1 ###################################################
4 # Creator [Xcode -> Makefile Ver: Feb 14 2007 09:18:41]
5 # Created: April 16, 2010
7 ###################################################
16 # if you do not want to use the readline library set to no, default yes.
17 # make sure you have the library installed
21 ifeq ($(strip $(64BIT_VERSION)),yes)
22 CC_OPTIONS += -arch x86_64
23 LNK_OPTIONS += -arch x86_64
28 ifeq ($(strip $(USEREADLINE)),yes)
29 CC_OPTIONS += -DUSE_READLINE
38 ifeq ($(strip $(USEMPI)),yes)
40 CC_OPTIONS += -DUSE_MPI
44 # INCLUDE directories for mothur
55 ./treegroupscommand.o\
56 ./bootstrapsharedcommand.o\
57 ./matrixoutputcommand.o\
59 ./screenseqscommand.o\
81 ./unifracweightedcommand.o\
84 ./unifracunweightedcommand.o\
100 ./sharedkulczynskicody.o\
101 ./sharedmorisitahorn.o\
106 ./consensuscommand.o\
107 ./heatmapsimcommand.o\
110 ./filterseqscommand.o\
114 ./sharedmarczewski.o\
117 ./parsimonycommand.o\
119 ./seqsummarycommand.o\
120 ./chimeraccodecommand.o\
121 ./chimerabellerophoncommand.o\
122 ./chimeracheckcommand.o\
123 ./chimeraslayercommand.o\
124 ./chimerapintailcommand.o\
125 ./chimeraseqscommand.o\
126 ./sharedlistvector.o\
129 ./sharedsobscollectsummary.o\
130 ./deconvolutecommand.o\
133 ./removeseqscommand.o\
134 ./degapseqscommand.o\
136 ./binsequencecommand.o\
147 ./collectsharedcommand.o\
148 ./commandoptionparser.o\
157 ./makegroupcommand.o\
161 ./splitabundcommand.o\
163 ./clustersplitcommand.o\
181 ./rarefactsharedcommand.o\
191 ./sharedordervector.o\
192 ./sharedrabundvector.o\
193 ./sharedsabundvector.o\
204 ./summarysharedcommand.o\
215 ./mergefilecommand.o\
218 ./preclustercommand.o\
219 ./otuhierarchycommand.o\
223 ./secondarystructurecommand.o\
225 ./parselistscommand.o\
230 ./getlistcountcommand.o\
233 ./taxonomyequalizer.o\
234 ./phylotypecommand.o\
235 ./classifyseqscommand.o\
236 ./classifyotucommand.o\
241 ./phylodiversitycommand.o\
252 ./mgclustercommand.o\
253 ./getsharedotucommand.o\
255 ./chimerarealigner.o\
263 ./setlogfilecommand.o
264 $(CC) $(LNK_OPTIONS) \
266 ./treegroupscommand.o\
267 ./bootstrapsharedcommand.o\
268 ./matrixoutputcommand.o\
269 ./getoturepcommand.o\
270 ./screenseqscommand.o\
280 ./needlemanoverlap.o\
292 ./unifracweightedcommand.o\
295 ./unifracunweightedcommand.o\
296 ./getsabundcommand.o\
297 ./getrabundcommand.o\
300 ./sharedanderbergs.o\
308 ./sharedbraycurtis.o\
309 ./sharedkulczynski.o\
311 ./sharedkulczynskicody.o\
312 ./sharedmorisitahorn.o\
317 ./consensuscommand.o\
318 ./heatmapsimcommand.o\
321 ./filterseqscommand.o\
325 ./sharedmarczewski.o\
328 ./parsimonycommand.o\
330 ./seqsummarycommand.o\
331 ./chimeraccodecommand.o\
332 ./chimerabellerophoncommand.o\
333 ./chimeracheckcommand.o\
334 ./chimeraslayercommand.o\
335 ./chimerapintailcommand.o\
336 ./chimeraseqscommand.o\
337 ./sharedlistvector.o\
340 ./sharedsobscollectsummary.o\
341 ./deconvolutecommand.o\
344 ./removeseqscommand.o\
345 ./degapseqscommand.o\
347 ./binsequencecommand.o\
358 ./collectsharedcommand.o\
359 ./commandoptionparser.o\
368 ./makegroupcommand.o\
372 ./splitabundcommand.o\
374 ./clustersplitcommand.o\
392 ./rarefactsharedcommand.o\
402 ./sharedordervector.o\
403 ./sharedrabundvector.o\
404 ./sharedsabundvector.o\
415 ./summarysharedcommand.o\
426 ./mergefilecommand.o\
429 ./preclustercommand.o\
430 ./otuhierarchycommand.o\
434 ./secondarystructurecommand.o\
436 ./parselistscommand.o\
441 ./getlistcountcommand.o\
444 ./taxonomyequalizer.o\
445 ./phylotypecommand.o\
446 ./classifyseqscommand.o\
447 ./classifyotucommand.o\
452 ./phylodiversitycommand.o\
463 ./mgclustercommand.o\
464 ./getsharedotucommand.o\
466 ./chimerarealigner.o\
474 ./setlogfilecommand.o\
480 ./treegroupscommand.o\
481 ./bootstrapsharedcommand.o\
482 ./matrixoutputcommand.o\
483 ./getoturepcommand.o\
484 ./screenseqscommand.o\
494 ./needlemanoverlap.o\
506 ./unifracweightedcommand.o\
509 ./unifracunweightedcommand.o\
510 ./getsabundcommand.o\
511 ./getrabundcommand.o\
514 ./sharedanderbergs.o\
522 ./sharedbraycurtis.o\
523 ./sharedkulczynski.o\
525 ./sharedkulczynskicody.o\
526 ./sharedmorisitahorn.o\
531 ./consensuscommand.o\
532 ./heatmapsimcommand.o\
535 ./filterseqscommand.o\
539 ./sharedmarczewski.o\
542 ./parsimonycommand.o\
544 ./seqsummarycommand.o\
545 ./chimeraccodecommand.o\
546 ./chimerabellerophoncommand.o\
547 ./chimeracheckcommand.o\
548 ./chimeraslayercommand.o\
549 ./chimerapintailcommand.o\
550 ./chimeraseqscommand.o\
551 ./sharedlistvector.o\
554 ./sharedsobscollectsummary.o\
555 ./deconvolutecommand.o\
558 ./removeseqscommand.o\
559 ./degapseqscommand.o\
561 ./binsequencecommand.o\
572 ./collectsharedcommand.o\
573 ./commandoptionparser.o\
582 ./makegroupcommand.o\
586 ./splitabundcommand.o\
588 ./clustersplitcommand.o\
606 ./rarefactsharedcommand.o\
616 ./sharedordervector.o\
617 ./sharedrabundvector.o\
618 ./sharedsabundvector.o\
629 ./summarysharedcommand.o\
640 ./mergefilecommand.o\
643 ./preclustercommand.o\
644 ./otuhierarchycommand.o\
648 ./secondarystructurecommand.o\
650 ./parselistscommand.o\
655 ./getlistcountcommand.o\
658 ./taxonomyequalizer.o\
659 ./phylotypecommand.o\
660 ./classifyseqscommand.o\
661 ./classifyotucommand.o\
666 ./phylodiversitycommand.o\
677 ./mgclustercommand.o\
678 ./getsharedotucommand.o\
680 ./chimerarealigner.o\
688 ./setlogfilecommand.o\
692 #cp mothur ../Release/mothur
695 # Build the parts of mothur
699 # Item # 1 -- sharedutilities --
700 ./sharedutilities.o : sharedutilities.cpp
701 $(CC) $(CC_OPTIONS) sharedutilities.cpp -c $(INCLUDE) -o ./sharedutilities.o
704 # Item # 2 -- treegroupscommand --
705 ./treegroupscommand.o : treegroupscommand.cpp
706 $(CC) $(CC_OPTIONS) treegroupscommand.cpp -c $(INCLUDE) -o ./treegroupscommand.o
709 # Item # 3 -- bootstrapsharedcommand --
710 ./bootstrapsharedcommand.o : bootstrapsharedcommand.cpp
711 $(CC) $(CC_OPTIONS) bootstrapsharedcommand.cpp -c $(INCLUDE) -o ./bootstrapsharedcommand.o
714 # Item # 4 -- matrixoutputcommand --
715 ./matrixoutputcommand.o : matrixoutputcommand.cpp
716 $(CC) $(CC_OPTIONS) matrixoutputcommand.cpp -c $(INCLUDE) -o ./matrixoutputcommand.o
719 # Item # 5 -- getoturepcommand --
720 ./getoturepcommand.o : getoturepcommand.cpp
721 $(CC) $(CC_OPTIONS) getoturepcommand.cpp -c $(INCLUDE) -o ./getoturepcommand.o
724 # Item # 6 -- screenseqscommand --
725 ./screenseqscommand.o : screenseqscommand.cpp
726 $(CC) $(CC_OPTIONS) screenseqscommand.cpp -c $(INCLUDE) -o ./screenseqscommand.o
729 # Item # 7 -- chimera --
730 ./chimera.o : chimera.cpp
731 $(CC) $(CC_OPTIONS) chimera.cpp -c $(INCLUDE) -o ./chimera.o
734 # Item # 8 -- decalc --
735 ./decalc.o : decalc.cpp
736 $(CC) $(CC_OPTIONS) decalc.cpp -c $(INCLUDE) -o ./decalc.o
739 # Item # 9 -- readotucommand --
740 ./readotucommand.o : readotucommand.cpp
741 $(CC) $(CC_OPTIONS) readotucommand.cpp -c $(INCLUDE) -o ./readotucommand.o
744 # Item # 10 -- readdistcommand --
745 ./readdistcommand.o : readdistcommand.cpp
746 $(CC) $(CC_OPTIONS) readdistcommand.cpp -c $(INCLUDE) -o ./readdistcommand.o
749 # Item # 11 -- commandfactory --
750 ./commandfactory.o : commandfactory.cpp
751 $(CC) $(CC_OPTIONS) commandfactory.cpp -c $(INCLUDE) -o ./commandfactory.o
754 # Item # 12 -- alignment --
755 ./alignment.o : alignment.cpp
756 $(CC) $(CC_OPTIONS) alignment.cpp -c $(INCLUDE) -o ./alignment.o
759 # Item # 13 -- alignmentcell --
760 ./alignmentcell.o : alignmentcell.cpp
761 $(CC) $(CC_OPTIONS) alignmentcell.cpp -c $(INCLUDE) -o ./alignmentcell.o
764 # Item # 14 -- gotohoverlap --
765 ./gotohoverlap.o : gotohoverlap.cpp
766 $(CC) $(CC_OPTIONS) gotohoverlap.cpp -c $(INCLUDE) -o ./gotohoverlap.o
769 # Item # 15 -- overlap --
770 ./overlap.o : overlap.cpp
771 $(CC) $(CC_OPTIONS) overlap.cpp -c $(INCLUDE) -o ./overlap.o
774 # Item # 16 -- needlemanoverlap --
775 ./needlemanoverlap.o : needlemanoverlap.cpp
776 $(CC) $(CC_OPTIONS) needlemanoverlap.cpp -c $(INCLUDE) -o ./needlemanoverlap.o
779 # Item # 17 -- blastalign --
780 ./blastalign.o : blastalign.cpp
781 $(CC) $(CC_OPTIONS) blastalign.cpp -c $(INCLUDE) -o ./blastalign.o
784 # Item # 18 -- noalign --
785 ./noalign.o : noalign.cpp
786 $(CC) $(CC_OPTIONS) noalign.cpp -c $(INCLUDE) -o ./noalign.o
789 # Item # 19 -- suffixdb --
790 ./suffixdb.o : suffixdb.cpp
791 $(CC) $(CC_OPTIONS) suffixdb.cpp -c $(INCLUDE) -o ./suffixdb.o
794 # Item # 20 -- suffixnodes --
795 ./suffixnodes.o : suffixnodes.cpp
796 $(CC) $(CC_OPTIONS) suffixnodes.cpp -c $(INCLUDE) -o ./suffixnodes.o
799 # Item # 21 -- suffixtree --
800 ./suffixtree.o : suffixtree.cpp
801 $(CC) $(CC_OPTIONS) suffixtree.cpp -c $(INCLUDE) -o ./suffixtree.o
804 # Item # 22 -- blastdb --
805 ./blastdb.o : blastdb.cpp
806 $(CC) $(CC_OPTIONS) blastdb.cpp -c $(INCLUDE) -o ./blastdb.o
809 # Item # 23 -- nast --
811 $(CC) $(CC_OPTIONS) nast.cpp -c $(INCLUDE) -o ./nast.o
814 # Item # 24 -- nastreport --
815 ./nastreport.o : nastreport.cpp
816 $(CC) $(CC_OPTIONS) nastreport.cpp -c $(INCLUDE) -o ./nastreport.o
819 # Item # 25 -- boneh --
820 ./boneh.o : boneh.cpp
821 $(CC) $(CC_OPTIONS) boneh.cpp -c $(INCLUDE) -o ./boneh.o
824 # Item # 26 -- efron --
825 ./efron.o : efron.cpp
826 $(CC) $(CC_OPTIONS) efron.cpp -c $(INCLUDE) -o ./efron.o
829 # Item # 27 -- solow --
830 ./solow.o : solow.cpp
831 $(CC) $(CC_OPTIONS) solow.cpp -c $(INCLUDE) -o ./solow.o
834 # Item # 28 -- unifracweightedcommand --
835 ./unifracweightedcommand.o : unifracweightedcommand.cpp
836 $(CC) $(CC_OPTIONS) unifracweightedcommand.cpp -c $(INCLUDE) -o ./unifracweightedcommand.o
839 # Item # 29 -- weighted --
840 ./weighted.o : weighted.cpp
841 $(CC) $(CC_OPTIONS) weighted.cpp -c $(INCLUDE) -o ./weighted.o
844 # Item # 30 -- unweighted --
845 ./unweighted.o : unweighted.cpp
846 $(CC) $(CC_OPTIONS) unweighted.cpp -c $(INCLUDE) -o ./unweighted.o
849 # Item # 31 -- unifracunweightedcommand --
850 ./unifracunweightedcommand.o : unifracunweightedcommand.cpp
851 $(CC) $(CC_OPTIONS) unifracunweightedcommand.cpp -c $(INCLUDE) -o ./unifracunweightedcommand.o
854 # Item # 32 -- getsabundcommand --
855 ./getsabundcommand.o : getsabundcommand.cpp
856 $(CC) $(CC_OPTIONS) getsabundcommand.cpp -c $(INCLUDE) -o ./getsabundcommand.o
859 # Item # 33 -- getrabundcommand --
860 ./getrabundcommand.o : getrabundcommand.cpp
861 $(CC) $(CC_OPTIONS) getrabundcommand.cpp -c $(INCLUDE) -o ./getrabundcommand.o
864 # Item # 34 -- bellerophon --
865 ./bellerophon.o : bellerophon.cpp
866 $(CC) $(CC_OPTIONS) bellerophon.cpp -c $(INCLUDE) -o ./bellerophon.o
869 # Item # 35 -- pintail --
870 ./pintail.o : pintail.cpp
871 $(CC) $(CC_OPTIONS) pintail.cpp -c $(INCLUDE) -o ./pintail.o
874 # Item # 36 -- sharedanderbergs --
875 ./sharedanderbergs.o : sharedanderbergs.cpp
876 $(CC) $(CC_OPTIONS) sharedanderbergs.cpp -c $(INCLUDE) -o ./sharedanderbergs.o
879 # Item # 37 -- venncommand --
880 ./venncommand.o : venncommand.cpp
881 $(CC) $(CC_OPTIONS) venncommand.cpp -c $(INCLUDE) -o ./venncommand.o
884 # Item # 38 -- venn --
886 $(CC) $(CC_OPTIONS) venn.cpp -c $(INCLUDE) -o ./venn.o
889 # Item # 39 -- fullmatrix --
890 ./fullmatrix.o : fullmatrix.cpp
891 $(CC) $(CC_OPTIONS) fullmatrix.cpp -c $(INCLUDE) -o ./fullmatrix.o
894 # Item # 40 -- heatmap --
895 ./heatmap.o : heatmap.cpp
896 $(CC) $(CC_OPTIONS) heatmap.cpp -c $(INCLUDE) -o ./heatmap.o
899 # Item # 41 -- heatmapcommand --
900 ./heatmapcommand.o : heatmapcommand.cpp
901 $(CC) $(CC_OPTIONS) heatmapcommand.cpp -c $(INCLUDE) -o ./heatmapcommand.o
904 # Item # 42 -- libshuffcommand --
905 ./libshuffcommand.o : libshuffcommand.cpp
906 $(CC) $(CC_OPTIONS) libshuffcommand.cpp -c $(INCLUDE) -o ./libshuffcommand.o
909 # Item # 43 -- nocommands --
910 ./nocommands.o : nocommands.cpp
911 $(CC) $(CC_OPTIONS) nocommands.cpp -c $(INCLUDE) -o ./nocommands.o
914 # Item # 44 -- sharedbraycurtis --
915 ./sharedbraycurtis.o : sharedbraycurtis.cpp
916 $(CC) $(CC_OPTIONS) sharedbraycurtis.cpp -c $(INCLUDE) -o ./sharedbraycurtis.o
919 # Item # 45 -- sharedkulczynski --
920 ./sharedkulczynski.o : sharedkulczynski.cpp
921 $(CC) $(CC_OPTIONS) sharedkulczynski.cpp -c $(INCLUDE) -o ./sharedkulczynski.o
924 # Item # 46 -- sharedlennon --
925 ./sharedlennon.o : sharedlennon.cpp
926 $(CC) $(CC_OPTIONS) sharedlennon.cpp -c $(INCLUDE) -o ./sharedlennon.o
929 # Item # 47 -- sharedkulczynskicody --
930 ./sharedkulczynskicody.o : sharedkulczynskicody.cpp
931 $(CC) $(CC_OPTIONS) sharedkulczynskicody.cpp -c $(INCLUDE) -o ./sharedkulczynskicody.o
934 # Item # 48 -- sharedmorisitahorn --
935 ./sharedmorisitahorn.o : sharedmorisitahorn.cpp
936 $(CC) $(CC_OPTIONS) sharedmorisitahorn.cpp -c $(INCLUDE) -o ./sharedmorisitahorn.o
939 # Item # 49 -- sharedochiai --
940 ./sharedochiai.o : sharedochiai.cpp
941 $(CC) $(CC_OPTIONS) sharedochiai.cpp -c $(INCLUDE) -o ./sharedochiai.o
944 # Item # 50 -- readcolumn --
945 ./readcolumn.o : readcolumn.cpp
946 $(CC) $(CC_OPTIONS) readcolumn.cpp -c $(INCLUDE) -o ./readcolumn.o
949 # Item # 51 -- readotu --
950 ./readotu.o : readotu.cpp
951 $(CC) $(CC_OPTIONS) readotu.cpp -c $(INCLUDE) -o ./readotu.o
954 # Item # 52 -- readphylip --
955 ./readphylip.o : readphylip.cpp
956 $(CC) $(CC_OPTIONS) readphylip.cpp -c $(INCLUDE) -o ./readphylip.o
959 # Item # 53 -- consensuscommand --
960 ./consensuscommand.o : consensuscommand.cpp
961 $(CC) $(CC_OPTIONS) consensuscommand.cpp -c $(INCLUDE) -o ./consensuscommand.o
964 # Item # 54 -- heatmapsimcommand --
965 ./heatmapsimcommand.o : heatmapsimcommand.cpp
966 $(CC) $(CC_OPTIONS) heatmapsimcommand.cpp -c $(INCLUDE) -o ./heatmapsimcommand.o
969 # Item # 55 -- heatmapsim --
970 ./heatmapsim.o : heatmapsim.cpp
971 $(CC) $(CC_OPTIONS) heatmapsim.cpp -c $(INCLUDE) -o ./heatmapsim.o
974 # Item # 56 -- optionparser --
975 ./optionparser.o : optionparser.cpp
976 $(CC) $(CC_OPTIONS) optionparser.cpp -c $(INCLUDE) -o ./optionparser.o
979 # Item # 57 -- filterseqscommand --
980 ./filterseqscommand.o : filterseqscommand.cpp
981 $(CC) $(CC_OPTIONS) filterseqscommand.cpp -c $(INCLUDE) -o ./filterseqscommand.o
984 # Item # 58 -- goodscoverage --
985 ./goodscoverage.o : goodscoverage.cpp
986 $(CC) $(CC_OPTIONS) goodscoverage.cpp -c $(INCLUDE) -o ./goodscoverage.o
989 # Item # 59 -- sequencedb --
990 ./sequencedb.o : sequencedb.cpp
991 $(CC) $(CC_OPTIONS) sequencedb.cpp -c $(INCLUDE) -o ./sequencedb.o
994 # Item # 60 -- sharedjackknife --
995 ./sharedjackknife.o : sharedjackknife.cpp
996 $(CC) $(CC_OPTIONS) sharedjackknife.cpp -c $(INCLUDE) -o ./sharedjackknife.o
999 # Item # 61 -- sharedmarczewski --
1000 ./sharedmarczewski.o : sharedmarczewski.cpp
1001 $(CC) $(CC_OPTIONS) sharedmarczewski.cpp -c $(INCLUDE) -o ./sharedmarczewski.o
1004 # Item # 62 -- aligncommand --
1005 ./aligncommand.o : aligncommand.cpp
1006 $(CC) $(CC_OPTIONS) aligncommand.cpp -c $(INCLUDE) -o ./aligncommand.o
1009 # Item # 63 -- treemap --
1010 ./treemap.o : treemap.cpp
1011 $(CC) $(CC_OPTIONS) treemap.cpp -c $(INCLUDE) -o ./treemap.o
1014 # Item # 64 -- parsimonycommand --
1015 ./parsimonycommand.o : parsimonycommand.cpp
1016 $(CC) $(CC_OPTIONS) parsimonycommand.cpp -c $(INCLUDE) -o ./parsimonycommand.o
1019 # Item # 65 -- parsimony --
1020 ./parsimony.o : parsimony.cpp
1021 $(CC) $(CC_OPTIONS) parsimony.cpp -c $(INCLUDE) -o ./parsimony.o
1024 # Item # 66 -- seqsummarycommand --
1025 ./seqsummarycommand.o : seqsummarycommand.cpp
1026 $(CC) $(CC_OPTIONS) seqsummarycommand.cpp -c $(INCLUDE) -o ./seqsummarycommand.o
1029 # Item # 67 -- chimeraseqscommand --
1030 ./chimeraseqscommand.o : chimeraseqscommand.cpp
1031 $(CC) $(CC_OPTIONS) chimeraseqscommand.cpp -c $(INCLUDE) -o ./chimeraseqscommand.o
1034 # Item # 68 -- sharedlistvector --
1035 ./sharedlistvector.o : sharedlistvector.cpp
1036 $(CC) $(CC_OPTIONS) sharedlistvector.cpp -c $(INCLUDE) -o ./sharedlistvector.o
1039 # Item # 69 -- tree --
1041 $(CC) $(CC_OPTIONS) tree.cpp -c $(INCLUDE) -o ./tree.o
1044 # Item # 70 -- readtree --
1045 ./readtree.o : readtree.cpp
1046 $(CC) $(CC_OPTIONS) readtree.cpp -c $(INCLUDE) -o ./readtree.o
1049 # Item # 71 -- sharedsobscollectsummary --
1050 ./sharedsobscollectsummary.o : sharedsobscollectsummary.cpp
1051 $(CC) $(CC_OPTIONS) sharedsobscollectsummary.cpp -c $(INCLUDE) -o ./sharedsobscollectsummary.o
1054 # Item # 72 -- deconvolutecommand --
1055 ./deconvolutecommand.o : deconvolutecommand.cpp
1056 $(CC) $(CC_OPTIONS) deconvolutecommand.cpp -c $(INCLUDE) -o ./deconvolutecommand.o
1059 # Item # 73 -- listseqscommand --
1060 ./listseqscommand.o : listseqscommand.cpp
1061 $(CC) $(CC_OPTIONS) listseqscommand.cpp -c $(INCLUDE) -o ./listseqscommand.o
1064 # Item # 74 -- getseqscommand --
1065 ./getseqscommand.o : getseqscommand.cpp
1066 $(CC) $(CC_OPTIONS) getseqscommand.cpp -c $(INCLUDE) -o ./getseqscommand.o
1069 # Item # 75 -- removeseqscommand --
1070 ./removeseqscommand.o : removeseqscommand.cpp
1071 $(CC) $(CC_OPTIONS) removeseqscommand.cpp -c $(INCLUDE) -o ./removeseqscommand.o
1074 # Item # 76 -- systemcommand --
1075 ./systemcommand.o : systemcommand.cpp
1076 $(CC) $(CC_OPTIONS) systemcommand.cpp -c $(INCLUDE) -o ./systemcommand.o
1079 # Item # 77 -- binsequencecommand --
1080 ./binsequencecommand.o : binsequencecommand.cpp
1081 $(CC) $(CC_OPTIONS) binsequencecommand.cpp -c $(INCLUDE) -o ./binsequencecommand.o
1084 # Item # 78 -- distancecommand --
1085 ./distancecommand.o : distancecommand.cpp
1086 $(CC) $(CC_OPTIONS) distancecommand.cpp -c $(INCLUDE) -o ./distancecommand.o
1089 # Item # 79 -- ace --
1091 $(CC) $(CC_OPTIONS) ace.cpp -c $(INCLUDE) -o ./ace.o
1094 # Item # 80 -- averagelinkage --
1095 ./averagelinkage.o : averagelinkage.cpp
1096 $(CC) $(CC_OPTIONS) averagelinkage.cpp -c $(INCLUDE) -o ./averagelinkage.o
1099 # Item # 81 -- bootstrap --
1100 ./bootstrap.o : bootstrap.cpp
1101 $(CC) $(CC_OPTIONS) bootstrap.cpp -c $(INCLUDE) -o ./bootstrap.o
1104 # Item # 82 -- calculator --
1105 ./calculator.o : calculator.cpp
1106 $(CC) $(CC_OPTIONS) calculator.cpp -c $(INCLUDE) -o ./calculator.o
1109 # Item # 83 -- chao1 --
1110 ./chao1.o : chao1.cpp
1111 $(CC) $(CC_OPTIONS) chao1.cpp -c $(INCLUDE) -o ./chao1.o
1114 # Item # 84 -- cluster --
1115 ./cluster.o : cluster.cpp
1116 $(CC) $(CC_OPTIONS) cluster.cpp -c $(INCLUDE) -o ./cluster.o
1119 # Item # 85 -- clustercommand --
1120 ./clustercommand.o : clustercommand.cpp
1121 $(CC) $(CC_OPTIONS) clustercommand.cpp -c $(INCLUDE) -o ./clustercommand.o
1124 # Item # 86 -- collect --
1125 ./collect.o : collect.cpp
1126 $(CC) $(CC_OPTIONS) collect.cpp -c $(INCLUDE) -o ./collect.o
1129 # Item # 87 -- collectcommand --
1130 ./collectcommand.o : collectcommand.cpp
1131 $(CC) $(CC_OPTIONS) collectcommand.cpp -c $(INCLUDE) -o ./collectcommand.o
1134 # Item # 88 -- collectsharedcommand --
1135 ./collectsharedcommand.o : collectsharedcommand.cpp
1136 $(CC) $(CC_OPTIONS) collectsharedcommand.cpp -c $(INCLUDE) -o ./collectsharedcommand.o
1139 # Item # 89 -- commandoptionparser --
1140 ./commandoptionparser.o : commandoptionparser.cpp
1141 $(CC) $(CC_OPTIONS) commandoptionparser.cpp -c $(INCLUDE) -o ./commandoptionparser.o
1144 # Item # 90 -- completelinkage --
1145 ./completelinkage.o : completelinkage.cpp
1146 $(CC) $(CC_OPTIONS) completelinkage.cpp -c $(INCLUDE) -o ./completelinkage.o
1149 # Item # 91 -- database --
1150 ./database.o : database.cpp
1151 $(CC) $(CC_OPTIONS) database.cpp -c $(INCLUDE) -o ./database.o
1154 # Item # 92 -- engine --
1155 ./engine.o : engine.cpp
1156 $(CC) $(CC_OPTIONS) engine.cpp -c $(INCLUDE) -o ./engine.o
1159 # Item # 93 -- fastamap --
1160 ./fastamap.o : fastamap.cpp
1161 $(CC) $(CC_OPTIONS) fastamap.cpp -c $(INCLUDE) -o ./fastamap.o
1164 # Item # 94 -- fileoutput --
1165 ./fileoutput.o : fileoutput.cpp
1166 $(CC) $(CC_OPTIONS) fileoutput.cpp -c $(INCLUDE) -o ./fileoutput.o
1169 # Item # 95 -- globaldata --
1170 ./globaldata.o : globaldata.cpp
1171 $(CC) $(CC_OPTIONS) globaldata.cpp -c $(INCLUDE) -o ./globaldata.o
1174 # Item # 96 -- groupmap --
1175 ./groupmap.o : groupmap.cpp
1176 $(CC) $(CC_OPTIONS) groupmap.cpp -c $(INCLUDE) -o ./groupmap.o
1179 # Item # 97 -- helpcommand --
1180 ./helpcommand.o : helpcommand.cpp
1181 $(CC) $(CC_OPTIONS) helpcommand.cpp -c $(INCLUDE) -o ./helpcommand.o
1184 # Item # 98 -- inputdata --
1185 ./inputdata.o : inputdata.cpp
1186 $(CC) $(CC_OPTIONS) inputdata.cpp -c $(INCLUDE) -o ./inputdata.o
1189 # Item # 99 -- jackknife --
1190 ./jackknife.o : jackknife.cpp
1191 $(CC) $(CC_OPTIONS) jackknife.cpp -c $(INCLUDE) -o ./jackknife.o
1194 # Item # 100 -- kmer --
1196 $(CC) $(CC_OPTIONS) kmer.cpp -c $(INCLUDE) -o ./kmer.o
1199 # Item # 101 -- kmerdb --
1200 ./kmerdb.o : kmerdb.cpp
1201 $(CC) $(CC_OPTIONS) kmerdb.cpp -c $(INCLUDE) -o ./kmerdb.o
1204 # Item # 102 -- listvector --
1205 ./listvector.o : listvector.cpp
1206 $(CC) $(CC_OPTIONS) listvector.cpp -c $(INCLUDE) -o ./listvector.o
1209 # Item # 103 -- mothur --
1210 ./mothur.o : mothur.cpp
1211 $(CC) $(CC_OPTIONS) mothur.cpp -c $(INCLUDE) -o ./mothur.o
1214 # Item # 104 -- nameassignment --
1215 ./nameassignment.o : nameassignment.cpp
1216 $(CC) $(CC_OPTIONS) nameassignment.cpp -c $(INCLUDE) -o ./nameassignment.o
1219 # Item # 105 -- npshannon --
1220 ./npshannon.o : npshannon.cpp
1221 $(CC) $(CC_OPTIONS) npshannon.cpp -c $(INCLUDE) -o ./npshannon.o
1224 # Item # 106 -- ordervector --
1225 ./ordervector.o : ordervector.cpp
1226 $(CC) $(CC_OPTIONS) ordervector.cpp -c $(INCLUDE) -o ./ordervector.o
1229 # Item # 107 -- progress --
1230 ./progress.o : progress.cpp
1231 $(CC) $(CC_OPTIONS) progress.cpp -c $(INCLUDE) -o ./progress.o
1234 # Item # 108 -- quitcommand --
1235 ./quitcommand.o : quitcommand.cpp
1236 $(CC) $(CC_OPTIONS) quitcommand.cpp -c $(INCLUDE) -o ./quitcommand.o
1239 # Item # 109 -- rabundvector --
1240 ./rabundvector.o : rabundvector.cpp
1241 $(CC) $(CC_OPTIONS) rabundvector.cpp -c $(INCLUDE) -o ./rabundvector.o
1244 # Item # 110 -- rarecalc --
1245 ./rarecalc.o : rarecalc.cpp
1246 $(CC) $(CC_OPTIONS) rarecalc.cpp -c $(INCLUDE) -o ./rarecalc.o
1249 # Item # 111 -- raredisplay --
1250 ./raredisplay.o : raredisplay.cpp
1251 $(CC) $(CC_OPTIONS) raredisplay.cpp -c $(INCLUDE) -o ./raredisplay.o
1254 # Item # 112 -- rarefact --
1255 ./rarefact.o : rarefact.cpp
1256 $(CC) $(CC_OPTIONS) rarefact.cpp -c $(INCLUDE) -o ./rarefact.o
1259 # Item # 113 -- rarefactcommand --
1260 ./rarefactcommand.o : rarefactcommand.cpp
1261 $(CC) $(CC_OPTIONS) rarefactcommand.cpp -c $(INCLUDE) -o ./rarefactcommand.o
1264 # Item # 114 -- rarefactsharedcommand --
1265 ./rarefactsharedcommand.o : rarefactsharedcommand.cpp
1266 $(CC) $(CC_OPTIONS) rarefactsharedcommand.cpp -c $(INCLUDE) -o ./rarefactsharedcommand.o
1269 # Item # 115 -- sabundvector --
1270 ./sabundvector.o : sabundvector.cpp
1271 $(CC) $(CC_OPTIONS) sabundvector.cpp -c $(INCLUDE) -o ./sabundvector.o
1274 # Item # 116 -- sequence --
1275 ./sequence.o : sequence.cpp
1276 $(CC) $(CC_OPTIONS) sequence.cpp -c $(INCLUDE) -o ./sequence.o
1279 # Item # 117 -- shannon --
1280 ./shannon.o : shannon.cpp
1281 $(CC) $(CC_OPTIONS) shannon.cpp -c $(INCLUDE) -o ./shannon.o
1284 # Item # 118 -- sharedace --
1285 ./sharedace.o : sharedace.cpp
1286 $(CC) $(CC_OPTIONS) sharedace.cpp -c $(INCLUDE) -o ./sharedace.o
1289 # Item # 119 -- sharedchao1 --
1290 ./sharedchao1.o : sharedchao1.cpp
1291 $(CC) $(CC_OPTIONS) sharedchao1.cpp -c $(INCLUDE) -o ./sharedchao1.o
1294 # Item # 120 -- sharedcommand --
1295 ./sharedcommand.o : sharedcommand.cpp
1296 $(CC) $(CC_OPTIONS) sharedcommand.cpp -c $(INCLUDE) -o ./sharedcommand.o
1299 # Item # 121 -- sharedjabund --
1300 ./sharedjabund.o : sharedjabund.cpp
1301 $(CC) $(CC_OPTIONS) sharedjabund.cpp -c $(INCLUDE) -o ./sharedjabund.o
1304 # Item # 122 -- sharedjclass --
1305 ./sharedjclass.o : sharedjclass.cpp
1306 $(CC) $(CC_OPTIONS) sharedjclass.cpp -c $(INCLUDE) -o ./sharedjclass.o
1309 # Item # 123 -- sharedjest --
1310 ./sharedjest.o : sharedjest.cpp
1311 $(CC) $(CC_OPTIONS) sharedjest.cpp -c $(INCLUDE) -o ./sharedjest.o
1314 # Item # 124 -- sharedordervector --
1315 ./sharedordervector.o : sharedordervector.cpp
1316 $(CC) $(CC_OPTIONS) sharedordervector.cpp -c $(INCLUDE) -o ./sharedordervector.o
1319 # Item # 125 -- sharedrabundvector --
1320 ./sharedrabundvector.o : sharedrabundvector.cpp
1321 $(CC) $(CC_OPTIONS) sharedrabundvector.cpp -c $(INCLUDE) -o ./sharedrabundvector.o
1324 # Item # 126 -- sharedsabundvector --
1325 ./sharedsabundvector.o : sharedsabundvector.cpp
1326 $(CC) $(CC_OPTIONS) sharedsabundvector.cpp -c $(INCLUDE) -o ./sharedsabundvector.o
1329 # Item # 127 -- sharedsobs --
1330 ./sharedsobs.o : sharedsobs.cpp
1331 $(CC) $(CC_OPTIONS) sharedsobs.cpp -c $(INCLUDE) -o ./sharedsobs.o
1334 # Item # 128 -- sharedsorabund --
1335 ./sharedsorabund.o : sharedsorabund.cpp
1336 $(CC) $(CC_OPTIONS) sharedsorabund.cpp -c $(INCLUDE) -o ./sharedsorabund.o
1339 # Item # 129 -- sharedsorclass --
1340 ./sharedsorclass.o : sharedsorclass.cpp
1341 $(CC) $(CC_OPTIONS) sharedsorclass.cpp -c $(INCLUDE) -o ./sharedsorclass.o
1344 # Item # 130 -- sharedsorest --
1345 ./sharedsorest.o : sharedsorest.cpp
1346 $(CC) $(CC_OPTIONS) sharedsorest.cpp -c $(INCLUDE) -o ./sharedsorest.o
1349 # Item # 131 -- sharedthetan --
1350 ./sharedthetan.o : sharedthetan.cpp
1351 $(CC) $(CC_OPTIONS) sharedthetan.cpp -c $(INCLUDE) -o ./sharedthetan.o
1354 # Item # 132 -- sharedthetayc --
1355 ./sharedthetayc.o : sharedthetayc.cpp
1356 $(CC) $(CC_OPTIONS) sharedthetayc.cpp -c $(INCLUDE) -o ./sharedthetayc.o
1359 # Item # 133 -- simpson --
1360 ./simpson.o : simpson.cpp
1361 $(CC) $(CC_OPTIONS) simpson.cpp -c $(INCLUDE) -o ./simpson.o
1364 # Item # 134 -- singlelinkage --
1365 ./singlelinkage.o : singlelinkage.cpp
1366 $(CC) $(CC_OPTIONS) singlelinkage.cpp -c $(INCLUDE) -o ./singlelinkage.o
1369 # Item # 135 -- sparsematrix --
1370 ./sparsematrix.o : sparsematrix.cpp
1371 $(CC) $(CC_OPTIONS) sparsematrix.cpp -c $(INCLUDE) -o ./sparsematrix.o
1374 # Item # 136 -- summarycommand --
1375 ./summarycommand.o : summarycommand.cpp
1376 $(CC) $(CC_OPTIONS) summarycommand.cpp -c $(INCLUDE) -o ./summarycommand.o
1379 # Item # 137 -- summarysharedcommand --
1380 ./summarysharedcommand.o : summarysharedcommand.cpp
1381 $(CC) $(CC_OPTIONS) summarysharedcommand.cpp -c $(INCLUDE) -o ./summarysharedcommand.o
1384 # Item # 138 -- uvest --
1385 ./uvest.o : uvest.cpp
1386 $(CC) $(CC_OPTIONS) uvest.cpp -c $(INCLUDE) -o ./uvest.o
1389 # Item # 139 -- validcalculator --
1390 ./validcalculator.o : validcalculator.cpp
1391 $(CC) $(CC_OPTIONS) validcalculator.cpp -c $(INCLUDE) -o ./validcalculator.o
1394 # Item # 140 -- validparameter --
1395 ./validparameter.o : validparameter.cpp
1396 $(CC) $(CC_OPTIONS) validparameter.cpp -c $(INCLUDE) -o ./validparameter.o
1399 # Item # 141 -- treenode --
1400 ./treenode.o : treenode.cpp
1401 $(CC) $(CC_OPTIONS) treenode.cpp -c $(INCLUDE) -o ./treenode.o
1404 # Item # 142 -- readtreecommand --
1405 ./readtreecommand.o : readtreecommand.cpp
1406 $(CC) $(CC_OPTIONS) readtreecommand.cpp -c $(INCLUDE) -o ./readtreecommand.o
1409 # Item # 143 -- reversecommand --
1410 ./reversecommand.o : reversecommand.cpp
1411 $(CC) $(CC_OPTIONS) reversecommand.cpp -c $(INCLUDE) -o ./reversecommand.o
1414 # Item # 144 -- trimseqscommand --
1415 ./trimseqscommand.o : trimseqscommand.cpp
1416 $(CC) $(CC_OPTIONS) trimseqscommand.cpp -c $(INCLUDE) -o ./trimseqscommand.o
1419 # Item # 145 -- slibshuff --
1420 ./slibshuff.o : slibshuff.cpp
1421 $(CC) $(CC_OPTIONS) slibshuff.cpp -c $(INCLUDE) -o ./slibshuff.o
1424 # Item # 146 -- libshuff --
1425 ./libshuff.o : libshuff.cpp
1426 $(CC) $(CC_OPTIONS) libshuff.cpp -c $(INCLUDE) -o ./libshuff.o
1429 # Item # 147 -- dlibshuff --
1430 ./dlibshuff.o : dlibshuff.cpp
1431 $(CC) $(CC_OPTIONS) dlibshuff.cpp -c $(INCLUDE) -o ./dlibshuff.o
1434 # Item # 148 -- mergefilecommand --
1435 ./mergefilecommand.o : mergefilecommand.cpp
1436 $(CC) $(CC_OPTIONS) mergefilecommand.cpp -c $(INCLUDE) -o ./mergefilecommand.o
1439 # Item # 149 -- coverage --
1440 ./coverage.o : coverage.cpp
1441 $(CC) $(CC_OPTIONS) coverage.cpp -c $(INCLUDE) -o ./coverage.o
1444 # Item # 150 -- whittaker --
1445 ./whittaker.o : whittaker.cpp
1446 $(CC) $(CC_OPTIONS) whittaker.cpp -c $(INCLUDE) -o ./whittaker.o
1449 # Item # 151 -- preclustercommand --
1450 ./preclustercommand.o : preclustercommand.cpp
1451 $(CC) $(CC_OPTIONS) preclustercommand.cpp -c $(INCLUDE) -o ./preclustercommand.o
1454 # Item # 152 -- otuhierarchycommand --
1455 ./otuhierarchycommand.o : otuhierarchycommand.cpp
1456 $(CC) $(CC_OPTIONS) otuhierarchycommand.cpp -c $(INCLUDE) -o ./otuhierarchycommand.o
1459 # Item # 153 -- setdircommand --
1460 ./setdircommand.o : setdircommand.cpp
1461 $(CC) $(CC_OPTIONS) setdircommand.cpp -c $(INCLUDE) -o ./setdircommand.o
1464 # Item # 154 -- getgroupcommand --
1465 ./getgroupcommand.o : getgroupcommand.cpp
1466 $(CC) $(CC_OPTIONS) getgroupcommand.cpp -c $(INCLUDE) -o ./getgroupcommand.o
1469 # Item # 155 -- getlabelcommand --
1470 ./getlabelcommand.o : getlabelcommand.cpp
1471 $(CC) $(CC_OPTIONS) getlabelcommand.cpp -c $(INCLUDE) -o ./getlabelcommand.o
1474 # Item # 156 -- secondarystructurecommand --
1475 ./secondarystructurecommand.o : secondarystructurecommand.cpp
1476 $(CC) $(CC_OPTIONS) secondarystructurecommand.cpp -c $(INCLUDE) -o ./secondarystructurecommand.o
1479 # Item # 157 -- mothurout --
1480 ./mothurout.o : mothurout.cpp
1481 $(CC) $(CC_OPTIONS) mothurout.cpp -c $(INCLUDE) -o ./mothurout.o
1484 # Item # 158 -- parselistscommand --
1485 ./parselistscommand.o : parselistscommand.cpp
1486 $(CC) $(CC_OPTIONS) parselistscommand.cpp -c $(INCLUDE) -o ./parselistscommand.o
1489 # Item # 159 -- readblast --
1490 ./readblast.o : readblast.cpp
1491 $(CC) $(CC_OPTIONS) readblast.cpp -c $(INCLUDE) -o ./readblast.o
1494 # Item # 160 -- chimeracheckrdp --
1495 ./chimeracheckrdp.o : chimeracheckrdp.cpp
1496 $(CC) $(CC_OPTIONS) chimeracheckrdp.cpp -c $(INCLUDE) -o ./chimeracheckrdp.o
1499 # Item # 161 -- hclustercommand --
1500 ./hclustercommand.o : hclustercommand.cpp
1501 $(CC) $(CC_OPTIONS) hclustercommand.cpp -c $(INCLUDE) -o ./hclustercommand.o
1504 # Item # 162 -- hcluster --
1505 ./hcluster.o : hcluster.cpp
1506 $(CC) $(CC_OPTIONS) hcluster.cpp -c $(INCLUDE) -o ./hcluster.o
1509 # Item # 163 -- getlistcountcommand --
1510 ./getlistcountcommand.o : getlistcountcommand.cpp
1511 $(CC) $(CC_OPTIONS) getlistcountcommand.cpp -c $(INCLUDE) -o ./getlistcountcommand.o
1514 # Item # 164 -- readcluster --
1515 ./readcluster.o : readcluster.cpp
1516 $(CC) $(CC_OPTIONS) readcluster.cpp -c $(INCLUDE) -o ./readcluster.o
1519 # Item # 165 -- ccode --
1520 ./ccode.o : ccode.cpp
1521 $(CC) $(CC_OPTIONS) ccode.cpp -c $(INCLUDE) -o ./ccode.o
1524 # Item # 166 -- taxonomyequalizer --
1525 ./taxonomyequalizer.o : taxonomyequalizer.cpp
1526 $(CC) $(CC_OPTIONS) taxonomyequalizer.cpp -c $(INCLUDE) -o ./taxonomyequalizer.o
1529 # Item # 167 -- phylotypecommand --
1530 ./phylotypecommand.o : phylotypecommand.cpp
1531 $(CC) $(CC_OPTIONS) phylotypecommand.cpp -c $(INCLUDE) -o ./phylotypecommand.o
1534 # Item # 168 -- classifyseqscommand --
1535 ./classifyseqscommand.o : classifyseqscommand.cpp
1536 $(CC) $(CC_OPTIONS) classifyseqscommand.cpp -c $(INCLUDE) -o ./classifyseqscommand.o
1539 # Item # 169 -- classify --
1540 ./classify.o : classify.cpp
1541 $(CC) $(CC_OPTIONS) classify.cpp -c $(INCLUDE) -o ./classify.o
1544 # Item # 170 -- phylotree --
1545 ./phylotree.o : phylotree.cpp
1546 $(CC) $(CC_OPTIONS) phylotree.cpp -c $(INCLUDE) -o ./phylotree.o
1549 # Item # 171 -- bayesian --
1550 ./bayesian.o : bayesian.cpp
1551 $(CC) $(CC_OPTIONS) bayesian.cpp -c $(INCLUDE) -o ./bayesian.o
1554 # Item # 172 -- alignmentdb --
1555 ./alignmentdb.o : alignmentdb.cpp
1556 $(CC) $(CC_OPTIONS) alignmentdb.cpp -c $(INCLUDE) -o ./alignmentdb.o
1559 # Item # 173 -- knn --
1561 $(CC) $(CC_OPTIONS) knn.cpp -c $(INCLUDE) -o ./knn.o
1564 # Item # 174 -- distancedb --
1565 ./distancedb.o : distancedb.cpp
1566 $(CC) $(CC_OPTIONS) distancedb.cpp -c $(INCLUDE) -o ./distancedb.o
1569 # Item # 175 -- chimeraslayer --
1570 ./chimeraslayer.o : chimeraslayer.cpp
1571 $(CC) $(CC_OPTIONS) chimeraslayer.cpp -c $(INCLUDE) -o ./chimeraslayer.o
1574 # Item # 176 -- slayer --
1575 ./slayer.o : slayer.cpp
1576 $(CC) $(CC_OPTIONS) slayer.cpp -c $(INCLUDE) -o ./slayer.o
1579 # Item # 177 -- pcacommand --
1580 ./pcacommand.o : pcacommand.cpp
1581 $(CC) $(CC_OPTIONS) pcacommand.cpp -c $(INCLUDE) -o ./pcacommand.o
1584 # Item # 178 -- formatcolumn --
1585 ./formatcolumn.o : formatcolumn.cpp
1586 $(CC) $(CC_OPTIONS) formatcolumn.cpp -c $(INCLUDE) -o ./formatcolumn.o
1589 # Item # 179 -- formatphylip --
1590 ./formatphylip.o : formatphylip.cpp
1591 $(CC) $(CC_OPTIONS) formatphylip.cpp -c $(INCLUDE) -o ./formatphylip.o
1594 # Item # 180 -- mgclustercommand --
1595 ./mgclustercommand.o : mgclustercommand.cpp
1596 $(CC) $(CC_OPTIONS) mgclustercommand.cpp -c $(INCLUDE) -o ./mgclustercommand.o
1599 # Item # 181 -- getsharedotucommand --
1600 ./getsharedotucommand.o : getsharedotucommand.cpp
1601 $(CC) $(CC_OPTIONS) getsharedotucommand.cpp -c $(INCLUDE) -o ./getsharedotucommand.o
1604 # Item # 182 -- maligner --
1605 ./maligner.o : maligner.cpp
1606 $(CC) $(CC_OPTIONS) maligner.cpp -c $(INCLUDE) -o ./maligner.o
1609 # Item # 183 -- chimerarealigner --
1610 ./chimerarealigner.o : chimerarealigner.cpp
1611 $(CC) $(CC_OPTIONS) chimerarealigner.cpp -c $(INCLUDE) -o ./chimerarealigner.o
1614 # Item # 184 -- bergerparker --
1615 ./bergerparker.o : bergerparker.cpp
1616 $(CC) $(CC_OPTIONS) bergerparker.cpp -c $(INCLUDE) -o ./bergerparker.o
1619 # Item # 185 -- bstick --
1620 ./bstick.o : bstick.cpp
1621 $(CC) $(CC_OPTIONS) bstick.cpp -c $(INCLUDE) -o ./bstick.o
1624 # Item # 186 -- sharedkstest --
1625 ./sharedkstest.o : sharedkstest.cpp
1626 $(CC) $(CC_OPTIONS) sharedkstest.cpp -c $(INCLUDE) -o ./sharedkstest.o
1629 # Item # 187 -- qstat --
1630 ./qstat.o : qstat.cpp
1631 $(CC) $(CC_OPTIONS) qstat.cpp -c $(INCLUDE) -o ./qstat.o
1634 # Item # 188 -- shen --
1636 $(CC) $(CC_OPTIONS) shen.cpp -c $(INCLUDE) -o ./shen.o
1639 # Item # 189 -- logsd --
1640 ./logsd.o : logsd.cpp
1641 $(CC) $(CC_OPTIONS) logsd.cpp -c $(INCLUDE) -o ./logsd.o
1644 # Item # 190 -- geom --
1646 $(CC) $(CC_OPTIONS) geom.cpp -c $(INCLUDE) -o ./geom.o
1648 # Item # 191 -- parsesffcommand --
1649 ./parsesffcommand.o : parsesffcommand.cpp
1650 $(CC) $(CC_OPTIONS) parsesffcommand.cpp -c $(INCLUDE) -o ./parsesffcommand.o
1652 # Item # 192 -- chimeraccodecommand --
1653 ./chimeraccodecommand.o : chimeraccodecommand.cpp
1654 $(CC) $(CC_OPTIONS) chimeraccodecommand.cpp -c $(INCLUDE) -o ./chimeraccodecommand.o
1656 # Item # 193 -- chimeracheckcommand --
1657 ./chimeracheckcommand.o : chimeracheckcommand.cpp
1658 $(CC) $(CC_OPTIONS) chimeracheckcommand.cpp -c $(INCLUDE) -o ./chimeracheckcommand.o
1661 # Item # 194 -- chimeraslayercommand --
1662 ./chimeraslayercommand.o : chimeraslayercommand.cpp
1663 $(CC) $(CC_OPTIONS) chimeraslayercommand.cpp -c $(INCLUDE) -o ./chimeraslayercommand.o
1665 # Item # 195 -- chimerapintailcommand --
1666 ./chimerapintailcommand.o : chimerapintailcommand.cpp
1667 $(CC) $(CC_OPTIONS) chimerapintailcommand.cpp -c $(INCLUDE) -o ./chimerapintailcommand.o
1669 # Item # 196 -- chimerabellerophoncommand --
1670 ./chimerabellerophoncommand.o : chimerabellerophoncommand.cpp
1671 $(CC) $(CC_OPTIONS) chimerabellerophoncommand.cpp -c $(INCLUDE) -o ./chimerabellerophoncommand.o
1673 # Item # 197 -- phylosummary --
1674 ./phylosummary.o : phylosummary.cpp
1675 $(CC) $(CC_OPTIONS) phylosummary.cpp -c $(INCLUDE) -o ./phylosummary.o
1677 # Item # 198 -- setlogfilecommand --
1678 ./setlogfilecommand.o : setlogfilecommand.cpp
1679 $(CC) $(CC_OPTIONS) setlogfilecommand.cpp -c $(INCLUDE) -o ./setlogfilecommand.o
1681 # Item # 199 -- phylodiversity --
1682 ./phylodiversity.o : phylodiversity.cpp
1683 $(CC) $(CC_OPTIONS) phylodiversity.cpp -c $(INCLUDE) -o ./phylodiversity.o
1685 # Item # 200 -- phylodiversitycommand --
1686 ./phylodiversitycommand.o : phylodiversitycommand.cpp
1687 $(CC) $(CC_OPTIONS) phylodiversitycommand.cpp -c $(INCLUDE) -o ./phylodiversitycommand.o
1689 # Item # 201 -- makegroupcommand --
1690 ./makegroupcommand.o : makegroupcommand.cpp
1691 $(CC) $(CC_OPTIONS) makegroupcommand.cpp -c $(INCLUDE) -o ./makegroupcommand.o
1693 # Item # 202 -- chopseqscommand --
1694 ./chopseqscommand.o : chopseqscommand.cpp
1695 $(CC) $(CC_OPTIONS) chopseqscommand.cpp -c $(INCLUDE) -o ./chopseqscommand.o
1697 # Item # 203 -- clearcutcommand --
1698 ./clearcutcommand.o : clearcutcommand.cpp
1699 $(CC) $(CC_OPTIONS) clearcutcommand.cpp -c $(INCLUDE) -o ./clearcutcommand.o
1701 # Item # 204 -- catchallcommand --
1702 ./catchallcommand.o : catchallcommand.cpp
1703 $(CC) $(CC_OPTIONS) catchallcommand.cpp -c $(INCLUDE) -o ./catchallcommand.o
1705 # Item # 205 -- splitabundcommand --
1706 ./splitabundcommand.o : splitabundcommand.cpp
1707 $(CC) $(CC_OPTIONS) splitabundcommand.cpp -c $(INCLUDE) -o ./splitabundcommand.o
1709 # Item # 206 -- splitmatrix --
1710 ./splitmatrix.o : splitmatrix.cpp
1711 $(CC) $(CC_OPTIONS) splitmatrix.cpp -c $(INCLUDE) -o ./splitmatrix.o
1713 # Item # 207 -- clustersplit --
1714 ./clustersplitcommand.o : clustersplitcommand.cpp
1715 $(CC) $(CC_OPTIONS) clustersplitcommand.cpp -c $(INCLUDE) -o ./clustersplitcommand.o
1717 # Item # 208 -- classifyotu --
1718 ./classifyotucommand.o : classifyotucommand.cpp
1719 $(CC) $(CC_OPTIONS) classifyotucommand.cpp -c $(INCLUDE) -o ./classifyotucommand.o
1721 # Item # 209 -- weightedlinkage --
1722 ./weightedlinkage.o : weightedlinkage.cpp
1723 $(CC) $(CC_OPTIONS) weightedlinkage.cpp -c $(INCLUDE) -o ./weightedlinkage.o
1725 # Item # 210 -- degapseqscommand --
1726 ./degapseqscommand.o : degapseqscommand.cpp
1727 $(CC) $(CC_OPTIONS) degapseqscommand.cpp -c $(INCLUDE) -o ./degapseqscommand.o