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 $(USEREADLINE)),yes)
22 CC_OPTIONS += -DUSE_READLINE
31 ifeq ($(strip $(USEMPI)),yes)
33 CC_OPTIONS += -DUSE_MPI
37 # INCLUDE directories for mothur
48 ./treegroupscommand.o\
49 ./bootstrapsharedcommand.o\
50 ./matrixoutputcommand.o\
52 ./screenseqscommand.o\
74 ./unifracweightedcommand.o\
77 ./unifracunweightedcommand.o\
93 ./sharedkulczynskicody.o\
94 ./sharedmorisitahorn.o\
100 ./heatmapsimcommand.o\
103 ./filterseqscommand.o\
107 ./sharedmarczewski.o\
110 ./parsimonycommand.o\
112 ./seqsummarycommand.o\
113 ./chimeraccodecommand.o\
114 ./chimerabellerophoncommand.o\
115 ./chimeracheckcommand.o\
116 ./chimeraslayercommand.o\
117 ./chimerapintailcommand.o\
118 ./chimeraseqscommand.o\
119 ./sharedlistvector.o\
122 ./sharedsobscollectsummary.o\
123 ./deconvolutecommand.o\
126 ./removeseqscommand.o\
128 ./binsequencecommand.o\
139 ./collectsharedcommand.o\
140 ./commandoptionparser.o\
149 ./makegroupcommand.o\
153 ./splitabundcommand.o\
155 ./clustersplitcommand.o\
172 ./rarefactsharedcommand.o\
182 ./sharedordervector.o\
183 ./sharedrabundvector.o\
184 ./sharedsabundvector.o\
195 ./summarysharedcommand.o\
206 ./mergefilecommand.o\
209 ./preclustercommand.o\
210 ./otuhierarchycommand.o\
214 ./secondarystructurecommand.o\
216 ./parselistscommand.o\
221 ./getlistcountcommand.o\
224 ./taxonomyequalizer.o\
225 ./phylotypecommand.o\
226 ./classifyseqscommand.o\
231 ./phylodiversitycommand.o\
242 ./mgclustercommand.o\
243 ./getsharedotucommand.o\
245 ./chimerarealigner.o\
253 ./setlogfilecommand.o
254 $(CC) $(LNK_OPTIONS) \
256 ./treegroupscommand.o\
257 ./bootstrapsharedcommand.o\
258 ./matrixoutputcommand.o\
259 ./getoturepcommand.o\
260 ./screenseqscommand.o\
270 ./needlemanoverlap.o\
282 ./unifracweightedcommand.o\
285 ./unifracunweightedcommand.o\
286 ./getsabundcommand.o\
287 ./getrabundcommand.o\
290 ./sharedanderbergs.o\
298 ./sharedbraycurtis.o\
299 ./sharedkulczynski.o\
301 ./sharedkulczynskicody.o\
302 ./sharedmorisitahorn.o\
307 ./consensuscommand.o\
308 ./heatmapsimcommand.o\
311 ./filterseqscommand.o\
315 ./sharedmarczewski.o\
318 ./parsimonycommand.o\
320 ./seqsummarycommand.o\
321 ./chimeraccodecommand.o\
322 ./chimerabellerophoncommand.o\
323 ./chimeracheckcommand.o\
324 ./chimeraslayercommand.o\
325 ./chimerapintailcommand.o\
326 ./chimeraseqscommand.o\
327 ./sharedlistvector.o\
330 ./sharedsobscollectsummary.o\
331 ./deconvolutecommand.o\
334 ./removeseqscommand.o\
336 ./binsequencecommand.o\
347 ./collectsharedcommand.o\
348 ./commandoptionparser.o\
357 ./makegroupcommand.o\
361 ./splitabundcommand.o\
363 ./clustersplitcommand.o\
380 ./rarefactsharedcommand.o\
390 ./sharedordervector.o\
391 ./sharedrabundvector.o\
392 ./sharedsabundvector.o\
403 ./summarysharedcommand.o\
414 ./mergefilecommand.o\
417 ./preclustercommand.o\
418 ./otuhierarchycommand.o\
422 ./secondarystructurecommand.o\
424 ./parselistscommand.o\
429 ./getlistcountcommand.o\
432 ./taxonomyequalizer.o\
433 ./phylotypecommand.o\
434 ./classifyseqscommand.o\
439 ./phylodiversitycommand.o\
450 ./mgclustercommand.o\
451 ./getsharedotucommand.o\
453 ./chimerarealigner.o\
461 ./setlogfilecommand.o\
467 ./treegroupscommand.o\
468 ./bootstrapsharedcommand.o\
469 ./matrixoutputcommand.o\
470 ./getoturepcommand.o\
471 ./screenseqscommand.o\
481 ./needlemanoverlap.o\
493 ./unifracweightedcommand.o\
496 ./unifracunweightedcommand.o\
497 ./getsabundcommand.o\
498 ./getrabundcommand.o\
501 ./sharedanderbergs.o\
509 ./sharedbraycurtis.o\
510 ./sharedkulczynski.o\
512 ./sharedkulczynskicody.o\
513 ./sharedmorisitahorn.o\
518 ./consensuscommand.o\
519 ./heatmapsimcommand.o\
522 ./filterseqscommand.o\
526 ./sharedmarczewski.o\
529 ./parsimonycommand.o\
531 ./seqsummarycommand.o\
532 ./chimeraccodecommand.o\
533 ./chimerabellerophoncommand.o\
534 ./chimeracheckcommand.o\
535 ./chimeraslayercommand.o\
536 ./chimerapintailcommand.o\
537 ./chimeraseqscommand.o\
538 ./sharedlistvector.o\
541 ./sharedsobscollectsummary.o\
542 ./deconvolutecommand.o\
545 ./removeseqscommand.o\
547 ./binsequencecommand.o\
558 ./collectsharedcommand.o\
559 ./commandoptionparser.o\
568 ./makegroupcommand.o\
572 ./splitabundcommand.o\
574 ./clustersplitcommand.o\
591 ./rarefactsharedcommand.o\
601 ./sharedordervector.o\
602 ./sharedrabundvector.o\
603 ./sharedsabundvector.o\
614 ./summarysharedcommand.o\
625 ./mergefilecommand.o\
628 ./preclustercommand.o\
629 ./otuhierarchycommand.o\
633 ./secondarystructurecommand.o\
635 ./parselistscommand.o\
640 ./getlistcountcommand.o\
643 ./taxonomyequalizer.o\
644 ./phylotypecommand.o\
645 ./classifyseqscommand.o\
650 ./phylodiversitycommand.o\
661 ./mgclustercommand.o\
662 ./getsharedotucommand.o\
664 ./chimerarealigner.o\
672 ./setlogfilecommand.o\
676 #cp mothur ../Release/mothur
679 # Build the parts of mothur
683 # Item # 1 -- sharedutilities --
684 ./sharedutilities.o : sharedutilities.cpp
685 $(CC) $(CC_OPTIONS) sharedutilities.cpp -c $(INCLUDE) -o ./sharedutilities.o
688 # Item # 2 -- treegroupscommand --
689 ./treegroupscommand.o : treegroupscommand.cpp
690 $(CC) $(CC_OPTIONS) treegroupscommand.cpp -c $(INCLUDE) -o ./treegroupscommand.o
693 # Item # 3 -- bootstrapsharedcommand --
694 ./bootstrapsharedcommand.o : bootstrapsharedcommand.cpp
695 $(CC) $(CC_OPTIONS) bootstrapsharedcommand.cpp -c $(INCLUDE) -o ./bootstrapsharedcommand.o
698 # Item # 4 -- matrixoutputcommand --
699 ./matrixoutputcommand.o : matrixoutputcommand.cpp
700 $(CC) $(CC_OPTIONS) matrixoutputcommand.cpp -c $(INCLUDE) -o ./matrixoutputcommand.o
703 # Item # 5 -- getoturepcommand --
704 ./getoturepcommand.o : getoturepcommand.cpp
705 $(CC) $(CC_OPTIONS) getoturepcommand.cpp -c $(INCLUDE) -o ./getoturepcommand.o
708 # Item # 6 -- screenseqscommand --
709 ./screenseqscommand.o : screenseqscommand.cpp
710 $(CC) $(CC_OPTIONS) screenseqscommand.cpp -c $(INCLUDE) -o ./screenseqscommand.o
713 # Item # 7 -- chimera --
714 ./chimera.o : chimera.cpp
715 $(CC) $(CC_OPTIONS) chimera.cpp -c $(INCLUDE) -o ./chimera.o
718 # Item # 8 -- decalc --
719 ./decalc.o : decalc.cpp
720 $(CC) $(CC_OPTIONS) decalc.cpp -c $(INCLUDE) -o ./decalc.o
723 # Item # 9 -- readotucommand --
724 ./readotucommand.o : readotucommand.cpp
725 $(CC) $(CC_OPTIONS) readotucommand.cpp -c $(INCLUDE) -o ./readotucommand.o
728 # Item # 10 -- readdistcommand --
729 ./readdistcommand.o : readdistcommand.cpp
730 $(CC) $(CC_OPTIONS) readdistcommand.cpp -c $(INCLUDE) -o ./readdistcommand.o
733 # Item # 11 -- commandfactory --
734 ./commandfactory.o : commandfactory.cpp
735 $(CC) $(CC_OPTIONS) commandfactory.cpp -c $(INCLUDE) -o ./commandfactory.o
738 # Item # 12 -- alignment --
739 ./alignment.o : alignment.cpp
740 $(CC) $(CC_OPTIONS) alignment.cpp -c $(INCLUDE) -o ./alignment.o
743 # Item # 13 -- alignmentcell --
744 ./alignmentcell.o : alignmentcell.cpp
745 $(CC) $(CC_OPTIONS) alignmentcell.cpp -c $(INCLUDE) -o ./alignmentcell.o
748 # Item # 14 -- gotohoverlap --
749 ./gotohoverlap.o : gotohoverlap.cpp
750 $(CC) $(CC_OPTIONS) gotohoverlap.cpp -c $(INCLUDE) -o ./gotohoverlap.o
753 # Item # 15 -- overlap --
754 ./overlap.o : overlap.cpp
755 $(CC) $(CC_OPTIONS) overlap.cpp -c $(INCLUDE) -o ./overlap.o
758 # Item # 16 -- needlemanoverlap --
759 ./needlemanoverlap.o : needlemanoverlap.cpp
760 $(CC) $(CC_OPTIONS) needlemanoverlap.cpp -c $(INCLUDE) -o ./needlemanoverlap.o
763 # Item # 17 -- blastalign --
764 ./blastalign.o : blastalign.cpp
765 $(CC) $(CC_OPTIONS) blastalign.cpp -c $(INCLUDE) -o ./blastalign.o
768 # Item # 18 -- noalign --
769 ./noalign.o : noalign.cpp
770 $(CC) $(CC_OPTIONS) noalign.cpp -c $(INCLUDE) -o ./noalign.o
773 # Item # 19 -- suffixdb --
774 ./suffixdb.o : suffixdb.cpp
775 $(CC) $(CC_OPTIONS) suffixdb.cpp -c $(INCLUDE) -o ./suffixdb.o
778 # Item # 20 -- suffixnodes --
779 ./suffixnodes.o : suffixnodes.cpp
780 $(CC) $(CC_OPTIONS) suffixnodes.cpp -c $(INCLUDE) -o ./suffixnodes.o
783 # Item # 21 -- suffixtree --
784 ./suffixtree.o : suffixtree.cpp
785 $(CC) $(CC_OPTIONS) suffixtree.cpp -c $(INCLUDE) -o ./suffixtree.o
788 # Item # 22 -- blastdb --
789 ./blastdb.o : blastdb.cpp
790 $(CC) $(CC_OPTIONS) blastdb.cpp -c $(INCLUDE) -o ./blastdb.o
793 # Item # 23 -- nast --
795 $(CC) $(CC_OPTIONS) nast.cpp -c $(INCLUDE) -o ./nast.o
798 # Item # 24 -- nastreport --
799 ./nastreport.o : nastreport.cpp
800 $(CC) $(CC_OPTIONS) nastreport.cpp -c $(INCLUDE) -o ./nastreport.o
803 # Item # 25 -- boneh --
804 ./boneh.o : boneh.cpp
805 $(CC) $(CC_OPTIONS) boneh.cpp -c $(INCLUDE) -o ./boneh.o
808 # Item # 26 -- efron --
809 ./efron.o : efron.cpp
810 $(CC) $(CC_OPTIONS) efron.cpp -c $(INCLUDE) -o ./efron.o
813 # Item # 27 -- solow --
814 ./solow.o : solow.cpp
815 $(CC) $(CC_OPTIONS) solow.cpp -c $(INCLUDE) -o ./solow.o
818 # Item # 28 -- unifracweightedcommand --
819 ./unifracweightedcommand.o : unifracweightedcommand.cpp
820 $(CC) $(CC_OPTIONS) unifracweightedcommand.cpp -c $(INCLUDE) -o ./unifracweightedcommand.o
823 # Item # 29 -- weighted --
824 ./weighted.o : weighted.cpp
825 $(CC) $(CC_OPTIONS) weighted.cpp -c $(INCLUDE) -o ./weighted.o
828 # Item # 30 -- unweighted --
829 ./unweighted.o : unweighted.cpp
830 $(CC) $(CC_OPTIONS) unweighted.cpp -c $(INCLUDE) -o ./unweighted.o
833 # Item # 31 -- unifracunweightedcommand --
834 ./unifracunweightedcommand.o : unifracunweightedcommand.cpp
835 $(CC) $(CC_OPTIONS) unifracunweightedcommand.cpp -c $(INCLUDE) -o ./unifracunweightedcommand.o
838 # Item # 32 -- getsabundcommand --
839 ./getsabundcommand.o : getsabundcommand.cpp
840 $(CC) $(CC_OPTIONS) getsabundcommand.cpp -c $(INCLUDE) -o ./getsabundcommand.o
843 # Item # 33 -- getrabundcommand --
844 ./getrabundcommand.o : getrabundcommand.cpp
845 $(CC) $(CC_OPTIONS) getrabundcommand.cpp -c $(INCLUDE) -o ./getrabundcommand.o
848 # Item # 34 -- bellerophon --
849 ./bellerophon.o : bellerophon.cpp
850 $(CC) $(CC_OPTIONS) bellerophon.cpp -c $(INCLUDE) -o ./bellerophon.o
853 # Item # 35 -- pintail --
854 ./pintail.o : pintail.cpp
855 $(CC) $(CC_OPTIONS) pintail.cpp -c $(INCLUDE) -o ./pintail.o
858 # Item # 36 -- sharedanderbergs --
859 ./sharedanderbergs.o : sharedanderbergs.cpp
860 $(CC) $(CC_OPTIONS) sharedanderbergs.cpp -c $(INCLUDE) -o ./sharedanderbergs.o
863 # Item # 37 -- venncommand --
864 ./venncommand.o : venncommand.cpp
865 $(CC) $(CC_OPTIONS) venncommand.cpp -c $(INCLUDE) -o ./venncommand.o
868 # Item # 38 -- venn --
870 $(CC) $(CC_OPTIONS) venn.cpp -c $(INCLUDE) -o ./venn.o
873 # Item # 39 -- fullmatrix --
874 ./fullmatrix.o : fullmatrix.cpp
875 $(CC) $(CC_OPTIONS) fullmatrix.cpp -c $(INCLUDE) -o ./fullmatrix.o
878 # Item # 40 -- heatmap --
879 ./heatmap.o : heatmap.cpp
880 $(CC) $(CC_OPTIONS) heatmap.cpp -c $(INCLUDE) -o ./heatmap.o
883 # Item # 41 -- heatmapcommand --
884 ./heatmapcommand.o : heatmapcommand.cpp
885 $(CC) $(CC_OPTIONS) heatmapcommand.cpp -c $(INCLUDE) -o ./heatmapcommand.o
888 # Item # 42 -- libshuffcommand --
889 ./libshuffcommand.o : libshuffcommand.cpp
890 $(CC) $(CC_OPTIONS) libshuffcommand.cpp -c $(INCLUDE) -o ./libshuffcommand.o
893 # Item # 43 -- nocommands --
894 ./nocommands.o : nocommands.cpp
895 $(CC) $(CC_OPTIONS) nocommands.cpp -c $(INCLUDE) -o ./nocommands.o
898 # Item # 44 -- sharedbraycurtis --
899 ./sharedbraycurtis.o : sharedbraycurtis.cpp
900 $(CC) $(CC_OPTIONS) sharedbraycurtis.cpp -c $(INCLUDE) -o ./sharedbraycurtis.o
903 # Item # 45 -- sharedkulczynski --
904 ./sharedkulczynski.o : sharedkulczynski.cpp
905 $(CC) $(CC_OPTIONS) sharedkulczynski.cpp -c $(INCLUDE) -o ./sharedkulczynski.o
908 # Item # 46 -- sharedlennon --
909 ./sharedlennon.o : sharedlennon.cpp
910 $(CC) $(CC_OPTIONS) sharedlennon.cpp -c $(INCLUDE) -o ./sharedlennon.o
913 # Item # 47 -- sharedkulczynskicody --
914 ./sharedkulczynskicody.o : sharedkulczynskicody.cpp
915 $(CC) $(CC_OPTIONS) sharedkulczynskicody.cpp -c $(INCLUDE) -o ./sharedkulczynskicody.o
918 # Item # 48 -- sharedmorisitahorn --
919 ./sharedmorisitahorn.o : sharedmorisitahorn.cpp
920 $(CC) $(CC_OPTIONS) sharedmorisitahorn.cpp -c $(INCLUDE) -o ./sharedmorisitahorn.o
923 # Item # 49 -- sharedochiai --
924 ./sharedochiai.o : sharedochiai.cpp
925 $(CC) $(CC_OPTIONS) sharedochiai.cpp -c $(INCLUDE) -o ./sharedochiai.o
928 # Item # 50 -- readcolumn --
929 ./readcolumn.o : readcolumn.cpp
930 $(CC) $(CC_OPTIONS) readcolumn.cpp -c $(INCLUDE) -o ./readcolumn.o
933 # Item # 51 -- readotu --
934 ./readotu.o : readotu.cpp
935 $(CC) $(CC_OPTIONS) readotu.cpp -c $(INCLUDE) -o ./readotu.o
938 # Item # 52 -- readphylip --
939 ./readphylip.o : readphylip.cpp
940 $(CC) $(CC_OPTIONS) readphylip.cpp -c $(INCLUDE) -o ./readphylip.o
943 # Item # 53 -- consensuscommand --
944 ./consensuscommand.o : consensuscommand.cpp
945 $(CC) $(CC_OPTIONS) consensuscommand.cpp -c $(INCLUDE) -o ./consensuscommand.o
948 # Item # 54 -- heatmapsimcommand --
949 ./heatmapsimcommand.o : heatmapsimcommand.cpp
950 $(CC) $(CC_OPTIONS) heatmapsimcommand.cpp -c $(INCLUDE) -o ./heatmapsimcommand.o
953 # Item # 55 -- heatmapsim --
954 ./heatmapsim.o : heatmapsim.cpp
955 $(CC) $(CC_OPTIONS) heatmapsim.cpp -c $(INCLUDE) -o ./heatmapsim.o
958 # Item # 56 -- optionparser --
959 ./optionparser.o : optionparser.cpp
960 $(CC) $(CC_OPTIONS) optionparser.cpp -c $(INCLUDE) -o ./optionparser.o
963 # Item # 57 -- filterseqscommand --
964 ./filterseqscommand.o : filterseqscommand.cpp
965 $(CC) $(CC_OPTIONS) filterseqscommand.cpp -c $(INCLUDE) -o ./filterseqscommand.o
968 # Item # 58 -- goodscoverage --
969 ./goodscoverage.o : goodscoverage.cpp
970 $(CC) $(CC_OPTIONS) goodscoverage.cpp -c $(INCLUDE) -o ./goodscoverage.o
973 # Item # 59 -- sequencedb --
974 ./sequencedb.o : sequencedb.cpp
975 $(CC) $(CC_OPTIONS) sequencedb.cpp -c $(INCLUDE) -o ./sequencedb.o
978 # Item # 60 -- sharedjackknife --
979 ./sharedjackknife.o : sharedjackknife.cpp
980 $(CC) $(CC_OPTIONS) sharedjackknife.cpp -c $(INCLUDE) -o ./sharedjackknife.o
983 # Item # 61 -- sharedmarczewski --
984 ./sharedmarczewski.o : sharedmarczewski.cpp
985 $(CC) $(CC_OPTIONS) sharedmarczewski.cpp -c $(INCLUDE) -o ./sharedmarczewski.o
988 # Item # 62 -- aligncommand --
989 ./aligncommand.o : aligncommand.cpp
990 $(CC) $(CC_OPTIONS) aligncommand.cpp -c $(INCLUDE) -o ./aligncommand.o
993 # Item # 63 -- treemap --
994 ./treemap.o : treemap.cpp
995 $(CC) $(CC_OPTIONS) treemap.cpp -c $(INCLUDE) -o ./treemap.o
998 # Item # 64 -- parsimonycommand --
999 ./parsimonycommand.o : parsimonycommand.cpp
1000 $(CC) $(CC_OPTIONS) parsimonycommand.cpp -c $(INCLUDE) -o ./parsimonycommand.o
1003 # Item # 65 -- parsimony --
1004 ./parsimony.o : parsimony.cpp
1005 $(CC) $(CC_OPTIONS) parsimony.cpp -c $(INCLUDE) -o ./parsimony.o
1008 # Item # 66 -- seqsummarycommand --
1009 ./seqsummarycommand.o : seqsummarycommand.cpp
1010 $(CC) $(CC_OPTIONS) seqsummarycommand.cpp -c $(INCLUDE) -o ./seqsummarycommand.o
1013 # Item # 67 -- chimeraseqscommand --
1014 ./chimeraseqscommand.o : chimeraseqscommand.cpp
1015 $(CC) $(CC_OPTIONS) chimeraseqscommand.cpp -c $(INCLUDE) -o ./chimeraseqscommand.o
1018 # Item # 68 -- sharedlistvector --
1019 ./sharedlistvector.o : sharedlistvector.cpp
1020 $(CC) $(CC_OPTIONS) sharedlistvector.cpp -c $(INCLUDE) -o ./sharedlistvector.o
1023 # Item # 69 -- tree --
1025 $(CC) $(CC_OPTIONS) tree.cpp -c $(INCLUDE) -o ./tree.o
1028 # Item # 70 -- readtree --
1029 ./readtree.o : readtree.cpp
1030 $(CC) $(CC_OPTIONS) readtree.cpp -c $(INCLUDE) -o ./readtree.o
1033 # Item # 71 -- sharedsobscollectsummary --
1034 ./sharedsobscollectsummary.o : sharedsobscollectsummary.cpp
1035 $(CC) $(CC_OPTIONS) sharedsobscollectsummary.cpp -c $(INCLUDE) -o ./sharedsobscollectsummary.o
1038 # Item # 72 -- deconvolutecommand --
1039 ./deconvolutecommand.o : deconvolutecommand.cpp
1040 $(CC) $(CC_OPTIONS) deconvolutecommand.cpp -c $(INCLUDE) -o ./deconvolutecommand.o
1043 # Item # 73 -- listseqscommand --
1044 ./listseqscommand.o : listseqscommand.cpp
1045 $(CC) $(CC_OPTIONS) listseqscommand.cpp -c $(INCLUDE) -o ./listseqscommand.o
1048 # Item # 74 -- getseqscommand --
1049 ./getseqscommand.o : getseqscommand.cpp
1050 $(CC) $(CC_OPTIONS) getseqscommand.cpp -c $(INCLUDE) -o ./getseqscommand.o
1053 # Item # 75 -- removeseqscommand --
1054 ./removeseqscommand.o : removeseqscommand.cpp
1055 $(CC) $(CC_OPTIONS) removeseqscommand.cpp -c $(INCLUDE) -o ./removeseqscommand.o
1058 # Item # 76 -- systemcommand --
1059 ./systemcommand.o : systemcommand.cpp
1060 $(CC) $(CC_OPTIONS) systemcommand.cpp -c $(INCLUDE) -o ./systemcommand.o
1063 # Item # 77 -- binsequencecommand --
1064 ./binsequencecommand.o : binsequencecommand.cpp
1065 $(CC) $(CC_OPTIONS) binsequencecommand.cpp -c $(INCLUDE) -o ./binsequencecommand.o
1068 # Item # 78 -- distancecommand --
1069 ./distancecommand.o : distancecommand.cpp
1070 $(CC) $(CC_OPTIONS) distancecommand.cpp -c $(INCLUDE) -o ./distancecommand.o
1073 # Item # 79 -- ace --
1075 $(CC) $(CC_OPTIONS) ace.cpp -c $(INCLUDE) -o ./ace.o
1078 # Item # 80 -- averagelinkage --
1079 ./averagelinkage.o : averagelinkage.cpp
1080 $(CC) $(CC_OPTIONS) averagelinkage.cpp -c $(INCLUDE) -o ./averagelinkage.o
1083 # Item # 81 -- bootstrap --
1084 ./bootstrap.o : bootstrap.cpp
1085 $(CC) $(CC_OPTIONS) bootstrap.cpp -c $(INCLUDE) -o ./bootstrap.o
1088 # Item # 82 -- calculator --
1089 ./calculator.o : calculator.cpp
1090 $(CC) $(CC_OPTIONS) calculator.cpp -c $(INCLUDE) -o ./calculator.o
1093 # Item # 83 -- chao1 --
1094 ./chao1.o : chao1.cpp
1095 $(CC) $(CC_OPTIONS) chao1.cpp -c $(INCLUDE) -o ./chao1.o
1098 # Item # 84 -- cluster --
1099 ./cluster.o : cluster.cpp
1100 $(CC) $(CC_OPTIONS) cluster.cpp -c $(INCLUDE) -o ./cluster.o
1103 # Item # 85 -- clustercommand --
1104 ./clustercommand.o : clustercommand.cpp
1105 $(CC) $(CC_OPTIONS) clustercommand.cpp -c $(INCLUDE) -o ./clustercommand.o
1108 # Item # 86 -- collect --
1109 ./collect.o : collect.cpp
1110 $(CC) $(CC_OPTIONS) collect.cpp -c $(INCLUDE) -o ./collect.o
1113 # Item # 87 -- collectcommand --
1114 ./collectcommand.o : collectcommand.cpp
1115 $(CC) $(CC_OPTIONS) collectcommand.cpp -c $(INCLUDE) -o ./collectcommand.o
1118 # Item # 88 -- collectsharedcommand --
1119 ./collectsharedcommand.o : collectsharedcommand.cpp
1120 $(CC) $(CC_OPTIONS) collectsharedcommand.cpp -c $(INCLUDE) -o ./collectsharedcommand.o
1123 # Item # 89 -- commandoptionparser --
1124 ./commandoptionparser.o : commandoptionparser.cpp
1125 $(CC) $(CC_OPTIONS) commandoptionparser.cpp -c $(INCLUDE) -o ./commandoptionparser.o
1128 # Item # 90 -- completelinkage --
1129 ./completelinkage.o : completelinkage.cpp
1130 $(CC) $(CC_OPTIONS) completelinkage.cpp -c $(INCLUDE) -o ./completelinkage.o
1133 # Item # 91 -- database --
1134 ./database.o : database.cpp
1135 $(CC) $(CC_OPTIONS) database.cpp -c $(INCLUDE) -o ./database.o
1138 # Item # 92 -- engine --
1139 ./engine.o : engine.cpp
1140 $(CC) $(CC_OPTIONS) engine.cpp -c $(INCLUDE) -o ./engine.o
1143 # Item # 93 -- fastamap --
1144 ./fastamap.o : fastamap.cpp
1145 $(CC) $(CC_OPTIONS) fastamap.cpp -c $(INCLUDE) -o ./fastamap.o
1148 # Item # 94 -- fileoutput --
1149 ./fileoutput.o : fileoutput.cpp
1150 $(CC) $(CC_OPTIONS) fileoutput.cpp -c $(INCLUDE) -o ./fileoutput.o
1153 # Item # 95 -- globaldata --
1154 ./globaldata.o : globaldata.cpp
1155 $(CC) $(CC_OPTIONS) globaldata.cpp -c $(INCLUDE) -o ./globaldata.o
1158 # Item # 96 -- groupmap --
1159 ./groupmap.o : groupmap.cpp
1160 $(CC) $(CC_OPTIONS) groupmap.cpp -c $(INCLUDE) -o ./groupmap.o
1163 # Item # 97 -- helpcommand --
1164 ./helpcommand.o : helpcommand.cpp
1165 $(CC) $(CC_OPTIONS) helpcommand.cpp -c $(INCLUDE) -o ./helpcommand.o
1168 # Item # 98 -- inputdata --
1169 ./inputdata.o : inputdata.cpp
1170 $(CC) $(CC_OPTIONS) inputdata.cpp -c $(INCLUDE) -o ./inputdata.o
1173 # Item # 99 -- jackknife --
1174 ./jackknife.o : jackknife.cpp
1175 $(CC) $(CC_OPTIONS) jackknife.cpp -c $(INCLUDE) -o ./jackknife.o
1178 # Item # 100 -- kmer --
1180 $(CC) $(CC_OPTIONS) kmer.cpp -c $(INCLUDE) -o ./kmer.o
1183 # Item # 101 -- kmerdb --
1184 ./kmerdb.o : kmerdb.cpp
1185 $(CC) $(CC_OPTIONS) kmerdb.cpp -c $(INCLUDE) -o ./kmerdb.o
1188 # Item # 102 -- listvector --
1189 ./listvector.o : listvector.cpp
1190 $(CC) $(CC_OPTIONS) listvector.cpp -c $(INCLUDE) -o ./listvector.o
1193 # Item # 103 -- mothur --
1194 ./mothur.o : mothur.cpp
1195 $(CC) $(CC_OPTIONS) mothur.cpp -c $(INCLUDE) -o ./mothur.o
1198 # Item # 104 -- nameassignment --
1199 ./nameassignment.o : nameassignment.cpp
1200 $(CC) $(CC_OPTIONS) nameassignment.cpp -c $(INCLUDE) -o ./nameassignment.o
1203 # Item # 105 -- npshannon --
1204 ./npshannon.o : npshannon.cpp
1205 $(CC) $(CC_OPTIONS) npshannon.cpp -c $(INCLUDE) -o ./npshannon.o
1208 # Item # 106 -- ordervector --
1209 ./ordervector.o : ordervector.cpp
1210 $(CC) $(CC_OPTIONS) ordervector.cpp -c $(INCLUDE) -o ./ordervector.o
1213 # Item # 107 -- progress --
1214 ./progress.o : progress.cpp
1215 $(CC) $(CC_OPTIONS) progress.cpp -c $(INCLUDE) -o ./progress.o
1218 # Item # 108 -- quitcommand --
1219 ./quitcommand.o : quitcommand.cpp
1220 $(CC) $(CC_OPTIONS) quitcommand.cpp -c $(INCLUDE) -o ./quitcommand.o
1223 # Item # 109 -- rabundvector --
1224 ./rabundvector.o : rabundvector.cpp
1225 $(CC) $(CC_OPTIONS) rabundvector.cpp -c $(INCLUDE) -o ./rabundvector.o
1228 # Item # 110 -- rarecalc --
1229 ./rarecalc.o : rarecalc.cpp
1230 $(CC) $(CC_OPTIONS) rarecalc.cpp -c $(INCLUDE) -o ./rarecalc.o
1233 # Item # 111 -- raredisplay --
1234 ./raredisplay.o : raredisplay.cpp
1235 $(CC) $(CC_OPTIONS) raredisplay.cpp -c $(INCLUDE) -o ./raredisplay.o
1238 # Item # 112 -- rarefact --
1239 ./rarefact.o : rarefact.cpp
1240 $(CC) $(CC_OPTIONS) rarefact.cpp -c $(INCLUDE) -o ./rarefact.o
1243 # Item # 113 -- rarefactcommand --
1244 ./rarefactcommand.o : rarefactcommand.cpp
1245 $(CC) $(CC_OPTIONS) rarefactcommand.cpp -c $(INCLUDE) -o ./rarefactcommand.o
1248 # Item # 114 -- rarefactsharedcommand --
1249 ./rarefactsharedcommand.o : rarefactsharedcommand.cpp
1250 $(CC) $(CC_OPTIONS) rarefactsharedcommand.cpp -c $(INCLUDE) -o ./rarefactsharedcommand.o
1253 # Item # 115 -- sabundvector --
1254 ./sabundvector.o : sabundvector.cpp
1255 $(CC) $(CC_OPTIONS) sabundvector.cpp -c $(INCLUDE) -o ./sabundvector.o
1258 # Item # 116 -- sequence --
1259 ./sequence.o : sequence.cpp
1260 $(CC) $(CC_OPTIONS) sequence.cpp -c $(INCLUDE) -o ./sequence.o
1263 # Item # 117 -- shannon --
1264 ./shannon.o : shannon.cpp
1265 $(CC) $(CC_OPTIONS) shannon.cpp -c $(INCLUDE) -o ./shannon.o
1268 # Item # 118 -- sharedace --
1269 ./sharedace.o : sharedace.cpp
1270 $(CC) $(CC_OPTIONS) sharedace.cpp -c $(INCLUDE) -o ./sharedace.o
1273 # Item # 119 -- sharedchao1 --
1274 ./sharedchao1.o : sharedchao1.cpp
1275 $(CC) $(CC_OPTIONS) sharedchao1.cpp -c $(INCLUDE) -o ./sharedchao1.o
1278 # Item # 120 -- sharedcommand --
1279 ./sharedcommand.o : sharedcommand.cpp
1280 $(CC) $(CC_OPTIONS) sharedcommand.cpp -c $(INCLUDE) -o ./sharedcommand.o
1283 # Item # 121 -- sharedjabund --
1284 ./sharedjabund.o : sharedjabund.cpp
1285 $(CC) $(CC_OPTIONS) sharedjabund.cpp -c $(INCLUDE) -o ./sharedjabund.o
1288 # Item # 122 -- sharedjclass --
1289 ./sharedjclass.o : sharedjclass.cpp
1290 $(CC) $(CC_OPTIONS) sharedjclass.cpp -c $(INCLUDE) -o ./sharedjclass.o
1293 # Item # 123 -- sharedjest --
1294 ./sharedjest.o : sharedjest.cpp
1295 $(CC) $(CC_OPTIONS) sharedjest.cpp -c $(INCLUDE) -o ./sharedjest.o
1298 # Item # 124 -- sharedordervector --
1299 ./sharedordervector.o : sharedordervector.cpp
1300 $(CC) $(CC_OPTIONS) sharedordervector.cpp -c $(INCLUDE) -o ./sharedordervector.o
1303 # Item # 125 -- sharedrabundvector --
1304 ./sharedrabundvector.o : sharedrabundvector.cpp
1305 $(CC) $(CC_OPTIONS) sharedrabundvector.cpp -c $(INCLUDE) -o ./sharedrabundvector.o
1308 # Item # 126 -- sharedsabundvector --
1309 ./sharedsabundvector.o : sharedsabundvector.cpp
1310 $(CC) $(CC_OPTIONS) sharedsabundvector.cpp -c $(INCLUDE) -o ./sharedsabundvector.o
1313 # Item # 127 -- sharedsobs --
1314 ./sharedsobs.o : sharedsobs.cpp
1315 $(CC) $(CC_OPTIONS) sharedsobs.cpp -c $(INCLUDE) -o ./sharedsobs.o
1318 # Item # 128 -- sharedsorabund --
1319 ./sharedsorabund.o : sharedsorabund.cpp
1320 $(CC) $(CC_OPTIONS) sharedsorabund.cpp -c $(INCLUDE) -o ./sharedsorabund.o
1323 # Item # 129 -- sharedsorclass --
1324 ./sharedsorclass.o : sharedsorclass.cpp
1325 $(CC) $(CC_OPTIONS) sharedsorclass.cpp -c $(INCLUDE) -o ./sharedsorclass.o
1328 # Item # 130 -- sharedsorest --
1329 ./sharedsorest.o : sharedsorest.cpp
1330 $(CC) $(CC_OPTIONS) sharedsorest.cpp -c $(INCLUDE) -o ./sharedsorest.o
1333 # Item # 131 -- sharedthetan --
1334 ./sharedthetan.o : sharedthetan.cpp
1335 $(CC) $(CC_OPTIONS) sharedthetan.cpp -c $(INCLUDE) -o ./sharedthetan.o
1338 # Item # 132 -- sharedthetayc --
1339 ./sharedthetayc.o : sharedthetayc.cpp
1340 $(CC) $(CC_OPTIONS) sharedthetayc.cpp -c $(INCLUDE) -o ./sharedthetayc.o
1343 # Item # 133 -- simpson --
1344 ./simpson.o : simpson.cpp
1345 $(CC) $(CC_OPTIONS) simpson.cpp -c $(INCLUDE) -o ./simpson.o
1348 # Item # 134 -- singlelinkage --
1349 ./singlelinkage.o : singlelinkage.cpp
1350 $(CC) $(CC_OPTIONS) singlelinkage.cpp -c $(INCLUDE) -o ./singlelinkage.o
1353 # Item # 135 -- sparsematrix --
1354 ./sparsematrix.o : sparsematrix.cpp
1355 $(CC) $(CC_OPTIONS) sparsematrix.cpp -c $(INCLUDE) -o ./sparsematrix.o
1358 # Item # 136 -- summarycommand --
1359 ./summarycommand.o : summarycommand.cpp
1360 $(CC) $(CC_OPTIONS) summarycommand.cpp -c $(INCLUDE) -o ./summarycommand.o
1363 # Item # 137 -- summarysharedcommand --
1364 ./summarysharedcommand.o : summarysharedcommand.cpp
1365 $(CC) $(CC_OPTIONS) summarysharedcommand.cpp -c $(INCLUDE) -o ./summarysharedcommand.o
1368 # Item # 138 -- uvest --
1369 ./uvest.o : uvest.cpp
1370 $(CC) $(CC_OPTIONS) uvest.cpp -c $(INCLUDE) -o ./uvest.o
1373 # Item # 139 -- validcalculator --
1374 ./validcalculator.o : validcalculator.cpp
1375 $(CC) $(CC_OPTIONS) validcalculator.cpp -c $(INCLUDE) -o ./validcalculator.o
1378 # Item # 140 -- validparameter --
1379 ./validparameter.o : validparameter.cpp
1380 $(CC) $(CC_OPTIONS) validparameter.cpp -c $(INCLUDE) -o ./validparameter.o
1383 # Item # 141 -- treenode --
1384 ./treenode.o : treenode.cpp
1385 $(CC) $(CC_OPTIONS) treenode.cpp -c $(INCLUDE) -o ./treenode.o
1388 # Item # 142 -- readtreecommand --
1389 ./readtreecommand.o : readtreecommand.cpp
1390 $(CC) $(CC_OPTIONS) readtreecommand.cpp -c $(INCLUDE) -o ./readtreecommand.o
1393 # Item # 143 -- reversecommand --
1394 ./reversecommand.o : reversecommand.cpp
1395 $(CC) $(CC_OPTIONS) reversecommand.cpp -c $(INCLUDE) -o ./reversecommand.o
1398 # Item # 144 -- trimseqscommand --
1399 ./trimseqscommand.o : trimseqscommand.cpp
1400 $(CC) $(CC_OPTIONS) trimseqscommand.cpp -c $(INCLUDE) -o ./trimseqscommand.o
1403 # Item # 145 -- slibshuff --
1404 ./slibshuff.o : slibshuff.cpp
1405 $(CC) $(CC_OPTIONS) slibshuff.cpp -c $(INCLUDE) -o ./slibshuff.o
1408 # Item # 146 -- libshuff --
1409 ./libshuff.o : libshuff.cpp
1410 $(CC) $(CC_OPTIONS) libshuff.cpp -c $(INCLUDE) -o ./libshuff.o
1413 # Item # 147 -- dlibshuff --
1414 ./dlibshuff.o : dlibshuff.cpp
1415 $(CC) $(CC_OPTIONS) dlibshuff.cpp -c $(INCLUDE) -o ./dlibshuff.o
1418 # Item # 148 -- mergefilecommand --
1419 ./mergefilecommand.o : mergefilecommand.cpp
1420 $(CC) $(CC_OPTIONS) mergefilecommand.cpp -c $(INCLUDE) -o ./mergefilecommand.o
1423 # Item # 149 -- coverage --
1424 ./coverage.o : coverage.cpp
1425 $(CC) $(CC_OPTIONS) coverage.cpp -c $(INCLUDE) -o ./coverage.o
1428 # Item # 150 -- whittaker --
1429 ./whittaker.o : whittaker.cpp
1430 $(CC) $(CC_OPTIONS) whittaker.cpp -c $(INCLUDE) -o ./whittaker.o
1433 # Item # 151 -- preclustercommand --
1434 ./preclustercommand.o : preclustercommand.cpp
1435 $(CC) $(CC_OPTIONS) preclustercommand.cpp -c $(INCLUDE) -o ./preclustercommand.o
1438 # Item # 152 -- otuhierarchycommand --
1439 ./otuhierarchycommand.o : otuhierarchycommand.cpp
1440 $(CC) $(CC_OPTIONS) otuhierarchycommand.cpp -c $(INCLUDE) -o ./otuhierarchycommand.o
1443 # Item # 153 -- setdircommand --
1444 ./setdircommand.o : setdircommand.cpp
1445 $(CC) $(CC_OPTIONS) setdircommand.cpp -c $(INCLUDE) -o ./setdircommand.o
1448 # Item # 154 -- getgroupcommand --
1449 ./getgroupcommand.o : getgroupcommand.cpp
1450 $(CC) $(CC_OPTIONS) getgroupcommand.cpp -c $(INCLUDE) -o ./getgroupcommand.o
1453 # Item # 155 -- getlabelcommand --
1454 ./getlabelcommand.o : getlabelcommand.cpp
1455 $(CC) $(CC_OPTIONS) getlabelcommand.cpp -c $(INCLUDE) -o ./getlabelcommand.o
1458 # Item # 156 -- secondarystructurecommand --
1459 ./secondarystructurecommand.o : secondarystructurecommand.cpp
1460 $(CC) $(CC_OPTIONS) secondarystructurecommand.cpp -c $(INCLUDE) -o ./secondarystructurecommand.o
1463 # Item # 157 -- mothurout --
1464 ./mothurout.o : mothurout.cpp
1465 $(CC) $(CC_OPTIONS) mothurout.cpp -c $(INCLUDE) -o ./mothurout.o
1468 # Item # 158 -- parselistscommand --
1469 ./parselistscommand.o : parselistscommand.cpp
1470 $(CC) $(CC_OPTIONS) parselistscommand.cpp -c $(INCLUDE) -o ./parselistscommand.o
1473 # Item # 159 -- readblast --
1474 ./readblast.o : readblast.cpp
1475 $(CC) $(CC_OPTIONS) readblast.cpp -c $(INCLUDE) -o ./readblast.o
1478 # Item # 160 -- chimeracheckrdp --
1479 ./chimeracheckrdp.o : chimeracheckrdp.cpp
1480 $(CC) $(CC_OPTIONS) chimeracheckrdp.cpp -c $(INCLUDE) -o ./chimeracheckrdp.o
1483 # Item # 161 -- hclustercommand --
1484 ./hclustercommand.o : hclustercommand.cpp
1485 $(CC) $(CC_OPTIONS) hclustercommand.cpp -c $(INCLUDE) -o ./hclustercommand.o
1488 # Item # 162 -- hcluster --
1489 ./hcluster.o : hcluster.cpp
1490 $(CC) $(CC_OPTIONS) hcluster.cpp -c $(INCLUDE) -o ./hcluster.o
1493 # Item # 163 -- getlistcountcommand --
1494 ./getlistcountcommand.o : getlistcountcommand.cpp
1495 $(CC) $(CC_OPTIONS) getlistcountcommand.cpp -c $(INCLUDE) -o ./getlistcountcommand.o
1498 # Item # 164 -- readcluster --
1499 ./readcluster.o : readcluster.cpp
1500 $(CC) $(CC_OPTIONS) readcluster.cpp -c $(INCLUDE) -o ./readcluster.o
1503 # Item # 165 -- ccode --
1504 ./ccode.o : ccode.cpp
1505 $(CC) $(CC_OPTIONS) ccode.cpp -c $(INCLUDE) -o ./ccode.o
1508 # Item # 166 -- taxonomyequalizer --
1509 ./taxonomyequalizer.o : taxonomyequalizer.cpp
1510 $(CC) $(CC_OPTIONS) taxonomyequalizer.cpp -c $(INCLUDE) -o ./taxonomyequalizer.o
1513 # Item # 167 -- phylotypecommand --
1514 ./phylotypecommand.o : phylotypecommand.cpp
1515 $(CC) $(CC_OPTIONS) phylotypecommand.cpp -c $(INCLUDE) -o ./phylotypecommand.o
1518 # Item # 168 -- classifyseqscommand --
1519 ./classifyseqscommand.o : classifyseqscommand.cpp
1520 $(CC) $(CC_OPTIONS) classifyseqscommand.cpp -c $(INCLUDE) -o ./classifyseqscommand.o
1523 # Item # 169 -- classify --
1524 ./classify.o : classify.cpp
1525 $(CC) $(CC_OPTIONS) classify.cpp -c $(INCLUDE) -o ./classify.o
1528 # Item # 170 -- phylotree --
1529 ./phylotree.o : phylotree.cpp
1530 $(CC) $(CC_OPTIONS) phylotree.cpp -c $(INCLUDE) -o ./phylotree.o
1533 # Item # 171 -- bayesian --
1534 ./bayesian.o : bayesian.cpp
1535 $(CC) $(CC_OPTIONS) bayesian.cpp -c $(INCLUDE) -o ./bayesian.o
1538 # Item # 172 -- alignmentdb --
1539 ./alignmentdb.o : alignmentdb.cpp
1540 $(CC) $(CC_OPTIONS) alignmentdb.cpp -c $(INCLUDE) -o ./alignmentdb.o
1543 # Item # 173 -- knn --
1545 $(CC) $(CC_OPTIONS) knn.cpp -c $(INCLUDE) -o ./knn.o
1548 # Item # 174 -- distancedb --
1549 ./distancedb.o : distancedb.cpp
1550 $(CC) $(CC_OPTIONS) distancedb.cpp -c $(INCLUDE) -o ./distancedb.o
1553 # Item # 175 -- chimeraslayer --
1554 ./chimeraslayer.o : chimeraslayer.cpp
1555 $(CC) $(CC_OPTIONS) chimeraslayer.cpp -c $(INCLUDE) -o ./chimeraslayer.o
1558 # Item # 176 -- slayer --
1559 ./slayer.o : slayer.cpp
1560 $(CC) $(CC_OPTIONS) slayer.cpp -c $(INCLUDE) -o ./slayer.o
1563 # Item # 177 -- pcacommand --
1564 ./pcacommand.o : pcacommand.cpp
1565 $(CC) $(CC_OPTIONS) pcacommand.cpp -c $(INCLUDE) -o ./pcacommand.o
1568 # Item # 178 -- formatcolumn --
1569 ./formatcolumn.o : formatcolumn.cpp
1570 $(CC) $(CC_OPTIONS) formatcolumn.cpp -c $(INCLUDE) -o ./formatcolumn.o
1573 # Item # 179 -- formatphylip --
1574 ./formatphylip.o : formatphylip.cpp
1575 $(CC) $(CC_OPTIONS) formatphylip.cpp -c $(INCLUDE) -o ./formatphylip.o
1578 # Item # 180 -- mgclustercommand --
1579 ./mgclustercommand.o : mgclustercommand.cpp
1580 $(CC) $(CC_OPTIONS) mgclustercommand.cpp -c $(INCLUDE) -o ./mgclustercommand.o
1583 # Item # 181 -- getsharedotucommand --
1584 ./getsharedotucommand.o : getsharedotucommand.cpp
1585 $(CC) $(CC_OPTIONS) getsharedotucommand.cpp -c $(INCLUDE) -o ./getsharedotucommand.o
1588 # Item # 182 -- maligner --
1589 ./maligner.o : maligner.cpp
1590 $(CC) $(CC_OPTIONS) maligner.cpp -c $(INCLUDE) -o ./maligner.o
1593 # Item # 183 -- chimerarealigner --
1594 ./chimerarealigner.o : chimerarealigner.cpp
1595 $(CC) $(CC_OPTIONS) chimerarealigner.cpp -c $(INCLUDE) -o ./chimerarealigner.o
1598 # Item # 184 -- bergerparker --
1599 ./bergerparker.o : bergerparker.cpp
1600 $(CC) $(CC_OPTIONS) bergerparker.cpp -c $(INCLUDE) -o ./bergerparker.o
1603 # Item # 185 -- bstick --
1604 ./bstick.o : bstick.cpp
1605 $(CC) $(CC_OPTIONS) bstick.cpp -c $(INCLUDE) -o ./bstick.o
1608 # Item # 186 -- sharedkstest --
1609 ./sharedkstest.o : sharedkstest.cpp
1610 $(CC) $(CC_OPTIONS) sharedkstest.cpp -c $(INCLUDE) -o ./sharedkstest.o
1613 # Item # 187 -- qstat --
1614 ./qstat.o : qstat.cpp
1615 $(CC) $(CC_OPTIONS) qstat.cpp -c $(INCLUDE) -o ./qstat.o
1618 # Item # 188 -- shen --
1620 $(CC) $(CC_OPTIONS) shen.cpp -c $(INCLUDE) -o ./shen.o
1623 # Item # 189 -- logsd --
1624 ./logsd.o : logsd.cpp
1625 $(CC) $(CC_OPTIONS) logsd.cpp -c $(INCLUDE) -o ./logsd.o
1628 # Item # 190 -- geom --
1630 $(CC) $(CC_OPTIONS) geom.cpp -c $(INCLUDE) -o ./geom.o
1632 # Item # 191 -- parsesffcommand --
1633 ./parsesffcommand.o : parsesffcommand.cpp
1634 $(CC) $(CC_OPTIONS) parsesffcommand.cpp -c $(INCLUDE) -o ./parsesffcommand.o
1636 # Item # 192 -- chimeraccodecommand --
1637 ./chimeraccodecommand.o : chimeraccodecommand.cpp
1638 $(CC) $(CC_OPTIONS) chimeraccodecommand.cpp -c $(INCLUDE) -o ./chimeraccodecommand.o
1640 # Item # 193 -- chimeracheckcommand --
1641 ./chimeracheckcommand.o : chimeracheckcommand.cpp
1642 $(CC) $(CC_OPTIONS) chimeracheckcommand.cpp -c $(INCLUDE) -o ./chimeracheckcommand.o
1645 # Item # 194 -- chimeraslayercommand --
1646 ./chimeraslayercommand.o : chimeraslayercommand.cpp
1647 $(CC) $(CC_OPTIONS) chimeraslayercommand.cpp -c $(INCLUDE) -o ./chimeraslayercommand.o
1649 # Item # 195 -- chimerapintailcommand --
1650 ./chimerapintailcommand.o : chimerapintailcommand.cpp
1651 $(CC) $(CC_OPTIONS) chimerapintailcommand.cpp -c $(INCLUDE) -o ./chimerapintailcommand.o
1653 # Item # 196 -- chimerabellerophoncommand --
1654 ./chimerabellerophoncommand.o : chimerabellerophoncommand.cpp
1655 $(CC) $(CC_OPTIONS) chimerabellerophoncommand.cpp -c $(INCLUDE) -o ./chimerabellerophoncommand.o
1657 # Item # 197 -- phylosummary --
1658 ./phylosummary.o : phylosummary.cpp
1659 $(CC) $(CC_OPTIONS) phylosummary.cpp -c $(INCLUDE) -o ./phylosummary.o
1661 # Item # 198 -- setlogfilecommand --
1662 ./setlogfilecommand.o : setlogfilecommand.cpp
1663 $(CC) $(CC_OPTIONS) setlogfilecommand.cpp -c $(INCLUDE) -o ./setlogfilecommand.o
1665 # Item # 199 -- phylodiversity --
1666 ./phylodiversity.o : phylodiversity.cpp
1667 $(CC) $(CC_OPTIONS) phylodiversity.cpp -c $(INCLUDE) -o ./phylodiversity.o
1669 # Item # 200 -- phylodiversitycommand --
1670 ./phylodiversitycommand.o : phylodiversitycommand.cpp
1671 $(CC) $(CC_OPTIONS) phylodiversitycommand.cpp -c $(INCLUDE) -o ./phylodiversitycommand.o
1673 # Item # 201 -- makegroupcommand --
1674 ./makegroupcommand.o : makegroupcommand.cpp
1675 $(CC) $(CC_OPTIONS) makegroupcommand.cpp -c $(INCLUDE) -o ./makegroupcommand.o
1677 # Item # 202 -- chopseqscommand --
1678 ./chopseqscommand.o : chopseqscommand.cpp
1679 $(CC) $(CC_OPTIONS) chopseqscommand.cpp -c $(INCLUDE) -o ./chopseqscommand.o
1681 # Item # 203 -- clearcutcommand --
1682 ./clearcutcommand.o : clearcutcommand.cpp
1683 $(CC) $(CC_OPTIONS) clearcutcommand.cpp -c $(INCLUDE) -o ./clearcutcommand.o
1685 # Item # 204 -- catchallcommand --
1686 ./catchallcommand.o : catchallcommand.cpp
1687 $(CC) $(CC_OPTIONS) catchallcommand.cpp -c $(INCLUDE) -o ./catchallcommand.o
1689 # Item # 205 -- splitabundcommand --
1690 ./splitabundcommand : splitabundcommand
1691 $(CC) $(CC_OPTIONS) splitabundcommand -c $(INCLUDE) -o ./splitabundcommand
1693 # Item # 206 -- splitmatrix --
1694 ./splitmatrix : splitmatrix
1695 $(CC) $(CC_OPTIONS) splitmatrix -c $(INCLUDE) -o ./splitmatrix
1697 # Item # 207 -- splitmatrix --
1698 ./clustersplitcommand : clustersplitcommand
1699 $(CC) $(CC_OPTIONS) clustersplitcommand -c $(INCLUDE) -o ./clustersplitcommand