlistcountcommand.cpp -c $(INCLUDE) -o ./getlistcountcommand.o\r
+\r
+\r
+# Item # 164 -- readcluster --\r
+./readcluster.o : readcluster.cpp\r
+ $(CC) $(CC_OPTIONS) readcluster.cpp -c $(INCLUDE) -o ./readcluster.o\r
+\r
+\r
+# Item # 165 -- ccode --\r
+./ccode.o : ccode.cpp\r
+ $(CC) $(CC_OPTIONS) ccode.cpp -c $(INCLUDE) -o ./ccode.o\r
+\r
+\r
+# Item # 166 -- taxonomyequalizer --\r
+./taxonomyequalizer.o : taxonomyequalizer.cpp\r
+ $(CC) $(CC_OPTIONS) taxonomyequalizer.cpp -c $(INCLUDE) -o ./taxonomyequalizer.o\r
+\r
+\r
+# Item # 167 -- phylotypecommand --\r
+./phylotypecommand.o : phylotypecommand.cpp\r
+ $(CC) $(CC_OPTIONS) phylotypecommand.cpp -c $(INCLUDE) -o ./phylotypecommand.o\r
+\r
+\r
+# Item # 168 -- classifyseqscommand --\r
+./classifyseqscommand.o : classifyseqscommand.cpp\r
+ $(CC) $(CC_OPTIONS) classifyseqscommand.cpp -c $(INCLUDE) -o ./classifyseqscommand.o\r
+\r
+\r
+# Item # 169 -- classify --\r
+./classify.o : classify.cpp\r
+ $(CC) $(CC_OPTIONS) classify.cpp -c $(INCLUDE) -o ./classify.o\r
+\r
+\r
+# Item # 170 -- phylotree --\r
+./phylotree.o : phylotree.cpp\r
+ $(CC) $(CC_OPTIONS) phylotree.cpp -c $(INCLUDE) -o ./phylotree.o\r
+\r
+\r
+# Item # 171 -- bayesian --\r
+./bayesian.o : bayesian.cpp\r
+ $(CC) $(CC_OPTIONS) bayesian.cpp -c $(INCLUDE) -o ./bayesian.o\r
+\r
+\r
+# Item # 172 -- alignmentdb --\r
+./alignmentdb.o : alignmentdb.cpp\r
+ $(CC) $(CC_OPTIONS) alignmentdb.cpp -c $(INCLUDE) -o ./alignmentdb.o\r
+\r
+\r
+# Item # 173 -- knn --\r
+./knn.o : knn.cpp\r
+ $(CC) $(CC_OPTIONS) knn.cpp -c $(INCLUDE) -o ./knn.o\r
+\r
+\r
+# Item # 174 -- distancedb --\r
+./distancedb.o : distancedb.cpp\r
+ $(CC) $(CC_OPTIONS) distancedb.cpp -c $(INCLUDE) -o ./distancedb.o\r
+\r
+\r
+# Item # 175 -- chimeraslayer --\r
+./chimeraslayer.o : chimeraslayer.cpp\r
+ $(CC) $(CC_OPTIONS) chimeraslayer.cpp -c $(INCLUDE) -o ./chimeraslayer.o\r
+\r
+\r
+# Item # 176 -- slayer --\r
+./slayer.o : slayer.cpp\r
+ $(CC) $(CC_OPTIONS) slayer.cpp -c $(INCLUDE) -o ./slayer.o\r
+\r
+\r
+# Item # 177 -- pcacommand --\r
+./pcacommand.o : pcacommand.cpp\r
+ $(CC) $(CC_OPTIONS) pcacommand.cpp -c $(INCLUDE) -o ./pcacommand.o\r
+\r
+\r
+# Item # 178 -- formatcolumn --\r
+./formatcolumn.o : formatcolumn.cpp\r
+ $(CC) $(CC_OPTIONS) formatcolumn.cpp -c $(INCLUDE) -o ./formatcolumn.o\r
+\r
+\r
+# Item # 179 -- formatphylip --\r
+./formatphylip.o : formatphylip.cpp\r
+ $(CC) $(CC_OPTIONS) formatphylip.cpp -c $(INCLUDE) -o ./formatphylip.o\r
+\r
+\r
+# Item # 180 -- mgclustercommand --\r
+./mgclustercommand.o : mgclustercommand.cpp\r
+ $(CC) $(CC_OPTIONS) mgclustercommand.cpp -c $(INCLUDE) -o ./mgclustercommand.o\r
+\r
+\r
+# Item # 181 -- getsharedotucommand --\r
+./getsharedotucommand.o : getsharedotucommand.cpp\r
+ $(CC) $(CC_OPTIONS) getsharedotucommand.cpp -c $(INCLUDE) -o ./getsharedotucommand.o\r
+\r
+\r
+# Item # 182 -- maligner --\r
+./maligner.o : maligner.cpp\r
+ $(CC) $(CC_OPTIONS) maligner.cpp -c $(INCLUDE) -o ./maligner.o\r
+\r
+\r
+# Item # 183 -- chimerarealigner --\r
+./chimerarealigner.o : chimerarealigner.cpp\r
+ $(CC) $(CC_OPTIONS) chimerarealigner.cpp -c $(INCLUDE) -o ./chimerarealigner.o\r
+\r
+\r
+# Item # 184 -- bergerparker --\r
+./bergerparker.o : bergerparker.cpp\r
+ $(CC) $(CC_OPTIONS) bergerparker.cpp -c $(INCLUDE) -o ./bergerparker.o\r
+\r
+\r
+# Item # 185 -- bstick --\r
+./bstick.o : bstick.cpp\r
+ $(CC) $(CC_OPTIONS) bstick.cpp -c $(INCLUDE) -o ./bstick.o\r
+\r
+\r
+# Item # 186 -- sharedkstest --\r
+./sharedkstest.o : sharedkstest.cpp\r
+ $(CC) $(CC_OPTIONS) sharedkstest.cpp -c $(INCLUDE) -o ./sharedkstest.o\r
+\r
+\r
+# Item # 187 -- qstat --\r
+./qstat.o : qstat.cpp\r
+ $(CC) $(CC_OPTIONS) qstat.cpp -c $(INCLUDE) -o ./qstat.o\r
+\r
+\r
+# Item # 188 -- shen --\r
+./shen.o : shen.cpp\r
+ $(CC) $(CC_OPTIONS) shen.cpp -c $(INCLUDE) -o ./shen.o\r
+\r
+\r
+# Item # 189 -- logsd --\r
+./logsd.o : logsd.cpp\r
+ $(CC) $(CC_OPTIONS) logsd.cpp -c $(INCLUDE) -o ./logsd.o\r
+\r
+\r
+# Item # 190 -- geom --\r
+./geom.o : geom.cpp\r
+ $(CC) $(CC_OPTIONS) geom.cpp -c $(INCLUDE) -o ./geom.o\r
+\r
+# Item # 191 -- parsesffcommand --\r
+./parsesffcommand.o : parsesffcommand.cpp\r
+ $(CC) $(CC_OPTIONS) parsesffcommand.cpp -c $(INCLUDE) -o ./parsesffcommand.o\r
+\r
+# Item # 192 -- chimeraccodecommand --\r
+./chimeraccodecommand.o : chimeraccodecommand.cpp\r
+ $(CC) $(CC_OPTIONS) chimeraccodecommand.cpp -c $(INCLUDE) -o ./chimeraccodecommand.o\r
+\r
+# Item # 193 -- chimeracheckcommand --\r
+./chimeracheckcommand.o : chimeracheckcommand.cpp\r
+ $(CC) $(CC_OPTIONS) chimeracheckcommand.cpp -c $(INCLUDE) -o ./chimeracheckcommand.o\r
+\r
+\r
+# Item # 194 -- chimeraslayercommand --\r
+./chimeraslayercommand.o : chimeraslayercommand.cpp\r
+ $(CC) $(CC_OPTIONS) chimeraslayercommand.cpp -c $(INCLUDE) -o ./chimeraslayercommand.o\r
+\r
+# Item # 195 -- chimerapintailcommand --\r
+./chimerapintailcommand.o : chimerapintailcommand.cpp\r
+ $(CC) $(CC_OPTIONS) chimerapintailcommand.cpp -c $(INCLUDE) -o ./chimerapintailcommand.o\r
+\r
+# Item # 196 -- chimerabellerophoncommand --\r
+./chimerabellerophoncommand.o : chimerabellerophoncommand.cpp\r
+ $(CC) $(CC_OPTIONS) chimerabellerophoncommand.cpp -c $(INCLUDE) -o ./chimerabellerophoncommand.o\r
+\r
+\r
+##### END RUN ####\r